Starting phenix.real_space_refine (version: dev) on Tue Dec 13 12:17:22 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmu_33305/12_2022/7xmu_33305_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmu_33305/12_2022/7xmu_33305.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmu_33305/12_2022/7xmu_33305_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmu_33305/12_2022/7xmu_33305_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmu_33305/12_2022/7xmu_33305_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmu_33305/12_2022/7xmu_33305.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmu_33305/12_2022/7xmu_33305.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmu_33305/12_2022/7xmu_33305_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmu_33305/12_2022/7xmu_33305_updated.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A ASP 279": "OD1" <-> "OD2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D GLU 154": "OE1" <-> "OE2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D GLU 268": "OE1" <-> "OE2" Residue "D ASP 279": "OD1" <-> "OD2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D GLU 306": "OE1" <-> "OE2" Residue "B GLU 14": "OE1" <-> "OE2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B GLU 238": "OE1" <-> "OE2" Residue "B GLU 268": "OE1" <-> "OE2" Residue "B ASP 279": "OD1" <-> "OD2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "E GLU 14": "OE1" <-> "OE2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E ARG 195": "NH1" <-> "NH2" Residue "E GLU 238": "OE1" <-> "OE2" Residue "E GLU 268": "OE1" <-> "OE2" Residue "E ASP 279": "OD1" <-> "OD2" Residue "E GLU 280": "OE1" <-> "OE2" Residue "E ARG 302": "NH1" <-> "NH2" Residue "E GLU 306": "OE1" <-> "OE2" Residue "F GLU 14": "OE1" <-> "OE2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F GLU 154": "OE1" <-> "OE2" Residue "F ARG 195": "NH1" <-> "NH2" Residue "F GLU 238": "OE1" <-> "OE2" Residue "F GLU 268": "OE1" <-> "OE2" Residue "F ASP 279": "OD1" <-> "OD2" Residue "F GLU 280": "OE1" <-> "OE2" Residue "F ARG 302": "NH1" <-> "NH2" Residue "F GLU 306": "OE1" <-> "OE2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C ASP 279": "OD1" <-> "OD2" Residue "C GLU 280": "OE1" <-> "OE2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C GLU 306": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 15294 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2337 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Chain: "D" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2337 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Chain: "B" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2337 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Chain: "E" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2337 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Chain: "F" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2337 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Chain: "C" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2337 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 102 Unusual residues: {' MG': 2, 'ADP': 3, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {' MG': 2, 'ADP': 2, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {' MG': 2, 'ADP': 2, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {' MG': 2, 'ADP': 2, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {' MG': 2, 'ADP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {' MG': 2, 'ADP': 2, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 144 Classifications: {'water': 144} Link IDs: {None: 143} Chain: "D" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 141 Classifications: {'water': 141} Link IDs: {None: 140} Chain: "B" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 135 Classifications: {'water': 135} Link IDs: {None: 134} Chain: "E" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 135 Classifications: {'water': 135} Link IDs: {None: 134} Chain: "F" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 132 Classifications: {'water': 132} Link IDs: {None: 131} Chain: "C" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 135 Classifications: {'water': 135} Link IDs: {None: 134} Time building chain proxies: 9.52, per 1000 atoms: 0.62 Number of scatterers: 15294 At special positions: 0 Unit cell: (119.78, 126.14, 83.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 36 15.00 Mg 12 11.99 O 3696 8.00 N 2574 7.00 C 8898 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.92 Conformation dependent library (CDL) restraints added in 2.4 seconds 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3444 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 18 sheets defined 35.2% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 109 through 120 Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 149 through 158 removed outlier: 3.659A pdb=" N GLN A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 183 removed outlier: 4.932A pdb=" N VAL A 175 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 279 through 282 No H-bonds generated for 'chain 'A' and resid 279 through 282' Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 