Starting phenix.real_space_refine on Fri Mar 6 00:07:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o1l_0591/03_2026/6o1l_0591_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o1l_0591/03_2026/6o1l_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/cci-nas-00/data/ceres_data/6o1l_0591/03_2026/6o1l_0591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o1l_0591/03_2026/6o1l_0591.map" model { file = "/net/cci-nas-00/data/ceres_data/6o1l_0591/03_2026/6o1l_0591_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o1l_0591/03_2026/6o1l_0591_neut.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.98, per 1000 atoms: 0.19 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 888.2 milliseconds 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: 3.70 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: 5.95 Time building geometry restraints manager: 2.71 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: 0.00 - 4.20: 46394 4.20 - 8.40: 2836 8.40 - 12.61: 33 12.61 - 16.81: 6 16.81 - 21.01: 1 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 2.450 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 Time spend for trying shortcut: 0.00 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: 0.330 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: 0.160 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.440 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.270 ------------------------------------------------------------------------------- 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= 0.447 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 : 5.96 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.011 0.001 ARG I 16 TYR 0.081 0.004 TYR F 55 PHE 0.032 0.004 PHE F 42 TRP 0.046 0.004 TRP A 217 HIS 0.016 0.004 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.01017 (13938) covalent geometry : angle 1.19348 (19075) hydrogen bonds : bond 0.15798 ( 464) hydrogen bonds : angle 8.01779 ( 1284) *********************** 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 to be fit. rotamer outliers: 17 poor density : 334 time to evaluate : 0.633 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: 0.8679 (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: 0.3615 time to fit residues: 164.5725 Evaluate side-chains 261 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 255 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 F 57 HIS H 28 ASN 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** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.121820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.098492 restraints weight = 63271.064| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.24 r_work: 0.3198 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13938 Z= 0.144 Angle : 0.646 7.330 19075 Z= 0.335 Chirality : 0.047 0.170 2145 Planarity : 0.006 0.054 2317 Dihedral : 11.503 87.641 2242 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.90 % Allowed : 8.94 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.20), residues: 1549 helix: -1.84 (0.26), residues: 330 sheet: -2.10 (0.21), residues: 504 loop : -1.32 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 16 TYR 0.010 0.001 TYR A 150 PHE 0.016 0.002 PHE A 41 TRP 0.019 0.001 TRP A 217 HIS 0.007 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00313 (13938) covalent geometry : angle 0.64560 (19075) hydrogen bonds : bond 0.04472 ( 464) hydrogen bonds : angle 6.32974 ( 1284) *********************** 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 to be fit. rotamer outliers: 27 poor density : 290 time to evaluate : 0.695 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 62 LEU cc_start: 0.8991 (mt) cc_final: 0.8754 (mm) REVERT: B 202 SER cc_start: 0.8509 (m) cc_final: 0.8079 (t) REVERT: C 11 TYR cc_start: 0.6904 (t80) cc_final: 0.6570 (t80) REVERT: C 16 ARG cc_start: 0.8051 (tmm-80) cc_final: 0.7649 (tmm-80) REVERT: C 35 GLN cc_start: 0.8404 (mt0) cc_final: 0.8023 (mt0) REVERT: C 39 PHE cc_start: 0.7887 (p90) cc_final: 0.7617 (p90) REVERT: E 41 GLN cc_start: 0.7560 (tm-30) cc_final: 0.6995 (tm-30) REVERT: G 19 ARG cc_start: 0.8077 (mtt-85) cc_final: 0.7598 (mmt180) REVERT: H 41 GLN cc_start: 0.8192 (mp10) cc_final: 0.7684 (mp10) REVERT: H 42 PHE cc_start: 0.8504 (m-10) cc_final: 0.8277 (m-10) REVERT: J 19 ARG cc_start: 0.7911 (ttm-80) cc_final: 0.7636 (tpp80) REVERT: J 37 GLU cc_start: 0.8557 (tp30) cc_final: 0.8265 (mm-30) REVERT: K 37 GLU cc_start: 0.7960 (mp0) cc_final: 0.7365 (mp0) REVERT: K 40 ASP