Starting phenix.real_space_refine on Fri Sep 27 15:49:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqh_0945/09_2024/6lqh_0945.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqh_0945/09_2024/6lqh_0945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqh_0945/09_2024/6lqh_0945.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqh_0945/09_2024/6lqh_0945.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqh_0945/09_2024/6lqh_0945.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqh_0945/09_2024/6lqh_0945.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 10503 2.51 5 N 2853 2.21 5 O 3213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16623 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1589 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain: "a" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Restraints were copied for chains: f, c, g, b, h, e, i, d, C, B, E, D, G, F, I, H Time building chain proxies: 4.88, per 1000 atoms: 0.29 Number of scatterers: 16623 At special positions: 0 Unit cell: (112, 111, 115, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 3213 8.00 N 2853 7.00 C 10503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.86 Conformation dependent library (CDL) restraints added in 2.2 seconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3924 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 26.2% alpha, 42.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 81 through 90 Processing helix chain 'A' and resid 100 through 115 Processing helix chain 'A' and resid 226 through 249 Processing helix chain 'B' and resid 81 through 90 Processing helix chain 'B' and resid 100 through 115 Processing helix chain 'B' and resid 226 through 249 Processing helix chain 'C' and resid 81 through 90 Processing helix chain 'C' and resid 100 through 115 Processing helix chain 'C' and resid 226 through 249 Processing helix chain 'D' and resid 81 through 90 Processing helix chain 'D' and resid 100 through 115 Processing helix chain 'D' and resid 226 through 249 Processing helix chain 'E' and resid 81 through 90 Processing helix chain 'E' and resid 100 through 115 Processing helix chain 'E' and resid 226 through 249 Processing helix chain 'F' and resid 81 through 90 Processing helix chain 'F' and resid 100 through 115 Processing helix chain 'F' and resid 226 through 249 Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 100 through 115 Processing helix chain 'G' and resid 226 through 249 Processing helix chain 'H' and resid 81 through 90 Processing helix chain 'H' and resid 100 through 115 Processing helix chain 'H' and resid 226 through 249 Processing helix chain 'I' and resid 81 through 90 Processing helix chain 'I' and resid 100 through 115 Processing helix chain 'I' and resid 226 through 249 Processing helix chain 'a' and resid 35 through 47 removed outlier: 4.334A pdb=" N ALA a 39 " --> pdb=" O PRO a 35 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE a 40 " --> pdb=" O ASN a 36 " (cutoff:3.500A) Processing helix chain 'b' and resid 35 through 47 removed outlier: 4.335A pdb=" N ALA b 39 " --> pdb=" O PRO b 35 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE b 40 " --> pdb=" O ASN b 36 " (cutoff:3.500A) Processing helix chain 'c' and resid 35 through 47 removed outlier: 4.334A pdb=" N ALA c 39 " --> pdb=" O PRO c 35 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE c 40 " --> pdb=" O ASN c 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 35 through 47 removed outlier: 4.335A pdb=" N ALA d 39 " --> pdb=" O PRO d 35 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE d 40 " --> pdb=" O ASN d 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 35 through 47 removed outlier: 4.335A pdb=" N ALA e 39 " --> pdb=" O PRO e 35 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE e 40 " --> pdb=" O ASN e 36 " (cutoff:3.500A) Processing helix chain 'f' and resid 35 through 47 removed outlier: 4.334A pdb=" N ALA f 39 " --> pdb=" O PRO f 35 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE f 40 " --> pdb=" O ASN f 36 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 47 removed outlier: 4.334A pdb=" N ALA g 39 " --> pdb=" O PRO g 35 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE g 40 " --> pdb=" O ASN g 36 " (cutoff:3.500A) Processing helix chain 'h' and resid 35 through 47 removed outlier: 4.335A pdb=" N ALA h 39 " --> pdb=" O PRO h 35 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE h 40 " --> pdb=" O ASN h 36 " (cutoff:3.500A) Processing helix chain 'i' and resid 35 through 47 removed outlier: 4.335A pdb=" N ALA i 39 " --> pdb=" O PRO i 35 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE i 40 " --> pdb=" O ASN i 36 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 removed outlier: 7.100A pdb=" N GLN A 57 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLY A 144 " --> pdb=" O GLN A 57 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL A 149 " --> pdb=" O ASN B 224 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG B 207 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE B 186 " --> pdb=" O ASN B 180 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN B 180 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA B 163 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY B 155 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR B 165 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY B 153 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR B 167 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER B 151 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B 169 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN B 171 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER B 147 " --> pdb=" O GLN B 171 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA B 173 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR B 145 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASN B 175 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE B 143 " --> pdb=" O ASN B 175 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG B 177 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER B 141 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 179 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU B 139 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE B 136 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 52 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE B 49 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU B 96 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 51 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 56 through 57 removed outlier: 7.100A pdb=" N