63 through 79 Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'D' and resid 109 through 120 Processing helix chain 'D' and resid 133 through 138 Processing helix chain 'D' and resid 149 through 158 removed outlier: 3.658A pdb=" N GLN D 158 " --> pdb=" O GLU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 183 removed outlier: 4.932A pdb=" N VAL D 175 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 279 through 282 No H-bonds generated for 'chain 'D' and resid 279 through 282' Processing helix chain 'D' and resid 293 through 304 Processing helix chain 'D' and resid 310 through 312 No H-bonds generated for 'chain 'D' and resid 310 through 312' Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 63 through 79 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 109 through 120 Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 149 through 158 removed outlier: 3.659A pdb=" N GLN B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 183 removed outlier: 4.932A pdb=" N VAL B 175 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 279 through 282 No H-bonds generated for 'chain 'B' and resid 279 through 282' Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'B' and resid 310 through 312 No H-bonds generated for 'chain 'B' and resid 310 through 312' Processing helix chain 'E' and resid 13 through 22 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 101 through 103 No H-bonds generated for 'chain 'E' and resid 101 through 103' Processing helix chain 'E' and resid 109 through 120 Processing helix chain 'E' and resid 133 through 138 Processing helix chain 'E' and resid 149 through 158 removed outlier: 3.659A pdb=" N GLN E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 183 removed outlier: 4.932A pdb=" N VAL E 175 " --> pdb=" O GLY E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 238 Processing helix chain 'E' and resid 257 through 262 Processing helix chain 'E' and resid 279 through 282 No H-bonds generated for 'chain 'E' and resid 279 through 282' Processing helix chain 'E' and resid 293 through 304 Processing helix chain 'E' and resid 310 through 312 No H-bonds generated for 'chain 'E' and resid 310 through 312' Processing helix chain 'F' and resid 13 through 22 Processing helix chain 'F' and resid 63 through 79 Processing helix chain 'F' and resid 101 through 103 No H-bonds generated for 'chain 'F' and resid 101 through 103' Processing helix chain 'F' and resid 109 through 120 Processing helix chain 'F' and resid 133 through 138 Processing helix chain 'F' and resid 149 through 158 removed outlier: 3.659A pdb=" N GLN F 158 " --> pdb=" O GLU F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 183 removed outlier: 4.932A pdb=" N VAL F 175 " --> pdb=" O GLY F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 Processing helix chain 'F' and resid 257 through 262 Processing helix chain 'F' and resid 279 through 282 No H-bonds generated for 'chain 'F' and resid 279 through 282' Processing helix chain 'F' and resid 293 through 304 Processing helix chain 'F' and resid 310 through 312 No H-bonds generated for 'chain 'F' and resid 310 through 312' Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 109 through 120 Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 149 through 158 removed outlier: 3.659A pdb=" N GLN C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 183 removed outlier: 4.932A pdb=" N VAL C 175 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 279 through 282 No H-bonds generated for 'chain 'C' and resid 279 through 282' Processing helix chain 'C' and resid 293 through 304 Processing helix chain 'C' and resid 310 through 312 No H-bonds generated for 'chain 'C' and resid 310 through 312' Processing sheet with id= A, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.343A pdb=" N ASP A 52 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N PHE A 7 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE A 54 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG A 84 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE A 55 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR A 86 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ARG A 124 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE A 89 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU A 126 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N THR A 127 " --> pdb=" O PRO A 142 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASP A 144 " --> pdb=" O THR A 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 30 through 34 Processing sheet with id= C, first strand: chain 'A' and resid 287 through 289 removed outlier: 6.275A pdb=" N VAL A 269 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU A 268 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS A 216 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N TYR A 247 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU A 218 " --> pdb=" O TYR A 247 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE A 165 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL A 219 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A 167 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP A 188 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N SER A 168 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ALA A 190 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 204 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.343A pdb=" N ASP D 52 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N PHE D 7 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE D 54 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG D 84 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE D 55 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR D 86 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG D 124 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE D 89 " --> pdb=" O ARG D 124 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU D 126 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR D 127 " --> pdb=" O PRO D 142 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASP D 144 " --> pdb=" O THR D 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'D' and resid 30 through 34 Processing sheet with id= F, first strand: chain 'D' and resid 287 through 289 removed outlier: 6.275A pdb=" N VAL D 269 " --> pdb=" O ARG D 288 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU D 268 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS D 216 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N TYR D 247 " --> pdb=" O CYS D 216 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU D 218 " --> pdb=" O TYR D 247 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE D 165 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VAL D 219 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL D 167 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASP D 188 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N SER D 168 " --> pdb=" O ASP D 188 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ALA D 190 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL D 204 " --> pdb=" O ARG D 195 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.343A pdb=" N ASP B 52 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N PHE B 7 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE B 54 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG B 84 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE B 55 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR B 86 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG B 124 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE B 89 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU B 126 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR B 127 " --> pdb=" O PRO B 142 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASP B 144 " --> pdb=" O THR B 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 30 through 34 Processing sheet with id= I, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.275A pdb=" N VAL B 269 " --> pdb=" O ARG B 288 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU B 268 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS B 216 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N TYR B 247 " --> pdb=" O CYS B 216 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU B 218 " --> pdb=" O TYR B 247 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 165 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL B 219 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL B 167 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP B 188 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N SER B 168 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ALA B 190 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 204 " --> pdb=" O ARG B 195 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.343A pdb=" N ASP E 52 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N PHE E 7 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE E 54 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG E 84 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ILE E 55 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR E 86 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG E 124 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE E 89 " --> pdb=" O ARG E 124 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU E 126 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N THR E 127 " --> pdb=" O PRO E 142 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASP E 144 " --> pdb=" O THR E 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'E' and resid 30 through 34 Processing sheet with id= L, first strand: chain 'E' and resid 287 through 289 removed outlier: 6.275A pdb=" N VAL E 269 " --> pdb=" O ARG E 288 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU E 268 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS E 216 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N TYR E 247 " --> pdb=" O CYS E 216 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU E 218 " --> pdb=" O TYR E 247 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE E 165 " --> pdb=" O VAL E 217 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL E 219 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL E 167 