cc_start: 0.8594 (p0) cc_final: 0.8036 (p0) REVERT: K 65 SER cc_start: 0.8270 (m) cc_final: 0.8029 (m) REVERT: L 11 TYR cc_start: 0.8722 (t80) cc_final: 0.8383 (t80) REVERT: R 77 LYS cc_start: 0.8761 (mtpt) cc_final: 0.8559 (mtmm) REVERT: R 242 ARG cc_start: 0.4887 (OUTLIER) cc_final: 0.3910 (ptm-80) REVERT: R 256 GLN cc_start: 0.7569 (mp10) cc_final: 0.7294 (mp10) outliers start: 27 outliers final: 19 residues processed: 304 average time/residue: 0.3442 time to fit residues: 140.5811 Evaluate side-chains 276 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 256 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 212 MET Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 46 LEU 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 E residue 45 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 59 ILE 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 242 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 32 optimal weight: 0.0870 chunk 98 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN H 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.122500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.099671 restraints weight = 63309.502| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.20 r_work: 0.3211 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13938 Z= 0.118 Angle : 0.571 6.511 19075 Z= 0.292 Chirality : 0.045 0.159 2145 Planarity : 0.005 0.051 2317 Dihedral : 10.975 89.791 2240 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.18 % Allowed : 10.85 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.21), residues: 1549 helix: -1.10 (0.28), residues: 330 sheet: -1.89 (0.22), residues: 494 loop : -0.98 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 175 TYR 0.014 0.001 TYR R 91 PHE 0.012 0.001 PHE R 201 TRP 0.014 0.001 TRP A 217 HIS 0.010 0.001 HIS R 246 Details of bonding type rmsd covalent geometry : bond 0.00273 (13938) covalent geometry : angle 0.57052 (19075) hydrogen bonds : bond 0.03873 ( 464) hydrogen bonds : angle 5.80685 ( 1284) *********************** 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 296 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 265 time to evaluate : 0.690 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 191 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8960 (tp) REVERT: C 16 ARG cc_start: 0.8241 (tmm-80) cc_final: 0.7921 (tmm-80) REVERT: C 35 GLN cc_start: 0.8474 (mt0) cc_final: 0.8252 (mt0) REVERT: D 37 GLU cc_start: 0.7471 (pm20) cc_final: 0.7241 (pm20) REVERT: E 41 GLN cc_start: 0.7533 (tm-30) cc_final: 0.7003 (tm-30) REVERT: G 19 ARG cc_start: 0.8067 (mtt-85) cc_final: 0.7657 (mmt180) REVERT: H 41 GLN cc_start: 0.8256 (mp10) cc_final: 0.7877 (mp10) REVERT: J 37 GLU cc_start: 0.8571 (tp30) cc_final: 0.8317 (mm-30) REVERT: K 37 GLU cc_start: 0.7868 (mp0) cc_final: 0.7217 (mp0) REVERT: K 40 ASP cc_start: 0.8570 (p0) cc_final: 0.8031 (p0) REVERT: K 65 SER cc_start: 0.8215 (m) cc_final: 0.7967 (m) REVERT: L 11 TYR cc_start: 0.8744 (t80) cc_final: 0.8407 (t80) REVERT: L 19 ARG cc_start: 0.8606 (mtm-85) cc_final: 0.8321 (mtm110) REVERT: L 45 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7518 (mp) REVERT: R 9 ASN cc_start: 0.7434 (m110) cc_final: 0.7193 (m-40) REVERT: R 26 GLN cc_start: 0.6476 (tp-100) cc_final: 0.5914 (tp-100) REVERT: R 141 ARG cc_start: 0.7296 (mtp85) cc_final: 0.6939 (mmm-85) REVERT: R 242 ARG cc_start: 0.4732 (OUTLIER) cc_final: 0.3854 (ptm-80) REVERT: R 256 GLN cc_start: 0.7404 (mp10) cc_final: 0.7122 (mp10) outliers start: 31 outliers final: 21 residues processed: 284 average time/residue: 0.3349 time to fit residues: 128.8464 Evaluate side-chains 268 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 244 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 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 E residue 24 ILE 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 45 LEU Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 9 ASP Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 9 ASP 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 242 ARG Chi-restraints excluded: chain R residue 250 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 30 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN G 8 GLN G 57 HIS I 48 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.117301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.094244 restraints weight = 63364.118| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.18 r_work: 0.3121 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 