GLN B 57 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLY B 144 " --> pdb=" O GLN B 57 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL B 149 " --> pdb=" O ASN E 224 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG E 213 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG E 207 " --> pdb=" O LEU E 215 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE E 186 " --> pdb=" O ASN E 180 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN E 180 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA E 163 " --> pdb=" O GLY E 155 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY E 155 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR E 165 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY E 153 " --> pdb=" O THR E 165 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR E 167 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER E 151 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU E 169 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN E 171 " --> pdb=" O SER E 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER E 147 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA E 173 " --> pdb=" O TYR E 145 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR E 145 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN E 175 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE E 143 " --> pdb=" O ASN E 175 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG E 177 " --> pdb=" O SER E 141 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER E 141 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL E 179 " --> pdb=" O GLU E 139 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLU E 139 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE E 136 " --> pdb=" O PHE E 50 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER E 52 " --> pdb=" O ILE E 136 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 56 through 57 removed outlier: 7.100A pdb=" N GLN E 57 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLY E 144 " --> pdb=" O GLN E 57 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL E 149 " --> pdb=" O ASN H 224 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG H 213 " --> pdb=" O ILE H 209 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG H 207 " --> pdb=" O LEU H 215 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE H 186 " --> pdb=" O ASN H 180 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN H 180 " --> pdb=" O ILE H 186 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA H 163 " --> pdb=" O GLY H 155 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY H 155 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR H 165 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY H 153 " --> pdb=" O THR H 165 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR H 167 " --> pdb=" O SER H 151 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER H 151 " --> pdb=" O TYR H 167 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU H 169 " --> pdb=" O VAL H 149 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN H 171 " --> pdb=" O SER H 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER H 147 " --> pdb=" O GLN H 171 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA H 173 " --> pdb=" O TYR H 145 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR H 145 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN H 175 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE H 143 " --> pdb=" O ASN H 175 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG H 177 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER H 141 " --> pdb=" O ARG H 177 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL H 179 " --> pdb=" O GLU H 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU H 139 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE H 136 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER H 52 " --> pdb=" O ILE H 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 56 through 57 removed outlier: 7.099A pdb=" N GLN H 57 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLY H 144 " --> pdb=" O GLN H 57 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL H 149 " --> pdb=" O ASN F 224 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG F 213 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG F 207 " --> pdb=" O LEU F 215 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE F 186 " --> pdb=" O ASN F 180 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN F 180 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA F 163 " --> pdb=" O GLY F 155 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY F 155 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR F 165 " --> pdb=" O GLY F 153 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY F 153 " --> pdb=" O THR F 165 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR F 167 " --> pdb=" O SER F 151 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER F 151 " --> pdb=" O TYR F 167 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU F 169 " --> pdb=" O VAL F 149 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN F 171 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER F 147 " --> pdb=" O GLN F 171 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA F 173 " --> pdb=" O TYR F 145 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR F 145 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN F 175 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE F 143 " --> pdb=" O ASN F 175 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ARG F 177 " --> pdb=" O SER F 141 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N SER F 141 " --> pdb=" O ARG F 177 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL F 179 " --> pdb=" O GLU F 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU F 139 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE F 136 " --> pdb=" O PHE F 50 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER F 52 " --> pdb=" O ILE F 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 56 through 57 removed outlier: 7.100A pdb=" N GLN F 57 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLY F 144 " --> pdb=" O GLN F 57 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL F 149 " --> pdb=" O ASN D 224 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG D 207 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE D 186 " --> pdb=" O ASN D 180 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASN D 180 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA D 163 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY D 155 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR D 165 