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASP E 188 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N SER E 168 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ALA E 190 " --> pdb=" O SER E 168 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL E 204 " --> pdb=" O ARG E 195 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.343A pdb=" N ASP F 52 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N PHE F 7 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE F 54 " --> pdb=" O PHE F 7 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG F 84 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE F 55 " --> pdb=" O ARG F 84 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR F 86 " --> pdb=" O ILE F 55 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ARG F 124 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE F 89 " --> pdb=" O ARG F 124 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU F 126 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR F 127 " --> pdb=" O PRO F 142 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASP F 144 " --> pdb=" O THR F 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'F' and resid 30 through 34 Processing sheet with id= O, first strand: chain 'F' and resid 287 through 289 removed outlier: 6.275A pdb=" N VAL F 269 " --> pdb=" O ARG F 288 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU F 268 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS F 216 " --> pdb=" O PHE F 245 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TYR F 247 " --> pdb=" O CYS F 216 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU F 218 " --> pdb=" O TYR F 247 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE F 165 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL F 219 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL F 167 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP F 188 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N SER F 168 " --> pdb=" O ASP F 188 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ALA F 190 " --> pdb=" O SER F 168 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL F 204 " --> pdb=" O ARG F 195 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.344A pdb=" N ASP C 52 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N PHE C 7 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE C 54 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG C 84 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE C 55 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR C 86 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ARG C 124 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE C 89 " --> pdb=" O ARG C 124 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU C 126 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR C 127 " --> pdb=" O PRO C 142 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASP C 144 " --> pdb=" O THR C 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 30 through 34 Processing sheet with id= R, first strand: chain 'C' and resid 287 through 289 removed outlier: 6.274A pdb=" N VAL C 269 " --> pdb=" O ARG C 288 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU C 268 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS C 216 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TYR C 247 " --> pdb=" O CYS C 216 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU C 218 " --> pdb=" O TYR C 247 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE C 165 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL C 219 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL C 167 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP C 188 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N SER C 168 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ALA C 190 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 204 " --> pdb=" O ARG C 195 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1116 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: 4.35 Time building geometry restraints manager: 7.38 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: 4941 1.34 - 1.46: 1792 1.46 - 1.57: 7727 1.57 - 1.69: 54 1.69 - 1.81: 132 Bond restraints: 14646 Sorted by residual: bond pdb=" C1' ADP B 406 " pdb=" C2' ADP B 406 " ideal model delta sigma weight residual 1.267 1.516 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C1' ADP F 405 " pdb=" C2' ADP F 405 " ideal model delta sigma weight residual 1.267 1.516 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C1' ADP E 405 " pdb=" C2' ADP E 405 " ideal model delta sigma weight residual 1.267 1.516 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C1' ADP C 405 " pdb=" C2' ADP C 405 " ideal model delta sigma weight residual 1.267 1.516 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C1' ADP A 407 " pdb=" C2' ADP A 407 " ideal model delta sigma weight residual 1.267 1.516 -0.249 2.00e-02 2.50e+03 1.55e+02 ... (remaining 14641 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.48: 577 107.48 - 114.63: 8876 114.63 - 121.77: 7180 121.77 - 128.91: 3245 128.91 - 136.05: 54 Bond angle restraints: 19932 Sorted by residual: angle