13938 Z= 0.250 Angle : 0.631 6.508 19075 Z= 0.325 Chirality : 0.048 0.174 2145 Planarity : 0.005 0.049 2317 Dihedral : 10.995 91.605 2239 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.04 % Allowed : 12.11 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.21), residues: 1549 helix: -0.78 (0.29), residues: 330 sheet: -1.83 (0.22), residues: 466 loop : -1.03 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 192 TYR 0.015 0.002 TYR R 132 PHE 0.013 0.002 PHE B 201 TRP 0.016 0.001 TRP A 217 HIS 0.009 0.002 HIS R 246 Details of bonding type rmsd covalent geometry : bond 0.00593 (13938) covalent geometry : angle 0.63066 (19075) hydrogen bonds : bond 0.04352 ( 464) hydrogen bonds : angle 5.79697 ( 1284) *********************** 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 279 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 250 time to evaluate : 0.631 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: C 16 ARG cc_start: 0.8278 (tmm-80) cc_final: 0.7630 (tmm-80) REVERT: E 41 GLN cc_start: 0.7649 (tm-30) cc_final: 0.7065 (tm-30) REVERT: G 8 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6887 (tt0) REVERT: G 19 ARG cc_start: 0.8240 (mtt-85) cc_final: 0.7672 (mmt180) REVERT: G 47 LYS cc_start: 0.8692 (tptp) cc_final: 0.8058 (tptm) REVERT: H 41 GLN cc_start: 0.8298 (mp10) cc_final: 0.7810 (mp10) REVERT: J 37 GLU cc_start: 0.8545 (tp30) cc_final: 0.8317 (mm-30) REVERT: K 37 GLU cc_start: 0.7990 (mp0) cc_final: 0.7252 (mp0) REVERT: K 39 PHE cc_start: 0.8780 (p90) cc_final: 0.8570 (p90) REVERT: K 40 ASP cc_start: 0.8776 (p0) cc_final: 0.8160 (p0) REVERT: K 65 SER cc_start: 0.8121 (m) cc_final: 0.7815 (m) REVERT: L 19 ARG cc_start: 0.8603 (mtm-85) cc_final: 0.8305 (mtm110) REVERT: L 45 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7650 (mp) REVERT: M 33 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.7946 (mp10) REVERT: M 39 PHE cc_start: 0.7757 (p90) cc_final: 0.7199 (p90) REVERT: R 9 ASN cc_start: 0.7494 (m110) cc_final: 0.7252 (m-40) REVERT: R 141 ARG cc_start: 0.7531 (mtp85) cc_final: 0.7143 (mmm-85) REVERT: R 221 TYR cc_start: 0.7092 (m-10) cc_final: 0.6762 (m-10) REVERT: R 242 ARG cc_start: 0.4880 (OUTLIER) cc_final: 0.4188 (ptm-80) REVERT: R 256 GLN cc_start: 0.7237 (mp10) cc_final: 0.6933 (mp10) outliers start: 29 outliers final: 22 residues processed: 268 average time/residue: 0.3420 time to fit residues: 123.0424 Evaluate side-chains 264 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 238 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 E residue 23 SER 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 I residue 38 SER 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 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 156 MET Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 242 ARG Chi-restraints excluded: chain R residue 250 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 8 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 138 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 59 optimal weight: 0.0030 chunk 9 optimal weight: 0.6980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN H 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.120388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.097498 restraints weight = 62403.002| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.19 r_work: 0.3173 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13938 Z= 0.105 Angle : 0.555 8.194 19075 Z= 0.280 Chirality : 0.044 0.158 2145 Planarity : 0.004 0.047 2317 Dihedral : 10.699 90.667 2239 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.48 % Allowed : 13.38 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.22), residues: 1549 helix: -0.45 (0.29), residues: 330 sheet: -1.75 (0.22), residues: 478 loop : -0.71 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 19 TYR 0.018 0.001 TYR L 11 PHE 0.012 0.001 PHE A 243 TRP 0.009 0.001 TRP A 217 HIS 0.008 0.001 HIS R 246 Details of bonding type rmsd covalent geometry : bond 0.00246 (13938) covalent geometry : angle 0.55505 (19075) hydrogen bonds : bond 0.03558 ( 464) hydrogen bonds : angle 5.50041 ( 1284) *********************** 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 270 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 249 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 7 LEU cc_start: 0.7322 (tt) cc_final: 0.6929 (tp) REVERT: C 9 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.7126 (m-30) REVERT: C 16 ARG cc_start: 0.8289 (tmm-80) cc_final: 0.7622 (tmm-80) REVERT: C 37 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7532 (mt-10) REVERT: D 37 GLU cc_start: 0.7388 (pm20) cc_final: 0.7112 (pm20) REVERT: E 41 GLN cc_start: 0.7465 (tm-30) cc_final: 0.7070 (tm-30) REVERT: F 65 SER cc_start: 0.8780 (t) cc_final: 0.8225 (p) REVERT: G 19 ARG cc_start: 0.8168 (mtt-85) cc_final: 0.7654 (mmt180) REVERT: G 47 LYS cc_start: 0.8669 (tptp) cc_final: 0.8044 (tptm) REVERT: H 41 GLN cc_start: 0.8286 (mp10) cc_final: 0.7767 (mp10) REVERT: J 37 GLU cc_start: 0.8575 (tp30) cc_final: 0.8367 (mm-30) REVERT: K 37 GLU cc_start: 0.7927 (mp0) cc_final: 0.7176 (mp0) REVERT: K 39 PHE cc_start: 0.8719 (p90) cc_final: 0.8493 (p90) REVERT: K 40 ASP cc_start: 0.8645 (p0) cc_final: 0.8083 (p0) REVERT: K 65 SER cc_start: 0.8118 (m) cc_final: 0.7827 (m) REVERT: L 19 ARG cc_start: 0.8533 (mtm-85) cc_final: 0.8230 (mtm110) REVERT: L 45 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7544 (mp) REVERT: R 9 ASN cc_start: 0.7378 (m110) cc_final: 0.7150 (m-40) REVERT: R 141 ARG cc_start: 0.7344 (mtp85) cc_final: 0.6932 (mmm-85) REVERT: R 256 GLN cc_start: 0.7371 (mp10) cc_final: 0.7085 (mp10) outliers start: 21 outliers final: 15 residues processed: 258 average time/residue: 0.3378 time to fit residues: 117.6951 Evaluate side-chains 260 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 242 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 108 LEU Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain G residue 22 VAL 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 L residue 45 LEU Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain M residue 9 ASP 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 250 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 10 optimal weight: 0.2980 chunk 100 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.118505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.095507 restraints weight = 62926.265| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.17 r_work: 0.3141 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13938 Z= 0.172 Angle : 0.573 7.962 19075 Z= 0.291 Chirality : 0.045 0.166 2145 Planarity : 0.005 0.047 2317 Dihedral : 10.600 92.345 2232 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.18 % Allowed : 13.24 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.22), residues: 1549 helix: -0.49 (0.29), residues: 348 sheet: -1.65 (0.23), residues: 466 loop : -0.68 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 19 TYR 0.014 0.001 TYR R 91 PHE 0.012 0.001 PHE R 201 TRP 0.012 0.001 TRP A 217 HIS 0.010 0.001 HIS R 246 Details of bonding type rmsd covalent geometry : bond 0.00409 (13938) covalent geometry : angle 0.57307 (19075) hydrogen bonds : bond 0.03793 ( 464) hydrogen bonds : angle 5.46379 ( 1284) *********************** 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 to be fit. rotamer outliers: 31 poor density : 245 time to evaluate : 0.687 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: A 180 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7465 (tm-30) REVERT: B 180 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6977 (tm-30) REVERT: C 7 LEU cc_start: 0.7670 (tt) cc_final: 0.7325 (tp) REVERT: C 16 ARG cc_start: 0.8232 (tmm-80) cc_final: 0.7609 (tmm-80) REVERT: C 37 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7476 (mt-10) REVERT: D 37 GLU cc_start: 0.7317 (pm20) cc_final: 0.6984 (pm20) REVERT: E 41 GLN cc_start: 0.7670 (tm-30) cc_final: 0.7114 (tm-30) REVERT: F 65 SER cc_start: 0.8753 (t) cc_final: 0.8190 (p) REVERT: G 19 ARG cc_start: 0.8235 (mtt-85) cc_final: 0.7689 (mmt180) REVERT: G 47 LYS cc_start: 0.8685 (tptp) cc_final: 0.8077 (tptm) REVERT: H 41 GLN cc_start: 0.8305 (mp10) cc_final: 0.7851 (mp10) REVERT: J 37 GLU cc_start: 0.8603 (tp30) cc_final: 0.8400 (mm-30) REVERT: K 37 GLU cc_start: 0.7887 (mp0) cc_final: 0.7038 (mp0) REVERT: K 40 ASP cc_start: 0.8663 (p0) cc_final: 0.8091 (p0) REVERT: K 65 SER cc_start: 0.8136 (m) cc_final: 0.7849 (m) REVERT: L 11 TYR cc_start: 0.8704 (t80) cc_final: 0.8285 (t80) REVERT: L 19 ARG cc_start: 0.8562 (mtm-85) cc_final: 0.8256 (mtm110) REVERT: L 45 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7581 (mp) REVERT: M 33 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.7941 (mp10) REVERT: R 141 ARG cc_start: 0.7445 (mtp85) cc_final: 0.7115 (mmm-85) outliers start: 31 outliers final: 21 residues processed: 266 average time/residue: 0.3227 time to fit residues: 117.0027 Evaluate side-chains 262 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 238 