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY D 153 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR D 167 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER D 151 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU D 169 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLN D 171 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER D 147 " --> pdb=" O GLN D 171 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ALA D 173 " --> pdb=" O TYR D 145 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR D 145 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASN D 175 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE D 143 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG D 177 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER D 141 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL D 179 " --> pdb=" O GLU D 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU D 139 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE D 136 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER D 52 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 56 through 57 removed outlier: 7.100A pdb=" N GLN D 57 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLY D 144 " --> pdb=" O GLN D 57 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL D 149 " --> pdb=" O ASN C 224 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 207 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE C 186 " --> pdb=" O ASN C 180 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN C 180 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA C 163 " --> pdb=" O GLY C 155 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY C 155 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR C 165 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY C 153 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR C 167 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER C 151 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU C 169 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLN C 171 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER C 147 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA C 173 " --> pdb=" O TYR C 145 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR C 145 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN C 175 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE C 143 " --> pdb=" O ASN C 175 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG C 177 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N SER C 141 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL C 179 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU C 139 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE C 136 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 52 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE C 49 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU C 96 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C 51 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 57 removed outlier: 7.100A pdb=" N GLN C 57 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLY C 144 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL C 149 " --> pdb=" O ASN G 224 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG G 213 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG G 207 " --> pdb=" O LEU G 215 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE G 186 " --> pdb=" O ASN G 180 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN G 180 " --> pdb=" O ILE G 186 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA G 163 " --> pdb=" O GLY G 155 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY G 155 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR G 165 " --> pdb=" O GLY G 153 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY G 153 " --> pdb=" O THR G 165 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR G 167 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER G 151 " --> pdb=" O TYR G 167 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU G 169 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN G 171 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER G 147 " --> pdb=" O GLN G 171 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA G 173 " --> pdb=" O TYR G 145 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR G 145 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN G 175 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE G 143 " --> pdb=" O ASN G 175 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG G 177 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER G 141 " --> pdb=" O ARG G 177 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL G 179 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU G 139 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE G 136 " --> pdb=" O PHE G 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER G 52 " --> pdb=" O ILE G 136 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE G 49 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU G 96 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL G 51 " --> pdb=" O LEU G 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 56 through 57 removed outlier: 7.100A pdb=" N GLN G 57 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLY G 144 " --> pdb=" O GLN G 57 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL G 149 " --> pdb=" O ASN I 224 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG I 213 " --> pdb=" O ILE I 209 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG I 207 " --> pdb=" O LEU I 215 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE I 186 " --> pdb=" O ASN I 180 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASN I 180 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA I 163 " --> pdb=" O GLY I 155 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY I 155 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR I 165 " --> pdb=" O GLY I 153 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY I 153 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR I 167 " --> pdb=" O SER I 151 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER I 151 " --> pdb=" O TYR I 167 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU I 169 " --> pdb=" O VAL I 149 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN I 171 " --> pdb=" O SER I 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER I 147 " --> pdb=" O GLN I 171 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA I 173 " --> pdb=" O TYR I 145 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR I 145 " --> pdb=" O ALA I 173 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN I 175 " --> pdb=" O ILE I 143 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE I 143 " --> pdb=" O ASN I 175 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG I 177 " --> pdb=" O SER I 141 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER I 141 " --> pdb=" O ARG I 177 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL I 179 " --> pdb=" O GLU I 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU I 139 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE I 136 " --> pdb=" O PHE I 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER I 52 " --> pdb=" O ILE I 136 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 56 through 57 removed outlier: 7.099A pdb=" N GLN I 57 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLY I 144 " --> pdb=" O GLN I 57 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL I 149 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 207 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE A 186 " --> pdb=" O ASN A 180 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN A 180 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA A 163 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY A 155 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR A 165 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY A 153 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR A 167 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER A 151 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A 169 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN A 171 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N SER A 147 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ALA A 173 " --> pdb=" O TYR A 145 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR A 145 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN A 175 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE A 143 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ARG A 177 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER A 141 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A 179 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU A 139 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 136 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 52 " --> pdb=" O ILE A 136 " (cutoff:3.500A) 774 hydrogen bonds defined for protein. 2295 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: 4.40 Time building geometry restraints manager: 4.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5597 1.34 - 1.45: 2474 1.45 - 1.57: 8732 1.57 - 1.68: 0 1.68 - 1.80: 99 Bond restraints: 16902 Sorted by residual: bond pdb=" CG PRO C 67 " pdb=" CD PRO C 67 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.70e-02 1.37e+03 2.17e+00 bond pdb=" CG PRO H 67 " pdb=" CD PRO H 67 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.70e-02 1.37e+03 2.17e+00 bond pdb=" CG PRO I 67 " pdb=" CD PRO I 67 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.70e-02 1.37e+03 2.14e+00 bond pdb=" CG PRO G 67 " pdb=" CD PRO G 67 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.70e-02 1.37e+03 2.14e+00 bond pdb=" CG PRO D 67 " pdb=" CD PRO D 67 " ideal model delta sigma weight residual 1.512 1.473 0.039 2.70e-02 1.37e+03 2.10e+00 ... (remaining 16897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 21972 1.75 - 3.49: 780 3.49 - 5.24: 126 5.24 - 6.99: 18 6.99 - 8.73: 27 Bond angle restraints: 22923 Sorted by residual: angle pdb=" N GLY d 33 " pdb=" CA GLY d 33 " pdb=" C GLY d 33 " ideal model delta sigma weight residual 113.18 121.91 -8.73 2.37e+00 1.78e-01 1.36e+01 angle pdb=" N GLY g 33 " pdb=" CA GLY g 33 " pdb=" C GLY g 33 " ideal model delta sigma weight residual 113.18 121.89 -8.71 2.37e+00 1.78e-01 1.35e+01 angle pdb=" N GLY f 33 " pdb=" CA GLY f 33 " pdb=" C GLY f 33 " ideal model delta sigma weight residual 113.18 121.88 -8.70 2.37e+00 1.78e-01 1.35e+01 angle pdb=" N GLY a 33 " pdb=" CA GLY a 33 " pdb=" C GLY a 33 " ideal model delta sigma weight residual 113.18 121.88 -8.70 2.37e+00 1.78e-01 1.35e+01 angle pdb=" N GLY h 33 " pdb=" CA GLY h 33 " pdb=" C GLY h 33 " ideal model delta sigma weight residual 113.18 121.87 -8.69 2.37e+00 1.78e-01 1.35e+01 ... (remaining 22918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.68: 8668 15.68 - 31.37: 899 31.37 - 47.05: 243 47.05 - 62.73: 189 62.73 - 78.42: 36 Dihedral angle restraints: 10035 sinusoidal: 3888 harmonic: 6147 Sorted by residual: dihedral pdb=" CA GLN A 99 " pdb=" C GLN A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta harmonic sigma weight residual -180.00 -152.45 -27.55 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA GLN E 99 " pdb=" C GLN E 99 " pdb=" N GLY E 100 " pdb=" CA GLY E 100 " ideal model delta harmonic sigma weight residual -180.00 -152.45 -27.55 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA GLN H 99 " pdb=" C GLN H 99 " pdb=" N GLY H 100 " pdb=" CA GLY H 100 " ideal model delta harmonic sigma weight residual -180.00 -152.46 -27.54 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 10032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1410 0.037 - 0.074: 842 0.074 - 0.111: 244 0.111 - 0.148: 89 0.148 - 0.185: 16 Chirality restraints: 2601 Sorted by residual: chirality pdb=" CA PHE h 31 " pdb=" N PHE h 31 " pdb=" C PHE h 31 " pdb=" CB PHE h 31 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CA PHE d 31 " pdb=" N PHE d 31 " pdb=" C PHE d 31 " pdb=" CB PHE d 31 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA PHE c 31 " pdb=" N PHE c 31 " pdb=" C PHE c 31 " pdb=" CB PHE c 31 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 2598 not shown) Planarity restraints: 3024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE f 31 " 0.014 2.00e-02 2.50e+03 1.31e-02 3.02e+00 pdb=" CG PHE f 31 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE f 31 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE f 31 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE f 31 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE f 31 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE f 31 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE h 31 " 0.014 2.00e-02 2.50e+03 1.31e-02 3.00e+00 pdb=" CG PHE h 31 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE h 31 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE h 31 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE h 31 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE h 31 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE h 31 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE b 31 " -0.014 2.00e-02 2.50e+03 1.30e-02 2.98e+00 pdb=" CG PHE b 31 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE b 31 