pdb=" N1 ADP A 406 " pdb=" C6 ADP A 406 " pdb=" N6 ADP A 406 " ideal model delta sigma weight residual 106.84 121.65 -14.81 3.00e+00 1.11e-01 2.44e+01 angle pdb=" N1 ADP E 406 " pdb=" C6 ADP E 406 " pdb=" N6 ADP E 406 " ideal model delta sigma weight residual 106.84 121.65 -14.81 3.00e+00 1.11e-01 2.44e+01 angle pdb=" N1 ADP B 406 " pdb=" C6 ADP B 406 " pdb=" N6 ADP B 406 " ideal model delta sigma weight residual 106.84 121.64 -14.80 3.00e+00 1.11e-01 2.43e+01 angle pdb=" N1 ADP D 406 " pdb=" C6 ADP D 406 " pdb=" N6 ADP D 406 " ideal model delta sigma weight residual 106.84 121.63 -14.79 3.00e+00 1.11e-01 2.43e+01 angle pdb=" N1 ADP C 406 " pdb=" C6 ADP C 406 " pdb=" N6 ADP C 406 " ideal model delta sigma weight residual 106.84 121.62 -14.78 3.00e+00 1.11e-01 2.43e+01 ... (remaining 19927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.28: 8292 24.28 - 48.56: 498 48.56 - 72.84: 126 72.84 - 97.12: 30 97.12 - 121.40: 6 Dihedral angle restraints: 8952 sinusoidal: 3654 harmonic: 5298 Sorted by residual: dihedral pdb=" C4 HSX E 401 " pdb=" C5 HSX E 401 " pdb=" O5 HSX E 401 " pdb=" P' HSX E 401 " ideal model delta sinusoidal sigma weight residual 168.54 -70.06 -121.40 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" C4 HSX A 401 " pdb=" C5 HSX A 401 " pdb=" O5 HSX A 401 " pdb=" P' HSX A 401 " ideal model delta sinusoidal sigma weight residual 168.54 -70.06 -121.40 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" C4 HSX F 401 " pdb=" C5 HSX F 401 " pdb=" O5 HSX F 401 " pdb=" P' HSX F 401 " ideal model delta sinusoidal sigma weight residual 168.54 -70.07 -121.39 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 8949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1039 0.026 - 0.053: 655 0.053 - 0.079: 335 0.079 - 0.105: 201 0.105 - 0.132: 80 Chirality restraints: 2310 Sorted by residual: chirality pdb=" CA ILE C 275 " pdb=" N ILE C 275 " pdb=" C ILE C 275 " pdb=" CB ILE C 275 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE E 275 " pdb=" N ILE E 275 " pdb=" C ILE E 275 " pdb=" CB ILE E 275 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE D 275 " pdb=" N ILE D 275 " pdb=" C ILE D 275 " pdb=" CB ILE D 275 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 2307 not shown) Planarity restraints: 2568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 HSX C 401 " 0.212 2.00e-02 2.50e+03 6.71e-01 1.01e+04 pdb=" C2 HSX C 401 " 0.887 2.00e-02 2.50e+03 pdb=" C3 HSX C 401 " 0.069 2.00e-02 2.50e+03 pdb=" C4 HSX C 401 " -0.346 2.00e-02 2.50e+03 pdb=" C5 HSX C 401 " 0.504 2.00e-02 2.50e+03 pdb=" O1 HSX C 401 " -0.977 2.00e-02 2.50e+03 pdb=" O2 HSX C 401 " 0.868 2.00e-02 2.50e+03 pdb=" O3 HSX C 401 " -1.054 2.00e-02 2.50e+03 pdb=" O4 HSX C 401 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 HSX A 401 " 0.213 2.00e-02 2.50e+03 6.71e-01 1.01e+04 pdb=" C2 HSX A 401 " 0.886 2.00e-02 2.50e+03 pdb=" C3 HSX A 401 " 0.069 2.00e-02 2.50e+03 pdb=" C4 HSX A 401 " -0.345 2.00e-02 2.50e+03 pdb=" C5 HSX A 401 " 0.504 2.00e-02 2.50e+03 pdb=" O1 HSX A 401 " -0.976 2.00e-02 2.50e+03 pdb=" O2 HSX A 401 " 0.867 2.00e-02 2.50e+03 pdb=" O3 HSX A 401 " -1.055 2.00e-02 2.50e+03 pdb=" O4 HSX A 401 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 HSX F 401 " -0.212 2.00e-02 2.50e+03 6.71e-01 1.01e+04 pdb=" C2 HSX F 401 " -0.886 2.00e-02 2.50e+03 pdb=" C3 HSX F 401 " -0.069 2.00e-02 2.50e+03 pdb=" C4 HSX F 401 " 0.346 2.00e-02 2.50e+03 pdb=" C5 HSX F 401 " -0.504 2.00e-02 2.50e+03 pdb=" O1 HSX F 401 " 0.976 2.00e-02 2.50e+03 pdb=" O2 HSX F 401 " -0.867 2.00e-02 2.50e+03 pdb=" O3 HSX F 401 " 1.054 2.00e-02 2.50e+03 pdb=" O4 HSX F 401 " 0.164 2.00e-02 2.50e+03 ... (remaining 2565 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 262 2.50 - 3.10: 10947 3.10 - 3.70: 24147 3.70 - 4.30: 38487 4.30 - 4.90: 60144 Nonbonded interactions: 133987 Sorted by model distance: nonbonded pdb="MG MG E 404 " pdb=" O HOH E 501 " model vdw 1.897 2.170 nonbonded pdb="MG MG C 404 " pdb=" O HOH C 501 " model vdw 1.900 2.170 nonbonded pdb="MG MG B 404 " pdb=" O HOH B 508 " model vdw 1.902 2.170 nonbonded pdb="MG MG A 404 " pdb=" O HOH A 501 " model vdw 1.904 2.170 nonbonded pdb="MG MG B 404 " pdb=" O HOH B 501 " model vdw 1.905 2.170 ... (remaining 133982 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 315 or resid 401 through 405)) selection = (chain 'B' and (resid 3 through 315 or resid 401 through 405)) selection = (chain 'C' and (resid 3 through 315 or resid 401 through 405)) selection = (chain 'D' and (resid 3 through 315 or resid 401 through 405)) selection = (chain 'E' and (resid 3 through 315 or resid 401 through 405)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 78 5.16 5 C 8898 2.51 5 N 2574 2.21 5 O 3696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 5.370 Check model and map are aligned: 0.250 Convert atoms to be neutral: 0.150 Process input model: 42.210 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 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 : 0.016 0.249 14646 Z= 1.074 Angle : 0.968 14.813 19932 Z= 0.425 Chirality : 0.048 0.132 2310 Planarity : 0.042 0.671 2568 Dihedral : 17.306 121.400 5508 