Starting phenix.real_space_refine on Thu Feb 5 02:59:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e4j_47512/02_2026/9e4j_47512.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e4j_47512/02_2026/9e4j_47512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e4j_47512/02_2026/9e4j_47512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e4j_47512/02_2026/9e4j_47512.map" model { file = "/net/cci-nas-00/data/ceres_data/9e4j_47512/02_2026/9e4j_47512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e4j_47512/02_2026/9e4j_47512.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 156 5.16 5 C 9043 2.51 5 N 2408 2.21 5 O 2678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14285 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3349 Classifications: {'peptide': 418} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 399} Chain: "B" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3305 Classifications: {'peptide': 413} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 394} Chain: "C" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3305 Classifications: {'peptide': 413} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 394} Chain: "D" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 499 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 943 Classifications: {'peptide': 118} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 113} Chain: "F" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 499 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 943 Classifications: {'peptide': 118} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 113} Chain: "H" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 499 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 943 Classifications: {'peptide': 118} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 113} Time building chain proxies: 3.39, per 1000 atoms: 0.24 Number of scatterers: 14285 At special positions: 0 Unit cell: (134.196, 140.104, 133.352, 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 156 16.00 O 2678 8.00 N 2408 7.00 C 9043 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 314 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 310 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 314 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 325 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 314 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS C 325 " - pdb=" SG CYS C 337 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 58 " distance=2.03 Simple disulfide: pdb=" SG CYS D 17 " - pdb=" SG CYS D 41 " distance=2.03 Simple disulfide: pdb=" SG CYS D 33 " - pdb=" SG CYS D 54 " distance=2.03 Simple disulfide: pdb=" SG CYS E 11 " - pdb=" SG CYS E 70 " distance=2.03 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS E 118 " distance=2.03 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 43 " distance=2.03 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 100 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 93 " distance=2.03 Simple disulfide: pdb=" SG CYS E 59 " - pdb=" SG CYS E 86 " distance=2.03 Simple disulfide: pdb=" SG CYS E 79 " - pdb=" SG CYS E 91 " distance=2.03 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS F 17 " - pdb=" SG CYS F 41 " distance=2.03 Simple disulfide: pdb=" SG CYS F 33 " - pdb=" SG CYS F 54 " distance=2.03 Simple disulfide: pdb=" SG CYS G 11 " - pdb=" SG CYS G 70 " distance=2.03 Simple disulfide: pdb=" SG CYS G 25 " - pdb=" SG CYS G 118 " distance=2.03 Simple disulfide: pdb=" SG CYS G 27 " - pdb=" SG CYS G 43 " distance=2.03 Simple disulfide: pdb=" SG CYS G 42 " - pdb=" SG CYS G 100 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 93 " distance=2.03 Simple disulfide: pdb=" SG CYS G 59 " - pdb=" SG CYS G 86 " distance=2.03 Simple disulfide: pdb=" SG CYS G 79 " - pdb=" SG CYS G 91 " distance=2.03 Simple disulfide: pdb=" SG CYS H 7 " - pdb=" SG CYS H 58 " distance=2.03 Simple disulfide: pdb=" SG CYS H 17 " - pdb=" SG CYS H 41 " distance=2.03 Simple disulfide: pdb=" SG CYS H 33 " - pdb=" SG CYS H 54 " distance=2.03 Simple disulfide: pdb=" SG CYS I 11 " - pdb=" SG CYS I 70 " distance=2.03 Simple disulfide: pdb=" SG CYS I 25 " - pdb=" SG CYS I 118 " distance=2.03 Simple disulfide: pdb=" SG CYS I 27 " - pdb=" SG CYS I 43 " distance=2.03 Simple disulfide: pdb=" SG CYS I 42 " - pdb=" SG CYS I 100 " distance=2.03 Simple disulfide: pdb=" SG CYS I 49 " - pdb=" SG CYS I 93 " distance=2.03 Simple disulfide: pdb=" SG CYS I 59 " - pdb=" SG CYS I 86 " distance=2.03 Simple disulfide: pdb=" SG CYS I 79 " - pdb=" SG CYS I 91 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 439.0 milliseconds 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3364 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 15 sheets defined 