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE b 31 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE b 31 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE b 31 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE b 31 " -0.002 2.00e-02 2.50e+03 ... (remaining 3021 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4554 2.79 - 3.32: 15055 3.32 - 3.85: 29376 3.85 - 4.37: 35899 4.37 - 4.90: 62728 Nonbonded interactions: 147612 Sorted by model distance: nonbonded pdb=" O SER e 50 " pdb=" OG SER e 50 " model vdw 2.268 3.040 nonbonded pdb=" O SER f 50 " pdb=" OG SER f 50 " model vdw 2.268 3.040 nonbonded pdb=" O SER d 50 " pdb=" OG SER d 50 " model vdw 2.269 3.040 nonbonded pdb=" O SER b 50 " pdb=" OG SER b 50 " model vdw 2.269 3.040 nonbonded pdb=" O SER c 50 " pdb=" OG SER c 50 " model vdw 2.269 3.040 ... (remaining 147607 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 30.950 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 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:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 16902 Z= 0.543 Angle : 0.825 8.734 22923 Z= 0.461 Chirality : 0.051 0.185 2601 Planarity : 0.004 0.027 3024 Dihedral : 17.093 78.418 6111 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 9.05 % Allowed : 11.56 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.16), residues: 2124 helix: -1.15 (0.17), residues: 576 sheet: -0.81 (0.21), residues: 666 loop : -3.05 (0.16), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 252 PHE 0.031 0.002 PHE f 31 TYR 0.013 0.002 TYR E 158 ARG 0.003 0.001 ARG c 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 427 time to evaluate : 1.873 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8917 (mttp) cc_final: 0.8704 (mttt) REVERT: A 109 LYS cc_start: 0.8794 (mttp) cc_final: 0.8560 (mttt) REVERT: A 232 MET cc_start: 0.7953 (tpt) cc_final: 0.7439 (tpt) REVERT: B 70 ASN cc_start: 0.8423 (m-40) cc_final: 0.8151 (m-40) REVERT: B 170 ASP cc_start: 0.8106 (m-30) cc_final: 0.7904 (m-30) REVERT: C 48 LYS cc_start: 0.8463 (mttt) cc_final: 0.8263 (mttt) REVERT: C 70 ASN cc_start: 0.8420 (m-40) cc_final: 0.8018 (m-40) REVERT: C 166 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: C 185 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7557 (pt0) REVERT: D 70 ASN cc_start: 0.8450 (m-40) cc_final: 0.8060 (m-40) REVERT: D 88 LYS cc_start: 0.8891 (tptp) cc_final: 0.8677 (tptm) REVERT: D 109 LYS cc_start: 0.8838 (mttp) cc_final: 0.8537 (mtmt) REVERT: D 137 MET cc_start: 0.8463 (ttm) cc_final: 0.8125 (ttp) REVERT: D 141 SER cc_start: 0.9138 (OUTLIER) cc_final: 0.8909 (p) REVERT: D 166 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: D 170 ASP cc_start: 0.8182 (m-30) cc_final: 0.7972 (m-30) REVERT: E 109 LYS cc_start: 0.8863 (mttp) cc_final: 0.8661 (mttp) REVERT: E 166 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: E 170 ASP cc_start: 0.8193 (m-30) cc_final: 0.7934 (m-30) REVERT: E 185 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7472 (pt0) REVERT: F 70 ASN cc_start: 0.8410 (m-40) cc_final: 0.8143 (m110) REVERT: F 102 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7772 (tp40) REVERT: F 137 MET cc_start: 0.8380 (ttm) cc_final: 0.8083 (ttp) REVERT: F 141 SER cc_start: 0.9180 (OUTLIER) cc_final: 0.8898 (p) REVERT: F 166 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: F 213 ARG cc_start: 0.8306 (mmt-90) cc_final: 0.7918 (mmt180) REVERT: F 240 ILE cc_start: 0.8779 (mt) cc_final: 0.8549 (mp) REVERT: G 59 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7540 (mt-10) REVERT: G 88 LYS cc_start: 0.8909 (tptp) cc_final: 0.8581 (mtpp) REVERT: G 109 LYS cc_start: 0.8799 (mttp) cc_final: 0.8527 (mttt) REVERT: G 166 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: H 59 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7642 (mt-10) REVERT: H 109 LYS cc_start: 0.8825 (mttp) cc_final: 0.8595 (mttt) REVERT: H 141 SER cc_start: 0.9145 (OUTLIER) cc_final: 0.8942 (p) REVERT: H 185 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7431 (pt0) REVERT: H 193 SER cc_start: 0.8671 (OUTLIER) cc_final: 0.8467 (t) REVERT: H 200 GLU cc_start: 0.7820 (tt0) cc_final: 0.7604 (tt0) REVERT: I 64 LYS cc_start: 0.8904 (mttp) cc_final: 0.8660 (mttt) REVERT: I 70 ASN cc_start: 0.8486 (m-40) cc_final: 0.8273 (m110) REVERT: I 88 LYS cc_start: 0.8909 (tptp) cc_final: 0.8596 (mtpp) REVERT: I 109 LYS cc_start: 0.8795 (mttp) cc_final: 0.8573 (mttp) REVERT: I 167 TYR cc_start: 0.8685 (p90) cc_final: 0.8439 (p90) REVERT: I 185 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7516 (pt0) REVERT: e 44 SER cc_start: 0.8427 (p) cc_final: 0.8191 (p) REVERT: h 44 SER cc_start: 0.8536 (p) cc_final: 0.8317 (p) outliers start: 162 outliers final: 57 residues processed: 559 average time/residue: 1.3614 time to fit residues: 838.7665 Evaluate side-chains 376 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 306 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 166 GLN Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 166 GLN Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 252 TRP Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 198 SER Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 185 GLU Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 252 TRP Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 252 TRP Chi-restraints excluded: chain a residue 50 SER Chi-restraints excluded: chain b residue 50 SER Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain d residue 50 SER Chi-restraints excluded: chain e residue 50 SER Chi-restraints excluded: chain f residue 50 SER Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain h residue 50 SER Chi-restraints excluded: chain i residue 50 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 148 ASN A 212 GLN B 62 GLN B 148 ASN C 62 GLN D 62 GLN D 77 GLN D 148 ASN E 62 GLN E 148 ASN E 171 GLN F 62 GLN F 77 GLN F 148 ASN F 212 GLN G 62 GLN G 70 ASN G 77 GLN ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN H 168 GLN I 62 GLN I 77 GLN I 148 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16902 Z= 0.242 Angle : 0.665 8.040 22923 Z= 0.349 Chirality : 0.047 0.141 2601 Planarity : 0.004 0.024 3024 Dihedral : 9.102 84.655 2422 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.63 % Allowed : 17.76 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.17), residues: 2124 helix: 0.75 (0.20), residues: 585 sheet: -0.68 (0.22), residues: 612 loop : -2.34 (0.16), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 92 PHE 0.019 0.001 PHE d 31 TYR 0.010 0.001 TYR C 199 ARG 0.006 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 307 time to evaluate : 1.807 Fit