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.10 (0.19), residues: 1818 helix: 0.78 (0.19), residues: 726 sheet: 0.76 (0.24), residues: 414 loop : -1.51 (0.22), residues: 678 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 236 time to evaluate : 1.763 Fit side-chains outliers start: 24 outliers final: 3 residues processed: 236 average time/residue: 1.6463 time to fit residues: 419.9810 Evaluate side-chains 173 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 1.979 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 1.9114 time to fit residues: 4.7674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 0.4980 chunk 105 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN B 57 GLN B 158 GLN E 57 GLN E 158 GLN F 163 ASN C 158 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 14646 Z= 0.196 Angle : 1.440 19.052 19932 Z= 0.522 Chirality : 0.046 0.129 2310 Planarity : 0.004 0.041 2568 Dihedral : 14.611 100.871 2226 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.22 (0.19), residues: 1818 helix: 0.55 (0.19), residues: 726 sheet: 0.63 (0.22), residues: 468 loop : -1.54 (0.23), residues: 624 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 180 time to evaluate : 1.815 Fit side-chains outliers start: 27 outliers final: 3 residues processed: 194 average time/residue: 1.5161 time to fit residues: 320.4325 Evaluate side-chains 178 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 175 time to evaluate : 1.860 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.2701 time to fit residues: 3.2550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN F 163 ASN C 158 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 14646 Z= 0.318 Angle : 1.448 18.796 19932 Z= 0.531 Chirality : 0.048 0.131 2310 Planarity : 0.005 0.041 2568 Dihedral : 13.828 102.049 2226 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.19), residues: 1818 helix: 0.45 (0.19), residues: 726 sheet: 0.57 (0.23), residues: 450 loop : -1.63 (0.22), residues: 642 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 205 time to evaluate : 1.831 Fit side-chains outliers start: 19 outliers final: 5 residues processed: 208 average time/residue: 1.4848 time to fit residues: 337.0214 Evaluate side-chains 189 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 184 time to evaluate : 1.990 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 4 average time/residue: 0.9498 time to fit residues: 6.9565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 84 optimal weight: 0.0270 chunk 18 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 46 optimal weight: 0.0470 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 GLN E 158 GLN F 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 14646 Z= 0.141 Angle : 1.400 17.117 19932 Z= 0.498 Chirality : 0.045 0.126 2310 Planarity : 0.003 0.039 2568 Dihedral : 13.013 94.532 2226 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.08 (0.19), residues: 1818 helix: 0.59 (0.19), residues: 726 sheet: 0.85 (0.23), residues: 456 loop : -1.45 (0.23), residues: 636 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 201 time to evaluate : 1.976 Fit side-chains outliers start: 15 outliers final: 5 residues processed: 207 average time/residue: 1.4369 time to fit residues: 325.6218 Evaluate side-chains 185 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 180 time to evaluate : 1.872 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5216 time to fit residues: 5.6729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN F 163 ASN F 256 ASN C 158 GLN C 256 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.037 14646 Z= 0.421 Angle : 1.471 19.433 19932 Z= 0.547 Chirality : 0.050 0.143 2310 Planarity : 0.005 0.043 2568 Dihedral : 13.052 96.651 2226 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.43 (0.19), residues: 1818 helix: 0.45 (0.19), residues: 720 sheet: 0.48 (0.23), residues: 450 loop : -1.65 (0.22), residues: 648 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 1.912 Fit side-chains outliers start: 25 outliers final: 9 residues processed: 198 average time/residue: 1.4853 time to fit residues: 321.1401 Evaluate side-chains 198 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 189 time to evaluate : 1.939 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 1 residues processed: 8 average time/residue: 0.5391 time to fit residues: 7.7801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN B 158 GLN E 158 GLN F 163 ASN C 256 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 14646 Z= 0.213 Angle : 1.417 17.225 19932 Z= 0.511 Chirality : 0.046 0.128 2310 Planarity : 0.004 0.040 2568 Dihedral : 12.572 93.194 2226 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.28 (0.19), residues: 1818 helix: 0.56 (0.19), residues: 720 sheet: 0.60 (0.23), residues: 450 loop : -1.56 (0.23), residues: 648 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 190 time to evaluate : 1.936 Fit side-chains outliers start: 20 outliers final: 7 residues processed: 199 average time/residue: 1.5609 time to fit residues: 338.3174 Evaluate side-chains 194 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 187 time to evaluate : 1.864 