44.8% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 40 through 70 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.717A pdb=" N ALA A 130 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 199 through 203 removed outlier: 4.016A pdb=" N ASP A 202 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 345 through 356 Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 397 through 404 Processing helix chain 'A' and resid 427 through 451 removed outlier: 3.639A pdb=" N LEU A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 70 removed outlier: 3.917A pdb=" N LEU B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 126 through 130 removed outlier: 3.688A pdb=" N MET B 129 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA B 130 " --> pdb=" O THR B 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 126 through 130' Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 199 through 203 removed outlier: 4.166A pdb=" N ASP B 202 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 216 removed outlier: 3.508A pdb=" N ASN B 216 " --> pdb=" O GLY B 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 213 through 216' Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'B' and resid 338 through 345 Processing helix chain 'B' and resid 345 through 356 Processing helix chain 'B' and resid 386 through 394 Processing helix chain 'B' and resid 397 through 404 Processing helix chain 'B' and resid 427 through 450 removed outlier: 3.723A pdb=" N LEU B 448 " --> pdb=" O GLY B 444 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 42 No H-bonds generated for 'chain 'C' and resid 40 through 42' Processing helix chain 'C' and resid 43 through 69 removed outlier: 4.167A pdb=" N ALA C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.672A pdb=" N ALA C 130 " --> pdb=" O THR C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 294 through 298 removed outlier: 3.517A pdb=" N SER C 297 " --> pdb=" O THR C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 338 through 345 Processing helix chain 'C' and resid 345 through 355 Processing helix chain 'C' and resid 386 through 394 Processing helix chain 'C' and resid 397 through 404 Processing helix chain 'C' and resid 427 through 451 removed outlier: 3.588A pdb=" N LEU C 451 " --> pdb=" O ILE C 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 9 removed outlier: 3.526A pdb=" N TYR D 8 " --> pdb=" O ALA D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 58 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 16 through 20 Processing helix chain 'E' and resid 37 through 56 removed outlier: 3.507A pdb=" N CYS E 42 " --> pdb=" O ASP E 38 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 77 Processing helix chain 'E' and resid 84 through 104 removed outlier: 3.642A pdb=" N LEU E 102 " --> pdb=" O THR E 98 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR E 103 " --> pdb=" O LEU E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 111 Processing helix chain 'E' and resid 114 through 118 Processing helix chain 'F' and resid 4 through 9 Processing helix chain 'F' and resid 50 through 59 Processing helix chain 'G' and resid 2 through 13 Processing helix chain 'G' and resid 16 through 20 Processing helix chain 'G' and resid 37 through 56 removed outlier: 3.544A pdb=" N CYS G 43 " --> pdb=" O LEU G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 77 Processing helix chain 'G' and resid 84 through 104 removed outlier: 3.787A pdb=" N LEU G 102 " --> pdb=" O THR G 98 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR G 103 " --> pdb=" O LEU G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 111 Processing helix chain 'G' and resid 114 through 118 Processing helix chain 'H' and resid 4 through 9 Processing helix chain 'H' and resid 50 through 59 Processing helix chain 'I' and resid 2 through 13 Processing helix chain 'I' and resid 16 through 20 Processing helix chain 'I' and resid 37 through 56 Processing helix chain 'I' and resid 73 through 77 Processing helix chain 'I' and resid 84 through 104 removed outlier: 3.591A pdb=" N LEU I 102 " --> pdb=" O THR I 98 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR I 103 " --> pdb=" O LEU I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 111 Processing helix chain 'I' and resid 114 through 118 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 80 removed outlier: 9.863A pdb=" N GLU A 418 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU A 277 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ILE A 420 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARG A 279 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N GLN A 422 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE A 281 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N LYS A 424 