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 37 GLU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 65 SER 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 H residue 28 ASN 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 L 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 156 MET Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 250 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 69 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 128 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.119498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.096597 restraints weight = 62604.725| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.17 r_work: 0.3163 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13938 Z= 0.127 Angle : 0.550 6.382 19075 Z= 0.279 Chirality : 0.045 0.161 2145 Planarity : 0.004 0.046 2317 Dihedral : 10.525 92.095 2232 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.97 % Allowed : 13.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.22), residues: 1549 helix: -0.45 (0.29), residues: 354 sheet: -1.69 (0.23), residues: 458 loop : -0.52 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 16 TYR 0.013 0.001 TYR L 11 PHE 0.013 0.001 PHE R 41 TRP 0.010 0.001 TRP A 217 HIS 0.016 0.001 HIS R 246 Details of bonding type rmsd covalent geometry : bond 0.00301 (13938) covalent geometry : angle 0.55016 (19075) hydrogen bonds : bond 0.03570 ( 464) hydrogen bonds : angle 5.37949 ( 1284) *********************** 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 273 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 245 time to evaluate : 0.593 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 180 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7475 (tm-30) REVERT: C 7 LEU cc_start: 0.7512 (tt) cc_final: 0.7256 (tp) REVERT: C 9 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.7092 (m-30) REVERT: C 16 ARG cc_start: 0.8235 (tmm-80) cc_final: 0.7610 (tmm-80) REVERT: C 37 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7440 (mt-10) REVERT: D 37 GLU cc_start: 0.7377 (pm20) cc_final: 0.7045 (pm20) REVERT: E 41 GLN cc_start: 0.7623 (tm-30) cc_final: 0.7072 (tm-30) REVERT: F 65 SER cc_start: 0.8719 (t) cc_final: 0.8176 (p) REVERT: G 19 ARG cc_start: 0.8218 (mtt-85) cc_final: 0.7680 (mmt180) REVERT: G 47 LYS cc_start: 0.8675 (tptp) cc_final: 0.8070 (tptm) REVERT: K 37 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: K 40 ASP cc_start: 0.8614 (p0) cc_final: 0.8067 (p0) REVERT: K 65 SER cc_start: 0.8273 (m) cc_final: 0.8005 (m) REVERT: L 11 TYR cc_start: 0.8719 (t80) cc_final: 0.8238 (t80) REVERT: L 19 ARG cc_start: 0.8537 (mtm-85) cc_final: 0.8238 (mtm110) REVERT: L 45 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7561 (mp) REVERT: R 141 ARG cc_start: 0.7498 (mtp85) cc_final: 0.7099 (mmm-85) outliers start: 28 outliers final: 21 residues processed: 259 average time/residue: 0.3310 time to fit residues: 117.0739 Evaluate side-chains 264 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 239 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 215 LEU Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 65 SER 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 I residue 38 SER Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 37 GLU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 9 ASP Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain R residue 19 LEU 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 Chi-restraints excluded: chain R residue 250 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 100 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 87 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 160 ASN ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN I 57 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.116873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.093870 restraints weight = 62985.578| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.17 r_work: 0.3118 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 13938 Z= 0.244 Angle : 0.609 6.383 19075 Z= 0.313 Chirality : 0.047 0.169 2145 Planarity : 0.005 0.048 2317 Dihedral : 10.742 93.078 2232 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.39 % Allowed : 13.52 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.22), residues: 1549 helix: -0.17 (0.30), residues: 330 sheet: -1.69 (0.23), residues: 466 loop : -0.66 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 19 TYR 0.014 0.002 TYR R 132 PHE 0.012 0.002 PHE R 182 TRP 0.012 0.001 TRP A 