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4569 time to fit residues: 6.4879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 173 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN D 256 ASN B 256 ASN E 256 ASN F 163 ASN F 256 ASN C 158 GLN C 256 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 14646 Z= 0.338 Angle : 1.449 18.354 19932 Z= 0.532 Chirality : 0.048 0.132 2310 Planarity : 0.005 0.041 2568 Dihedral : 12.482 93.383 2226 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.44 (0.19), residues: 1818 helix: 0.45 (0.19), residues: 720 sheet: 0.41 (0.23), residues: 450 loop : -1.61 (0.22), residues: 648 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 185 time to evaluate : 1.955 Fit side-chains outliers start: 16 outliers final: 4 residues processed: 194 average time/residue: 1.4525 time to fit residues: 308.0360 Evaluate side-chains 193 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 189 time to evaluate : 1.916 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2758 time to fit residues: 4.0739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 85 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN F 163 ASN C 158 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 14646 Z= 0.166 Angle : 1.405 17.151 19932 Z= 0.502 Chirality : 0.045 0.127 2310 Planarity : 0.003 0.041 2568 Dihedral : 11.965 89.944 2226 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.15 (0.19), residues: 1818 helix: 0.59 (0.19), residues: 726 sheet: 0.66 (0.23), residues: 450 loop : -1.41 (0.23), residues: 642 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 190 time to evaluate : 1.933 Fit side-chains outliers start: 11 outliers final: 1 residues processed: 192 average time/residue: 1.4785 time to fit residues: 310.6454 Evaluate side-chains 183 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 1.915 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.6127 time to fit residues: 4.2298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 161 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 0.1980 chunk 126 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 146 optimal weight: 0.7980 chunk 152 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN D 256 ASN E 256 ASN F 163 ASN F 256 ASN C 158 GLN C 256 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 14646 Z= 0.210 Angle : 1.416 17.293 19932 Z= 0.509 Chirality : 0.046 0.126 2310 Planarity : 0.004 0.041 2568 Dihedral : 11.844 88.804 2226 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.15 (0.19), residues: 1818 helix: 0.68 (0.20), residues: 720 sheet: 0.60 (0.22), residues: 450 loop : -1.47 (0.23), residues: 648 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 181 time to evaluate : 1.902 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 185 average time/residue: 1.4976 time to fit residues: 302.5384 Evaluate side-chains 182 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 1.942 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2744 time to fit residues: 3.2805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 165 optimal weight: 0.5980 chunk 142 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 110 optimal weight: 0.0870 chunk 87 optimal weight: 0.0060 chunk 113 optimal weight: 4.9990 overall best weight: 0.4574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN E 256 ASN F 163 ASN F 256 ASN C 158 GLN C 256 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 14646 Z= 0.133 Angle : 1.398 17.094 19932 Z= 0.497 Chirality : 0.045 0.128 2310 Planarity : 0.003 0.041 2568 Dihedral : 11.346 85.526 2226 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.13 (0.20), residues: 1818 helix: 0.77 (0.20), residues: 726 sheet: 0.85 (0.22), residues: 468 loop : -1.27 (0.24), residues: 624 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 195 time to evaluate : 1.960 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 198 average time/residue: 1.5391 time to fit residues: 331.5987 Evaluate side-chains 190 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 1.852 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.5254 time to fit residues: 4.1522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.0020 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN D 43 GLN D 256 ASN B 43 GLN B 158 GLN E 43 GLN E 158 GLN E 256 ASN F 163 ASN F 256 ASN C 43 GLN C 158 GLN C 256 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.129712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.094780 restraints weight = 15170.239| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.58 r_work: 0.2933 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 14646 Z= 0.213 Angle : 1.416 17.305 19932 Z= 0.509 Chirality : 0.046 0.130 2310 Planarity : 0.004 0.040 2568 Dihedral : 11.337 83.706 2226 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.06 (0.19), residues: 1818 helix: 0.80 (0.20), residues: 726 sheet: 0.75 (0.23), residues: 450 loop : -1.32 (0.23), residues: 642 =============================================================================== Job complete usr+sys time: 5510.57 seconds wall clock time: 98 minutes 11.66 seconds (5891.66 seconds total)