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE A 269 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP A 223 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU A 169 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 80 removed outlier: 9.863A pdb=" N GLU A 418 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU A 277 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ILE A 420 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARG A 279 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N GLN A 422 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE A 281 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N LYS A 424 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 189 removed outlier: 7.053A pdb=" N LYS A 193 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASN A 94 " --> pdb=" O LYS A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 80 removed outlier: 9.841A pdb=" N GLU B 418 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU B 277 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ILE B 420 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG B 279 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLN B 422 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE B 281 " --> pdb=" O GLN B 422 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N LYS B 424 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE B 269 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASP B 223 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU B 169 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 80 removed outlier: 9.841A pdb=" N GLU B 418 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU B 277 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ILE B 420 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG B 279 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLN B 422 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE B 281 " --> pdb=" O GLN B 422 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N LYS B 424 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA8, first strand: chain 'B' and resid 184 through 189 removed outlier: 7.003A pdb=" N LYS B 193 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASN B 94 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 73 through 80 removed outlier: 10.058A pdb=" N GLU C 418 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU C 277 " --> pdb=" O GLU C 418 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ILE C 420 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG C 279 " --> pdb=" O ILE C 420 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLN C 422 " --> pdb=" O ARG C 279 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE C 281 " --> pdb=" O GLN C 422 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N LYS C 424 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE C 269 " --> pdb=" O ILE C 405 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP C 223 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU C 169 " --> pdb=" O ASP C 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 73 through 80 removed outlier: 10.058A pdb=" N GLU C 418 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU C 277 " --> pdb=" O GLU C 418 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ILE C 420 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG C 279 " --> pdb=" O ILE C 420 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLN C 422 " --> pdb=" O ARG C 279 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE C 281 " --> pdb=" O GLN C 422 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N LYS C 424 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AB3, first strand: chain 'C' and resid 184 through 189 removed outlier: 7.060A pdb=" N LYS C 193 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN C 94 " --> pdb=" O LYS C 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 21 through 27 Processing sheet with id=AB5, first strand: chain 'F' and resid 21 through 27 Processing sheet with id=AB6, first strand: chain 'H' and resid 21 through 27 710 hydrogen bonds defined for protein. 