217 HIS 0.007 0.001 HIS R 246 Details of bonding type rmsd covalent geometry : bond 0.00586 (13938) covalent geometry : angle 0.60941 (19075) hydrogen bonds : bond 0.04077 ( 464) hydrogen bonds : angle 5.53408 ( 1284) *********************** 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 274 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 240 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7515 (tm-30) REVERT: C 7 LEU cc_start: 0.7748 (tt) cc_final: 0.7501 (tp) REVERT: C 16 ARG cc_start: 0.8242 (tmm-80) cc_final: 0.8041 (tmm-80) REVERT: C 37 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7543 (mt-10) REVERT: D 37 GLU cc_start: 0.7363 (pm20) cc_final: 0.6988 (pm20) REVERT: E 41 GLN cc_start: 0.7707 (tm-30) cc_final: 0.7085 (tm-30) REVERT: F 65 SER cc_start: 0.8716 (t) cc_final: 0.8168 (p) REVERT: G 19 ARG cc_start: 0.8245 (mtt-85) cc_final: 0.7656 (mmt180) REVERT: G 47 LYS cc_start: 0.8716 (tptp) cc_final: 0.8124 (tptm) REVERT: K 37 GLU cc_start: 0.7924 (mp0) cc_final: 0.7088 (mp0) REVERT: K 40 ASP cc_start: 0.8685 (p0) cc_final: 0.8091 (p0) REVERT: K 65 SER cc_start: 0.8224 (m) cc_final: 0.7933 (m) REVERT: L 11 TYR cc_start: 0.8725 (t80) cc_final: 0.8317 (t80) REVERT: L 19 ARG cc_start: 0.8612 (mtm-85) cc_final: 0.8314 (mtm110) REVERT: L 45 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7658 (mp) REVERT: L 47 LYS cc_start: 0.8688 (mtmt) cc_final: 0.8445 (pttp) REVERT: M 33 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.7961 (mp10) REVERT: R 141 ARG cc_start: 0.7576 (mtp85) cc_final: 0.7084 (mmm-85) outliers start: 34 outliers final: 26 residues processed: 262 average time/residue: 0.3200 time to fit residues: 114.1165 Evaluate side-chains 265 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 236 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 215 LEU Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain H residue 28 ASN 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 L 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 Chi-restraints excluded: chain R residue 234 ASN Chi-restraints excluded: chain R residue 250 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 0 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.119180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.096034 restraints weight = 62604.252| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.18 r_work: 0.3151 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13938 Z= 0.126 Angle : 0.552 6.380 19075 Z= 0.279 Chirality : 0.045 0.162 2145 Planarity : 0.005 0.054 2317 Dihedral : 10.579 92.579 2232 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.97 % Allowed : 14.15 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.22), residues: 1549 helix: -0.11 (0.30), residues: 336 sheet: -1.66 (0.23), residues: 456 loop : -0.51 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 16 TYR 0.012 0.001 TYR L 11 PHE 0.014 0.001 PHE R 41 TRP 0.010 0.001 TRP A 217 HIS 0.004 0.001 HIS B 246 Details of bonding type rmsd covalent geometry : bond 0.00300 (13938) covalent geometry : angle 0.55181 (19075) hydrogen bonds : bond 0.03569 ( 464) hydrogen bonds : angle 5.33412 ( 1284) *********************** 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 264 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 236 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7465 (tm-30) REVERT: B 16 GLU cc_start: 0.7960 (tp30) cc_final: 0.7708 (tp30) REVERT: C 7 LEU cc_start: 0.7495 (tt) cc_final: 0.7245 (tp) REVERT: C 16 ARG cc_start: 0.8239 (tmm-80) cc_final: 0.8015 (tmm-80) REVERT: D 37 GLU cc_start: 0.7442 (pm20) cc_final: 0.7093 (pm20) REVERT: F 65 SER cc_start: 0.8716 (t) cc_final: 0.8181 (p) REVERT: G 19 ARG cc_start: 0.8228 (mtt-85) cc_final: 0.7681 (mmt180) REVERT: G 47 LYS cc_start: 0.8684 (tptp) cc_final: 0.8097 (tptm) REVERT: K 37 GLU cc_start: 0.7860 (mp0) cc_final: 0.7033 (mp0) REVERT: K 40 ASP cc_start: 0.8629 (p0) cc_final: 0.8059 (p0) REVERT: K 65 SER cc_start: 0.8164 (m) cc_final: 0.7902 (m) REVERT: L 11 TYR cc_start: 0.8713 (t80) cc_final: 0.8327 (t80) REVERT: L 19 ARG cc_start: 0.8594 (mtm-85) cc_final: 0.8294 (mtm110) REVERT: M 33 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.7911 (mp10) REVERT: R 141 ARG cc_start: 0.7541 (mtp85) cc_final: 0.7212 (mmm-85) outliers start: 28 outliers final: 26 residues processed: 254 average time/residue: 0.3393 time to fit residues: 117.4258 Evaluate side-chains 259 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 215 LEU Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain D residue 38 SER 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 45 LEU Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L 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 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 Chi-restraints excluded: chain R residue 250 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 143 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 115 optimal weight: 0.