side-chains REVERT: A 66 TYR cc_start: 0.8591 (t80) cc_final: 0.8311 (t80) REVERT: A 232 MET cc_start: 0.7800 (tpt) cc_final: 0.7584 (tpt) REVERT: B 70 ASN cc_start: 0.8280 (m-40) cc_final: 0.8010 (m-40) REVERT: B 146 GLU cc_start: 0.7301 (tp30) cc_final: 0.7022 (mm-30) REVERT: B 213 ARG cc_start: 0.8040 (mmt-90) cc_final: 0.7763 (mmt180) REVERT: B 249 ARG cc_start: 0.7457 (ptp90) cc_final: 0.7208 (ptp90) REVERT: C 59 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7488 (mt-10) REVERT: C 70 ASN cc_start: 0.8292 (m-40) cc_final: 0.7965 (m-40) REVERT: C 146 GLU cc_start: 0.7273 (tp30) cc_final: 0.7048 (mm-30) REVERT: C 185 GLU cc_start: 0.7795 (tt0) cc_final: 0.7569 (pt0) REVERT: C 249 ARG cc_start: 0.7468 (ptp90) cc_final: 0.7182 (ptp90) REVERT: D 70 ASN cc_start: 0.8347 (m-40) cc_final: 0.8034 (m-40) REVERT: D 88 LYS cc_start: 0.8758 (tptp) cc_final: 0.8495 (mtpp) REVERT: D 137 MET cc_start: 0.8430 (ttm) cc_final: 0.8022 (ttp) REVERT: D 146 GLU cc_start: 0.7425 (tp30) cc_final: 0.7140 (mm-30) REVERT: D 166 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: D 249 ARG cc_start: 0.7503 (ptt-90) cc_final: 0.7140 (ptm-80) REVERT: E 185 GLU cc_start: 0.7764 (tt0) cc_final: 0.7560 (pt0) REVERT: E 249 ARG cc_start: 0.7332 (ptp90) cc_final: 0.7051 (ptm-80) REVERT: F 131 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8120 (mp) REVERT: F 137 MET cc_start: 0.8355 (ttm) cc_final: 0.8143 (ttp) REVERT: F 166 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7732 (tt0) REVERT: F 213 ARG cc_start: 0.8221 (mmt-90) cc_final: 0.7948 (mmt-90) REVERT: F 249 ARG cc_start: 0.7662 (ptt-90) cc_final: 0.7212 (ptm-80) REVERT: G 88 LYS cc_start: 0.8735 (tptp) cc_final: 0.8398 (mtpp) REVERT: H 146 GLU cc_start: 0.7298 (tp30) cc_final: 0.7096 (mm-30) REVERT: H 249 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7080 (ptm-80) REVERT: I 59 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7560 (mt-10) REVERT: b 44 SER cc_start: 0.8693 (p) cc_final: 0.8371 (p) REVERT: e 44 SER cc_start: 0.8413 (p) cc_final: 0.8113 (p) REVERT: f 44 SER cc_start: 0.8549 (p) cc_final: 0.8246 (p) REVERT: h 44 SER cc_start: 0.8410 (p) cc_final: 0.8207 (p) outliers start: 65 outliers final: 28 residues processed: 359 average time/residue: 1.4092 time to fit residues: 555.9022 Evaluate side-chains 310 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 278 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 166 GLN Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 166 GLN Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 252 TRP Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain H residue 252 TRP Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 252 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 chunk 128 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 188 optimal weight: 9.9990 chunk 203 optimal weight: 9.9990 chunk 167 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 64 optimal weight: 0.0670 chunk 151 optimal weight: 10.0000 overall best weight: 3.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 148 ASN A 180 ASN B 148 ASN B 180 ASN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN D 148 ASN D 166 GLN D 180 ASN E 148 ASN E 180 ASN F 180 ASN G 70 ASN G 180 ASN H 57 GLN H 148 ASN H 180 ASN I 180 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 16902 Z= 0.407 Angle : 0.704 8.247 22923 Z= 0.367 Chirality : 0.049 0.148 2601 Planarity : 0.004 0.029 3024 Dihedral : 8.376 77.535 2362 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.96 % Allowed : 18.31 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.18), residues: 2124 helix: 1.10 (0.20), residues: 585 sheet: -0.55 (0.21), residues: 702 loop : -2.43 (0.18), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 92 PHE 0.027 0.002 PHE d 31 TYR 0.014 0.002 TYR C 199 ARG 0.005 0.001 ARG I 249 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 298 time to evaluate : 1.951 Fit side-chains REVERT: A 66 TYR cc_start: 0.8595 (t80) cc_final: 0.8333 (t80) REVERT: A 249 ARG cc_start: 0.7466 (ptt-90) cc_final: 0.6955 (ptm-80) REVERT: B 70 ASN cc_start: 0.8407 (m-40) cc_final: 0.8154 (m-40) REVERT: B 146 GLU cc_start: 0.7273 (tp30) cc_final: 0.6993 (mm-30) REVERT: B 249 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7222 (ptp90) REVERT: C 185 GLU cc_start: 0.7821 (tt0) cc_final: 0.7571 (pt0) REVERT: D 70 ASN cc_start: 0.8342 (m-40) cc_final: 0.8061 (m-40) REVERT: D 88 LYS cc_start: 0.8828 (tptp) cc_final: 0.8583 (tptm) REVERT: D 137 MET cc_start: 0.8434 (ttm) cc_final: 0.8031 (ttp) REVERT: D 146 GLU cc_start: 0.7405 (tp30) cc_final: 0.7162 (mm-30) REVERT: D 249 ARG cc_start: 0.7615 (ptt-90) cc_final: 0.7298 (ptm160) REVERT: E 59 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7444 (mt-10) REVERT: E 146 GLU cc_start: 0.7536 (tp30) cc_final: 0.7334 (tp30) REVERT: E 166 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7881 (tt0) REVERT: E 249 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7096 (ptm-80) REVERT: F 131 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8369 (mp) REVERT: F 166 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: F 249 ARG cc_start: 0.7622 (ptt-90) cc_final: 0.7301 (ptm160) REVERT: G 59 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7683 (mt-10) REVERT: G 88 LYS cc_start: 0.8864 (tptp) cc_final: 0.8493 (mtpp) REVERT: H 146 GLU cc_start: 0.7284 (tp30) cc_final: 0.7034 (mm-30) REVERT: H 249 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7137 (ptm160) REVERT: I 97 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6848 (tm-30) REVERT: I 170 ASP cc_start: 0.8192 (m-30) cc_final: 0.7952 (m-30) REVERT: e 44 SER cc_start: 0.8395 (p) cc_final: 0.8116 (p) REVERT: f 44 SER cc_start: 0.8510 (p) cc_final: 0.8234 (p) REVERT: h 44 SER cc_start: 0.8463 (p) cc_final: 0.8248 (p) outliers start: 71 outliers final: 39 residues processed: 356 average time/residue: 1.5165 time to fit residues: 591.3992 Evaluate side-chains 320 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 274 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 109 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 249 ARG Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 166 GLN Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 252 TRP Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain H residue 252 TRP Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 252 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 20 optimal weight: 0.2980 chunk 89 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 200 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN D 148 ASN E 148 ASN F 148 ASN ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 