1887 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: 2.03 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4710 1.35 - 1.47: 3573 1.47 - 1.59: 6139 1.59 - 1.71: 0 1.71 - 1.83: 198 Bond restraints: 14620 Sorted by residual: bond pdb=" CG MET I 64 " pdb=" SD MET I 64 " ideal model delta sigma weight residual 1.803 1.784 0.019 2.50e-02 1.60e+03 5.54e-01 bond pdb=" N PCA D 1 " pdb=" CD PCA D 1 " ideal model delta sigma weight residual 1.345 1.359 -0.014 2.00e-02 2.50e+03 5.11e-01 bond pdb=" C GLU B 403 " pdb=" N ASN B 404 " ideal model delta sigma weight residual 1.332 1.323 0.010 1.40e-02 5.10e+03 4.83e-01 bond pdb=" N PCA H 1 " pdb=" CD PCA H 1 " ideal model delta sigma weight residual 1.345 1.358 -0.013 2.00e-02 2.50e+03 3.99e-01 bond pdb=" CB PCA F 1 " pdb=" CG PCA F 1 " ideal model delta sigma weight residual 1.525 1.513 0.012 2.00e-02 2.50e+03 3.43e-01 ... (remaining 14615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 19630 1.95 - 3.89: 117 3.89 - 5.84: 17 5.84 - 7.78: 0 7.78 - 9.73: 6 Bond angle restraints: 19770 Sorted by residual: angle pdb=" CA PCA H 1 " pdb=" N PCA H 1 " pdb=" CD PCA H 1 " ideal model delta sigma weight residual 114.17 104.44 9.73 3.00e+00 1.11e-01 1.05e+01 angle pdb=" CA PCA F 1 " pdb=" N PCA F 1 " pdb=" CD PCA F 1 " ideal model delta sigma weight residual 114.17 104.45 9.72 3.00e+00 1.11e-01 1.05e+01 angle pdb=" CA PCA D 1 " pdb=" N PCA D 1 " pdb=" CD PCA D 1 " ideal model delta sigma weight residual 114.17 104.50 9.67 3.00e+00 1.11e-01 1.04e+01 angle pdb=" N PCA D 1 " pdb=" CD PCA D 1 " pdb=" CG PCA D 1 " ideal model delta sigma weight residual 107.23 115.93 -8.70 3.00e+00 1.11e-01 8.41e+00 angle pdb=" N PCA H 1 " pdb=" CD PCA H 1 " pdb=" CG PCA H 1 " ideal model delta sigma weight residual 107.23 115.91 -8.68 3.00e+00 1.11e-01 8.37e+00 ... (remaining 19765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 8142 17.19 - 34.38: 605 34.38 - 51.57: 115 51.57 - 68.76: 32 68.76 - 85.95: 13 Dihedral angle restraints: 8907 sinusoidal: 3683 harmonic: 5224 Sorted by residual: dihedral pdb=" CA ASP A 296 " pdb=" C ASP A 296 " pdb=" N SER A 297 " pdb=" CA SER A 297 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CB CYS C 93 " pdb=" SG CYS C 93 " pdb=" SG CYS C 194 " pdb=" CB CYS C 194 " ideal model delta sinusoidal sigma weight residual 93.00 121.23 -28.23 1 1.00e+01 1.00e-02 1.14e+01 dihedral pdb=" CB CYS E 42 " pdb=" SG CYS E 42 " pdb=" SG CYS E 100 " pdb=" CB CYS E 100 " ideal model delta sinusoidal sigma weight residual -86.00 -58.00 -28.00 1 1.00e+01 1.00e-02 1.12e+01 ... (remaining 8904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1342 0.029 - 0.058: 533 0.058 - 0.088: 141 0.088 - 0.117: 79 0.117 - 0.146: 8 Chirality restraints: 2103 Sorted by residual: chirality pdb=" CB ILE D 31 " pdb=" CA ILE D 31 " pdb=" CG1 ILE D 31 " pdb=" CG2 ILE D 31 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA ILE B 124 " pdb=" N ILE B 124 " pdb=" C ILE B 124 " pdb=" CB ILE B 124 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE A 124 " pdb=" N ILE A 124 " pdb=" C ILE A 124 " pdb=" CB ILE A 124 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 2100 not shown) Planarity restraints: 2597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 284 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO A 285 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 3 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO D 4 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO D 4 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 4 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 284 " 0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO C 285 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO C 285 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 285 " 0.016 5.00e-02 4.00e+02 ... (remaining 2594 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2996 2.78 - 3.31: 13647 3.31 - 3.84: 24409 3.84 - 4.37: 29916 4.37 - 4.90: 50532 Nonbonded interactions: 121500 Sorted by model distance: nonbonded pdb=" OD2 ASP C 126 " pdb=" NE2 GLN C 128 " model vdw 2.247 3.120 nonbonded pdb=" OD2 ASP A 126 " pdb=" NE2 GLN A 128 " model vdw 2.260 3.120 nonbonded pdb=" NE2 GLN A 276 " pdb=" OE2 GLU A 413 " model vdw 2.264 3.120 nonbonded pdb=" OG1 THR C 236 " pdb=" OG1 THR C 239 " model vdw 2.271 3.040 nonbonded pdb=" OE1 GLN A 358 " pdb=" NH2 ARG B 175 " model vdw 2.296 3.120 ... (remaining 121495 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' and resid 40 through 452) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.110 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.930 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:7.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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 : 0.002 0.021 14671 Z= 0.080 Angle : 0.451 9.727 19872 Z= 0.222 Chirality : 0.037 0.146 2103 Planarity : 0.003 0.032 2597 Dihedral : 12.927 85.949 5390 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.21), residues: 1757 helix: 1.62 (0.21), residues: 570 sheet: 0.18 (0.27), residues: 323 loop : 0.88 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 71 TYR 0.009 0.001 TYR B 342 PHE 0.009 0.001 PHE F 6 TRP 0.005 0.001 TRP C 233 HIS 0.002 0.000 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00178 (14620) covalent geometry : angle 0.44581 (19770) SS BOND : bond 0.00145 ( 51) SS BOND : angle 1.04331 ( 102) hydrogen bonds : bond 0.21023 ( 686) hydrogen bonds : angle 