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 ASN ** R 27 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 = 0.3609 r_free = 0.3609 target = 0.118569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.095320 restraints weight = 62440.697| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.18 r_work: 0.3135 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13938 Z= 0.163 Angle : 0.566 6.361 19075 Z= 0.287 Chirality : 0.045 0.164 2145 Planarity : 0.005 0.069 2317 Dihedral : 10.578 93.087 2232 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.11 % Allowed : 14.23 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.22), residues: 1549 helix: -0.28 (0.29), residues: 354 sheet: -1.67 (0.23), residues: 458 loop : -0.49 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 19 TYR 0.012 0.001 TYR L 11 PHE 0.013 0.001 PHE J 39 TRP 0.011 0.001 TRP A 217 HIS 0.004 0.001 HIS B 246 Details of bonding type rmsd covalent geometry : bond 0.00391 (13938) covalent geometry : angle 0.56554 (19075) hydrogen bonds : bond 0.03675 ( 464) hydrogen bonds : angle 5.31804 ( 1284) ********************** 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 266 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 236 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7468 (tm-30) REVERT: B 16 GLU cc_start: 0.7949 (tp30) cc_final: 0.7683 (tp30) REVERT: C 7 LEU cc_start: 0.7541 (tt) cc_final: 0.7317 (tp) REVERT: D 37 GLU cc_start: 0.7421 (pm20) cc_final: 0.7055 (pm20) REVERT: F 65 SER cc_start: 0.8777 (t) cc_final: 0.8238 (p) REVERT: G 19 ARG cc_start: 0.8243 (mtt-85) cc_final: 0.7683 (mmt180) REVERT: K 37 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: K 40 ASP cc_start: 0.8633 (p0) cc_final: 0.8068 (p0) REVERT: K 65 SER cc_start: 0.8129 (m) cc_final: 0.7864 (m) REVERT: L 11 TYR cc_start: 0.8712 (t80) cc_final: 0.8324 (t80) REVERT: L 19 ARG cc_start: 0.8608 (mtm-85) cc_final: 0.8301 (mtm110) REVERT: M 33 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.7929 (mp10) REVERT: R 141 ARG cc_start: 0.7582 (mtp85) cc_final: 0.7036 (mmm-85) REVERT: R 142 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7600 (mm-30) outliers start: 30 outliers final: 24 residues processed: 256 average time/residue: 0.3285 time to fit residues: 114.7423 Evaluate side-chains 259 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 233 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 215 LEU Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain D residue 38 SER 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 H residue 28 ASN Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 37 GLU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L 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 55 LEU Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 234 ASN Chi-restraints excluded: chain R residue 250 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 20 optimal weight: 0.2980 chunk 130 optimal weight: 10.0000 chunk 113 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.120390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097181 restraints weight = 62010.184| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.19 r_work: 0.3169 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13938 Z= 0.104 Angle : 0.537 6.327 19075 Z= 0.271 Chirality : 0.044 0.166 2145 Planarity : 0.005 0.064 2317 Dihedral : 10.447 92.175 2232 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.90 % Allowed : 14.37 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.22), residues: 1549 helix: -0.08 (0.29), residues: 352 sheet: -1.51 (0.23), residues: 476 loop : -0.32 (0.25), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 175 TYR 0.018 0.001 TYR R 91 PHE 0.016 0.001 PHE R 41 TRP 0.010 0.001 TRP R 217 HIS 0.004 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00248 (13938) covalent geometry : angle 0.53718 (19075) hydrogen bonds : bond 0.03335 ( 464) hydrogen bonds : angle 5.19274 ( 1284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6856.22 seconds wall clock time: 116 minutes 41.81 seconds (7001.81 seconds total)