GLN H 148 ASN I 148 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16902 Z= 0.201 Angle : 0.598 7.680 22923 Z= 0.310 Chirality : 0.045 0.137 2601 Planarity : 0.003 0.032 3024 Dihedral : 7.263 69.705 2354 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.85 % Allowed : 18.87 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.18), residues: 2124 helix: 1.99 (0.22), residues: 585 sheet: -0.34 (0.21), residues: 702 loop : -2.37 (0.18), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 92 PHE 0.016 0.001 PHE h 31 TYR 0.011 0.001 TYR C 199 ARG 0.005 0.000 ARG I 249 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 263 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 TYR cc_start: 0.8497 (t80) cc_final: 0.8186 (t80) REVERT: A 97 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6384 (tm-30) REVERT: A 219 VAL cc_start: 0.8713 (t) cc_final: 0.8467 (p) REVERT: A 249 ARG cc_start: 0.7534 (ptt-90) cc_final: 0.7077 (ptm160) REVERT: B 109 LYS cc_start: 0.8727 (mttp) cc_final: 0.8476 (mtmt) REVERT: B 146 GLU cc_start: 0.7212 (tp30) cc_final: 0.7002 (mm-30) REVERT: B 219 VAL cc_start: 0.8762 (t) cc_final: 0.8509 (p) REVERT: C 170 ASP cc_start: 0.7945 (m-30) cc_final: 0.7734 (m-30) REVERT: D 88 LYS cc_start: 0.8669 (tptp) cc_final: 0.8438 (tptm) REVERT: D 109 LYS cc_start: 0.8595 (mttt) cc_final: 0.8330 (mtmt) REVERT: D 137 MET cc_start: 0.8377 (ttm) cc_final: 0.7943 (ttp) REVERT: D 146 GLU cc_start: 0.7264 (tp30) cc_final: 0.7029 (mm-30) REVERT: D 228 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8512 (ptt) REVERT: D 249 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7218 (ptm160) REVERT: E 166 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: F 219 VAL cc_start: 0.8757 (t) cc_final: 0.8443 (p) REVERT: F 249 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7269 (ptm160) REVERT: G 48 LYS cc_start: 0.8236 (mttp) cc_final: 0.7997 (mttt) REVERT: G 88 LYS cc_start: 0.8766 (tptp) cc_final: 0.8432 (mtpp) REVERT: H 249 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.7042 (ptm-80) REVERT: I 131 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8066 (mp) REVERT: f 44 SER cc_start: 0.8394 (p) cc_final: 0.8194 (p) outliers start: 69 outliers final: 31 residues processed: 315 average time/residue: 1.5243 time to fit residues: 525.3822 Evaluate side-chains 289 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 251 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 249 ARG Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain F residue 252 TRP Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain H residue 252 TRP Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 252 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 148 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 170 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN D 148 ASN F 148 ASN ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN I 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 16902 Z= 0.342 Angle : 0.661 8.130 22923 Z= 0.346 Chirality : 0.047 0.159 2601 Planarity : 0.004 0.029 3024 Dihedral : 7.388 74.151 2347 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.96 % Allowed : 18.98 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.18), residues: 2124 helix: 1.78 (0.21), residues: 585 sheet: -0.15 (0.21), residues: 702 loop : -2.31 (0.18), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 92 PHE 0.022 0.002 PHE d 31 TYR 0.012 0.001 TYR F 199 ARG 0.004 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 278 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 TYR cc_start: 0.8519 (t80) cc_final: 0.8213 (t80) REVERT: A 97 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6431 (tm-30) REVERT: A 219 VAL cc_start: 0.8724 (t) cc_final: 0.8456 (p) REVERT: A 249 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7186 (ptm160) REVERT: B 70 ASN cc_start: 0.8430 (m-40) cc_final: 0.8171 (m-40) REVERT: B 219 VAL cc_start: 0.8779 (t) cc_final: 0.8569 (p) REVERT: C 170 ASP cc_start: 0.7957 (m-30) cc_final: 0.7754 (m-30) REVERT: C 216 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6798 (mt-10) REVERT: C 249 ARG cc_start: 0.7043 (ptm-80) cc_final: 0.6671 (ptm160) REVERT: D 70 ASN cc_start: 0.8311 (m-40) cc_final: 0.8061 (m-40) REVERT: D 88 LYS cc_start: 0.8759 (tptp) cc_final: 0.8519 (tptm) REVERT: D 109 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8387 (mtmt) REVERT: D 137 MET cc_start: 0.8418 (ttm) cc_final: 0.7997 (ttp) REVERT: D 146 GLU cc_start: 0.7398 (tp30) cc_final: 0.7155 (mm-30) REVERT: D 219 VAL cc_start: 0.8799 (t) cc_final: 0.8476 (p) REVERT: D 249 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7303 (ptm160) REVERT: E 59 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7439 (mt-10) REVERT: E 166 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: E 218 GLU cc_start: 0.7111 (tp30) cc_final: 0.6784 (tp30) REVERT: E 251 LEU cc_start: 0.7254 (mp) cc_final: 0.6876 (mp) REVERT: F 170 ASP cc_start: 0.7985 (m-30) cc_final: 0.7714 (m-30) REVERT: F 219 VAL cc_start: 0.8786 (t) cc_final: 0.8502 (p) REVERT: F 249 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7250 (ptm160) REVERT: G 48 LYS cc_start: 0.8272 (mttp) cc_final: 0.8032 (mttt) REVERT: G 59 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7622 (mt-10) REVERT: G 88 LYS cc_start: 0.8849 (tptp) cc_final: 0.8491 (mtpp) REVERT: H 225 GLU cc_start: 0.8089 (tt0) cc_final: 0.7666 (tt0) REVERT: H 249 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.7107 (ptm160) REVERT: I 97 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6775 (tm-30) outliers start: 71 outliers final: 31 residues processed: 331 average time/residue: 1.5483 time to fit residues: 560.6894 Evaluate side-chains 301 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 262 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 249 ARG Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain F residue 252 TRP Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain H residue 252 TRP Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 252 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 200 optimal weight: 20.0000 chunk 166 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 105 optimal weight: 0.2980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 168 GLN B 148 ASN D 148 ASN E 148 ASN F 148 ASN H 57 GLN H 148 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16902 Z= 0.261 Angle : 0.630 8.741 22923 Z= 0.330 Chirality : 0.046 0.149 2601 Planarity : 0.003 0.029 3024 Dihedral : 7.239 74.163 2347 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.35 % Allowed : 19.99 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.19), residues: 