8.71955 ( 1887) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7993 (mm-30) REVERT: A 399 GLN cc_start: 0.8711 (tt0) cc_final: 0.8101 (tp-100) REVERT: A 403 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7874 (mt-10) REVERT: A 418 GLU cc_start: 0.8533 (pt0) cc_final: 0.8269 (pt0) REVERT: B 45 LEU cc_start: 0.8705 (mt) cc_final: 0.8490 (mp) REVERT: B 48 LEU cc_start: 0.8727 (tt) cc_final: 0.8525 (mt) REVERT: B 129 MET cc_start: 0.8159 (mmm) cc_final: 0.7923 (tpp) REVERT: B 133 LYS cc_start: 0.8857 (mmmm) cc_final: 0.8567 (mtmm) REVERT: B 136 GLU cc_start: 0.8604 (tt0) cc_final: 0.8276 (tp30) REVERT: B 356 LYS cc_start: 0.8006 (mtpp) cc_final: 0.7698 (mttt) REVERT: B 371 ARG cc_start: 0.7320 (mtm180) cc_final: 0.7009 (mtm180) REVERT: B 380 LYS cc_start: 0.8291 (ttmm) cc_final: 0.7995 (ttpt) REVERT: B 438 GLN cc_start: 0.8630 (mm110) cc_final: 0.8349 (mm-40) REVERT: B 442 PHE cc_start: 0.8653 (t80) cc_final: 0.8381 (t80) REVERT: B 449 THR cc_start: 0.8837 (p) cc_final: 0.8608 (t) REVERT: C 177 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7774 (mt-10) REVERT: C 359 GLU cc_start: 0.8068 (mp0) cc_final: 0.7858 (mp0) REVERT: C 447 ILE cc_start: 0.8895 (mm) cc_final: 0.8646 (pp) REVERT: D 2 ILE cc_start: 0.8944 (tp) cc_final: 0.8723 (tt) REVERT: D 17 CYS cc_start: 0.6654 (m) cc_final: 0.6381 (m) REVERT: D 50 THR cc_start: 0.8312 (p) cc_final: 0.7989 (t) REVERT: E 15 ARG cc_start: 0.8864 (ttm-80) cc_final: 0.8590 (ttp-170) REVERT: E 22 ASP cc_start: 0.8795 (m-30) cc_final: 0.8332 (m-30) REVERT: E 78 ASP cc_start: 0.8436 (t0) cc_final: 0.8057 (t0) REVERT: E 85 LYS cc_start: 0.8714 (tptp) cc_final: 0.8453 (tptt) REVERT: E 107 ASN cc_start: 0.7774 (m-40) cc_final: 0.7501 (m-40) REVERT: F 10 ASP cc_start: 0.8800 (m-30) cc_final: 0.8435 (m-30) REVERT: F 28 ARG cc_start: 0.8217 (ptt-90) cc_final: 0.7801 (ptt-90) REVERT: F 56 ARG cc_start: 0.7979 (ttp80) cc_final: 0.7651 (ttm-80) REVERT: G 10 LYS cc_start: 0.8471 (tttt) cc_final: 0.8267 (tttp) REVERT: G 44 GLN cc_start: 0.8153 (tt0) cc_final: 0.7700 (tt0) REVERT: G 66 TYR cc_start: 0.9214 (p90) cc_final: 0.8901 (p90) REVERT: G 105 THR cc_start: 0.9270 (m) cc_final: 0.8802 (t) REVERT: H 2 ILE cc_start: 0.9080 (tp) cc_final: 0.8874 (tp) REVERT: H 9 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8137 (mm-30) REVERT: I 48 GLN cc_start: 0.8047 (mt0) cc_final: 0.7840 (mt0) REVERT: I 69 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7921 (mt-10) REVERT: I 109 ASN cc_start: 0.9035 (p0) cc_final: 0.8681 (p0) outliers start: 0 outliers final: 2 residues processed: 354 average time/residue: 0.6116 time to fit residues: 235.5694 Evaluate side-chains 222 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 220 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain G residue 113 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0060 chunk 91 optimal weight: 0.2980 chunk 149 optimal weight: 6.9990 overall best weight: 0.2314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN C 139 GLN C 329 HIS E 1 ASN E 44 GLN F 27 ASN G 46 GLN G 57 HIS I 1 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.084538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.066362 restraints weight = 26949.886| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.72 r_work: 0.2787 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14671 Z= 0.114 Angle : 0.565 8.954 19872 Z= 0.288 Chirality : 0.040 0.211 2103 Planarity : 0.004 0.043 2597 Dihedral : 4.381 29.944 1966 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.97 % Allowed : 12.02 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.20), residues: 1757 helix: 1.88 (0.21), residues: 595 sheet: 0.32 (0.26), residues: 306 loop : 0.95 (0.23), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 43 TYR 0.011 0.001 TYR I 23 PHE 0.010 0.001 PHE A 157 TRP 0.016 0.001 TRP B 46 HIS 0.004 0.001 HIS E 111 Details of bonding type rmsd covalent geometry : bond 0.00236 (14620) covalent geometry : angle 0.55701 (19770) SS BOND : bond 0.00289 ( 51) SS BOND : angle 1.45959 ( 102) hydrogen bonds : bond 0.04271 ( 686) hydrogen bonds : angle 6.30800 ( 1887) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 246 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 58 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7879 (mm) REVERT: A 62 THR cc_start: 0.8137 (m) cc_final: 0.7718 (t) REVERT: A 66 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7327 (mp10) REVERT: A 84 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8899 (tt0) REVERT: A 145 ARG cc_start: 0.8448 (ttp-110) cc_final: 0.8241 (ttp-110) REVERT: A 177 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8155 (mm-30) REVERT: A 399 GLN cc_start: 0.8384 (tt0) cc_final: 0.8176 (tp-100) REVERT: A 403 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8050 (pt0) REVERT: A 418 GLU cc_start: 0.8469 (pt0) cc_final: 0.8228 (pt0) REVERT: B 48 LEU cc_start: 0.8717 (tt) cc_final: 0.8485 (mt) REVERT: B 121 ARG cc_start: 0.8910 (mtm-85) cc_final: 0.8610 (mtm-85) REVERT: B 133 LYS cc_start: 0.8840 (mmmm) cc_final: 0.8590 (ptmt) REVERT: B 136 GLU cc_start: 0.8651 (tt0) cc_final: 0.8432 (tm-30) REVERT: B 210 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8279 (mpt) REVERT: B 356 LYS cc_start: 0.8050 (mtpp) cc_final: 0.7703 (mttt) REVERT: B 380 LYS cc_start: 0.8193 (ttmm) cc_final: 0.7909 (ttpt) REVERT: B 438 GLN cc_start: 0.8698 (mm110) cc_final: 0.8319 (mm-40) REVERT: B 449 THR cc_start: 0.8909 (p) cc_final: 0.8625 (t) REVERT: C 63 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7763 (tm-30) REVERT: C 177 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7947 (mt-10) REVERT: C 359 GLU cc_start: 0.8483 (mp0) cc_final: 0.8225 (mp0) REVERT: C 423 LYS cc_start: 0.8473 (mtpp) cc_final: 0.8216 (mtpt) REVERT: D 17 CYS cc_start: 0.6995 (m) cc_final: 0.6726 (m) REVERT: D 50 THR cc_start: 0.8298 (p) cc_final: 0.8058 (t) REVERT: E 15 ARG cc_start: 0.8868 (ttm-80) cc_final: 0.8605 (ttp-170) REVERT: E 22 ASP cc_start: 0.8987 (m-30) cc_final: 0.8578 (m-30) REVERT: E 66 TYR cc_start: 0.9235 (p90) cc_final: 0.8954 (p90) REVERT: E 112 LYS cc_start: 0.8945 (mmtt) cc_final: 0.8543 (mmtt) REVERT: F 22 ASP cc_start: 0.8968 (m-30) cc_final: 0.8731 (m-30) REVERT: F 59 HIS cc_start: 0.8038 (t70) cc_final: 0.7747 (t-90) REVERT: G 30 ARG cc_start: 0.7515 (mtp180) cc_final: 0.7104 (mtm110) REVERT: G 103 THR cc_start: 0.9381 (m) cc_final: 0.9120 (p) REVERT: G 105 THR cc_start: 0.8943 (m) cc_final: 0.8691 (t) REVERT: H 2 ILE cc_start: 0.8994 (tp) cc_final: 0.8792 (tp) REVERT: H 9 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8281 (mm-30) REVERT: I 55 LYS cc_start: 0.8476 (ttmm) cc_final: 0.8177 (tppp) outliers start: 31 outliers final: 10 residues processed: 264 average time/residue: 0.5532 time to fit residues: 159.5716 Evaluate side-chains 226 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 212 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain I residue 62 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 58 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 GLN D 15 GLN G 44 GLN G 46 GLN H 27 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.078284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.060159 restraints weight = 27965.226| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.68 r_work: 0.2652 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 14671 Z= 0.379 Angle : 0.680 10.465 19872 Z= 0.345 Chirality : 0.046 0.228 2103 Planarity : 0.004 0.030 2597 Dihedral : 4.733 31.541 1962 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.01 % Allowed : 12.78 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.20), residues: 1757 helix: 1.76 (0.21), residues: 590 sheet: -0.28 (0.25), residues: 303 loop : 0.73 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 41 TYR 0.023 0.002 TYR A 342 PHE 0.015 0.002 PHE C 69 TRP 0.014 0.002 TRP B 46 HIS 0.005 0.001 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00878 (14620) covalent geometry : angle 0.66807 (19770) SS BOND : bond 0.00481 ( 51) SS BOND : angle 1.88458 ( 102) hydrogen bonds : bond 0.04290 ( 686) hydrogen bonds : angle 6.04878 ( 1887) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 222 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 58 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7857 (mm) REVERT: A 66 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7473 (mp10) REVERT: A 177 GLU cc_start: 0.8254 (mt-10) cc_final: 0.8025 (mm-30) REVERT: A 204 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8397 (ttm110) REVERT: A 356 LYS cc_start: 0.8708 (mttt) cc_final: 0.8452 (mtpm) REVERT: A 399 GLN cc_start: 0.8445 (tt0) cc_final: 0.7899 (tp-100) REVERT: A 403 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8168 (mt-10) REVERT: A 418 GLU cc_start: 0.8564 (pt0) cc_final: 0.8306 (pt0) REVERT: B 48 LEU cc_start: 0.8768 (tt) cc_final: 0.8522 (mt) REVERT: B 133 LYS cc_start: 0.8883 (mmmm) cc_final: 0.8468 (tppt) REVERT: B 210 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8268 (mpt) REVERT: B 356 LYS cc_start: 0.8196 (mtpp) cc_final: 0.7863 (mttt) REVERT: B 380 LYS cc_start: 0.8243 (ttmm) cc_final: 0.7932 (ttpt) REVERT: B 438 GLN cc_start: 0.8705 (mm110) cc_final: 0.8253 (mm-40) REVERT: B 449 THR cc_start: 0.8890 (p) cc_final: 0.8655 (t) REVERT: C 50 PHE cc_start: 0.7212 (t80) cc_final: 0.6945 (t80) REVERT: C 129 MET cc_start: 0.8571 (mmt) cc_final: 0.8268 (mmm) REVERT: C 177 GLU cc_start: 0.8233 (mt-10) cc_final: 0.8008 (mt-10) REVERT: C 359 GLU cc_start: 0.8707 (mp0) cc_final: 0.8372 (mp0) REVERT: D 50 THR cc_start: 0.8299 (p) cc_final: 0.8056 (t) REVERT: E 22 ASP cc_start: 0.9030 (m-30) cc_final: 0.8811 (m-30) REVERT: E 41 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7374 (ttm110) REVERT: G 103 THR cc_start: 0.9381 (m) cc_final: 0.9117 (p) REVERT: H 2 ILE cc_start: 0.9062 (tp) cc_final: 0.8589 (tt) REVERT: H 9 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8342 (mm-30) REVERT: I 6 ARG cc_start: 0.8161 (ttp80) cc_final: 0.7904 (mtp-110) REVERT: I 10 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8134 (tttt) REVERT: I 55 LYS cc_start: 0.8499 (ttmm) cc_final: 0.8181 (tppp) outliers start: 63 outliers final: 27 residues processed: 254 average time/residue: 0.5195 time to fit residues: 144.6316 Evaluate side-chains 227 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 80 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 26 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 143 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 147 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 GLN D 15 GLN F 27 ASN G 46 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.080762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.062768 restraints weight = 27431.910| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.68 r_work: 0.2714 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14671 Z= 0.140 Angle : 0.553 10.803 19872 Z= 0.279 Chirality : 0.041 0.199 2103 Planarity : 0.003 0.036 2597 Dihedral : 4.621 28.601 1962 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.80 % Allowed : 15.32 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.20), residues: 1757 helix: 1.91 (0.21), residues: 591 sheet: -0.25 (0.26), residues: 301 loop : 0.81 (0.23), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 145 TYR 0.012 0.001 TYR G 23 PHE 0.012 0.001 PHE H 6 TRP 0.013 0.001 TRP B 46 HIS 0.004 0.001 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00316 (14620) covalent geometry : angle 0.54520 (19770) SS BOND : bond 0.00261 ( 51) SS BOND : angle 1.38840 ( 102) hydrogen bonds : bond 0.03514 ( 686) hydrogen bonds : angle 5.84362 ( 1887) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 214 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 58 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8053 (mm) REVERT: A 66 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7473 (mp10) REVERT: A 177 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8060 (mm-30) REVERT: A 399 GLN cc_start: 0.8397 (tt0) cc_final: 0.8154 (tp-100) REVERT: A 403 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8181 (pt0) REVERT: A 418 GLU cc_start: 0.8512 (pt0) cc_final: 0.8200 (pt0) REVERT: B 48 LEU cc_start: 0.8781 (tt) cc_final: 0.8564 (mt) REVERT: B 51 LEU cc_start: 0.8386 (tt) cc_final: 0.8132 (mm) REVERT: B 78 ASP cc_start: 0.8389 (t0) cc_final: 0.8059 (t0) REVERT: B 356 LYS cc_start: 0.8297 (mtpp) cc_final: 0.7962 (mttm) REVERT: B 359 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: B 380 LYS cc_start: 0.8294 (ttmm) cc_final: 0.7982 (ttpt) REVERT: B 418 GLU cc_start: 0.8112 (pt0) cc_final: 0.7677 (pt0) REVERT: B 438 GLN cc_start: 0.8728 (mm110) cc_final: 0.8296 (mm-40) REVERT: B 449 THR cc_start: 0.8979 (p) cc_final: 0.8705 (t) REVERT: C 50 PHE cc_start: 0.7299 (t80) cc_final: 0.7038 (t80) REVERT: C 129 MET cc_start: 0.8575 (mmt) cc_final: 0.8113 (mmm) REVERT: C 177 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8184 (mt-10) REVERT: C 359 GLU cc_start: 0.8660 (mp0) cc_final: 0.8447 (mp0) REVERT: D 50 THR cc_start: 0.8349 (p) cc_final: 0.8119 (t) REVERT: E 14 ASP cc_start: 0.8929 (OUTLIER) cc_final: 0.8714 (m-30) REVERT: E 22 ASP cc_start: 0.9019 (m-30) cc_final: 0.8819 (m-30) REVERT: E 60 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8088 (ptmt) REVERT: E 100 CYS cc_start: 0.7573 (OUTLIER) cc_final: 0.6971 (t) REVERT: G 103 THR cc_start: 0.9391 (m) cc_final: 0.9118 (p) REVERT: H 2 ILE cc_start: 0.9082 (tp) cc_final: 0.8637 (tt) REVERT: H 9 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8375 (mm-30) REVERT: I 6 ARG cc_start: 0.8234 (ttp80) cc_final: 0.7952 (mtp-110) REVERT: I 55 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8201 (tppp) REVERT: I 63 VAL cc_start: 0.8781 (m) cc_final: 0.8579 (p) outliers start: 44 outliers final: 17 residues processed: 239 average time/residue: 0.5169 time to fit residues: 135.6106 Evaluate side-chains 216 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 75 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 133 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN G 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.081176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.063240 restraints weight = 27396.685| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.67 r_work: 0.2711 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14671 