2124 helix: 2.07 (0.21), residues: 585 sheet: 0.15 (0.22), residues: 657 loop : -2.05 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 92 PHE 0.020 0.001 PHE d 31 TYR 0.013 0.001 TYR F 199 ARG 0.006 0.000 ARG I 249 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 265 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 TYR cc_start: 0.8470 (t80) cc_final: 0.8144 (t80) REVERT: A 97 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6442 (tm-30) REVERT: A 249 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7103 (ptm160) REVERT: B 109 LYS cc_start: 0.8727 (mttp) cc_final: 0.8416 (mtmt) REVERT: C 219 VAL cc_start: 0.8601 (t) cc_final: 0.8232 (p) REVERT: C 249 ARG cc_start: 0.6861 (ptm-80) cc_final: 0.6529 (ptm160) REVERT: C 251 LEU cc_start: 0.7293 (mp) cc_final: 0.7066 (mp) REVERT: D 70 ASN cc_start: 0.8266 (m-40) cc_final: 0.8028 (m-40) REVERT: D 88 LYS cc_start: 0.8702 (tptp) cc_final: 0.8272 (mtpp) REVERT: D 109 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8389 (mtmt) REVERT: D 137 MET cc_start: 0.8403 (ttm) cc_final: 0.7983 (ttp) REVERT: D 146 GLU cc_start: 0.7309 (tp30) cc_final: 0.7042 (mm-30) REVERT: D 219 VAL cc_start: 0.8769 (t) cc_final: 0.8481 (p) REVERT: D 249 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7258 (ptm160) REVERT: E 166 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: E 251 LEU cc_start: 0.7179 (mp) cc_final: 0.6918 (mp) REVERT: F 170 ASP cc_start: 0.7978 (m-30) cc_final: 0.7737 (m-30) REVERT: F 219 VAL cc_start: 0.8765 (t) cc_final: 0.8542 (p) REVERT: F 249 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.7149 (ptm160) REVERT: G 48 LYS cc_start: 0.8268 (mttp) cc_final: 0.8024 (mttt) REVERT: G 59 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7589 (mt-10) REVERT: G 88 LYS cc_start: 0.8824 (tptp) cc_final: 0.8482 (mtpp) REVERT: H 249 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7079 (ptm160) outliers start: 60 outliers final: 38 residues processed: 310 average time/residue: 1.5385 time to fit residues: 521.2672 Evaluate side-chains 299 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 254 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 249 ARG Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain F residue 252 TRP Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain H residue 252 TRP Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 252 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 168 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 199 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN D 148 ASN E 148 ASN F 148 ASN H 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 16902 Z= 0.349 Angle : 0.655 7.928 22923 Z= 0.345 Chirality : 0.047 0.156 2601 Planarity : 0.004 0.028 3024 Dihedral : 7.498 81.264 2347 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.13 % Allowed : 20.77 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.18), residues: 2124 helix: 1.87 (0.21), residues: 585 sheet: 0.13 (0.22), residues: 666 loop : -2.12 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP E 92 PHE 0.022 0.002 PHE d 31 TYR 0.016 0.001 TYR F 199 ARG 0.006 0.000 ARG I 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 263 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 TYR cc_start: 0.8474 (t80) cc_final: 0.8120 (t80) REVERT: A 97 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6521 (tm-30) REVERT: A 249 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7120 (ptm160) REVERT: B 70 ASN cc_start: 0.8401 (m-40) cc_final: 0.8145 (m-40) REVERT: C 219 VAL cc_start: 0.8626 (t) cc_final: 0.8273 (p) REVERT: D 70 ASN cc_start: 0.8316 (m-40) cc_final: 0.8061 (m-40) REVERT: D 88 LYS cc_start: 0.8755 (tptp) cc_final: 0.8468 (mtpp) REVERT: D 109 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8365 (mtmt) REVERT: D 137 MET cc_start: 0.8415 (ttm) cc_final: 0.8001 (ttp) REVERT: D 213 ARG cc_start: 0.8109 (mmt-90) cc_final: 0.7712 (mmt180) REVERT: D 219 VAL cc_start: 0.8765 (t) cc_final: 0.8485 (p) REVERT: D 249 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7249 (ptm160) REVERT: E 166 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7813 (tt0) REVERT: E 218 GLU cc_start: 0.7059 (tp30) cc_final: 0.6781 (tp30) REVERT: E 251 LEU cc_start: 0.7191 (mp) cc_final: 0.6940 (mp) REVERT: F 170 ASP cc_start: 0.8004 (m-30) cc_final: 0.7750 (m-30) REVERT: F 219 VAL cc_start: 0.8782 (t) cc_final: 0.8532 (p) REVERT: F 249 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7261 (ptm160) REVERT: G 48 LYS cc_start: 0.8277 (mttp) cc_final: 0.8029 (mttt) REVERT: G 59 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7650 (mt-10) REVERT: G 88 LYS cc_start: 0.8855 (tptp) cc_final: 0.8485 (mtpp) REVERT: H 225 GLU cc_start: 0.8095 (tt0) cc_final: 0.7660 (tt0) REVERT: H 249 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7151 (ptm-80) REVERT: I 59 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7586 (mt-10) REVERT: I 97 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6871 (tm-30) REVERT: I 249 ARG cc_start: 0.7005 (ptm-80) cc_final: 0.6658 (ppt170) REVERT: b 22 MET cc_start: 0.7668 (mtt) cc_final: 0.6920 (mtt) outliers start: 56 outliers final: 38 residues processed: 306 average time/residue: 1.5608 time to fit residues: 522.0556 Evaluate side-chains 306 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 260 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 249 ARG Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain F residue 252 TRP Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain H residue 252 TRP Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 252 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.4602 > 50: distance: 25 - 26: 56.052 distance: 27 - 28: 39.957 distance: 28 - 29: 40.594 distance: 29 - 30: 47.590 distance: 29 - 36: 40.093 distance: 31 - 32: 38.611 distance: 37 - 38: 40.281 distance: 39 - 142: 31.865 distance: 41 - 43: 34.095 distance: 45 - 48: 40.136 distance: 46 - 55: 38.991 distance: 49 - 50: 39.691 distance: 50 - 52: 40.720 distance: 53 - 54: 55.975 distance: 55 - 145: 33.429 distance: 56 - 57: 40.501 distance: 56 - 59: 39.708 distance: 58 - 157: 37.363 distance: 59 - 60: 38.745 distance: 59 - 61: 41.217 distance: 63 - 64: 39.006 distance: 64 - 65: 39.916 distance: 65 - 209: 36.788 distance: 69 - 72: 16.149 distance: 70 - 75: 40.242 distance: 72 - 73: 25.082 distance: 72 - 74: 44.076 distance: 75 - 76: 57.150 distance: 79 - 80: 8.554 distance: 80 - 81: 31.475 distance: 80 - 82: 9.101 distance: 84 - 85: 40.154 distance: 87 - 88: 40.396 distance: 89 - 95: 34.889 distance: 91 - 92: 38.919 distance: 92 - 93: 40.837 distance: 92 - 94: 55.769