Z= 0.145 Angle : 0.562 10.957 19872 Z= 0.282 Chirality : 0.040 0.197 2103 Planarity : 0.003 0.042 2597 Dihedral : 4.515 27.585 1962 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.99 % Allowed : 15.83 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.20), residues: 1757 helix: 1.92 (0.21), residues: 591 sheet: -0.31 (0.27), residues: 303 loop : 0.80 (0.23), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 145 TYR 0.014 0.001 TYR E 66 PHE 0.012 0.001 PHE H 6 TRP 0.016 0.001 TRP B 46 HIS 0.004 0.001 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00339 (14620) covalent geometry : angle 0.55123 (19770) SS BOND : bond 0.00291 ( 51) SS BOND : angle 1.60688 ( 102) hydrogen bonds : bond 0.03384 ( 686) hydrogen bonds : angle 5.67347 ( 1887) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8057 (mm) REVERT: A 66 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7511 (mp10) REVERT: A 145 ARG cc_start: 0.8577 (ttp-110) cc_final: 0.8257 (ttp-110) REVERT: A 177 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8123 (mm-30) REVERT: A 204 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8424 (ttm110) REVERT: A 327 MET cc_start: 0.8504 (mtp) cc_final: 0.7837 (mtm) REVERT: A 365 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8158 (mmm) REVERT: A 399 GLN cc_start: 0.8403 (tt0) cc_final: 0.8164 (tp-100) REVERT: A 403 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8195 (pt0) REVERT: A 418 GLU cc_start: 0.8543 (pt0) cc_final: 0.8218 (pt0) REVERT: B 48 LEU cc_start: 0.8755 (tt) cc_final: 0.8549 (mt) REVERT: B 51 LEU cc_start: 0.8377 (tt) cc_final: 0.8112 (mm) REVERT: B 133 LYS cc_start: 0.9122 (mppt) cc_final: 0.8908 (mppt) REVERT: B 356 LYS cc_start: 0.8364 (mtpp) cc_final: 0.8050 (mttm) REVERT: B 359 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7865 (mt-10) REVERT: B 365 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8459 (mmm) REVERT: B 380 LYS cc_start: 0.8318 (ttmm) cc_final: 0.8012 (ttpt) REVERT: B 418 GLU cc_start: 0.8106 (pt0) cc_final: 0.7691 (pt0) REVERT: B 438 GLN cc_start: 0.8729 (mm110) cc_final: 0.8293 (mm-40) REVERT: B 449 THR cc_start: 0.8945 (p) cc_final: 0.8687 (t) REVERT: C 50 PHE cc_start: 0.7299 (t80) cc_final: 0.7033 (t80) REVERT: C 177 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8217 (mt-10) REVERT: C 295 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.6307 (ttt) REVERT: C 359 GLU cc_start: 0.8674 (mp0) cc_final: 0.8464 (mp0) REVERT: D 50 THR cc_start: 0.8386 (p) cc_final: 0.8141 (t) REVERT: E 22 ASP cc_start: 0.9016 (m-30) cc_final: 0.8741 (m-30) REVERT: E 60 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8132 (ptmt) REVERT: E 112 LYS cc_start: 0.9096 (mmmm) cc_final: 0.8802 (mmmt) REVERT: G 103 THR cc_start: 0.9362 (m) cc_final: 0.9085 (p) REVERT: H 2 ILE cc_start: 0.9099 (tp) cc_final: 0.8646 (tt) REVERT: H 9 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8363 (mm-30) REVERT: I 6 ARG cc_start: 0.8280 (ttp80) cc_final: 0.7974 (mtp-110) REVERT: I 46 GLN cc_start: 0.8138 (tt0) cc_final: 0.7905 (tt0) REVERT: I 55 LYS cc_start: 0.8514 (ttmm) cc_final: 0.8201 (tppp) outliers start: 47 outliers final: 26 residues processed: 235 average time/residue: 0.4810 time to fit residues: 124.5375 Evaluate side-chains 231 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 93 CYS Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 11 CYS Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 59 HIS Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 76 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 40 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 67 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 60 optimal weight: 0.2980 chunk 53 optimal weight: 0.0670 chunk 138 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN G 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.082114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.064257 restraints weight = 27397.408| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.68 r_work: 0.2735 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 14671 Z= 0.114 Angle : 0.543 11.497 19872 Z= 0.272 Chirality : 0.040 0.203 2103 Planarity : 0.003 0.040 2597 Dihedral : 4.442 28.997 1962 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.12 % Allowed : 15.96 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.20), residues: 1757 helix: 1.98 (0.22), residues: 591 sheet: -0.21 (0.27), residues: 303 loop : 0.77 (0.23), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 145 TYR 0.012 0.001 TYR E 66 PHE 0.012 0.001 PHE H 6 TRP 0.015 0.001 TRP B 46 HIS 0.005 0.001 HIS H 59 Details of bonding type rmsd covalent geometry : bond 0.00267 (14620) covalent geometry : angle 0.53322 (19770) SS BOND : bond 0.00249 ( 51) SS BOND : angle 1.54823 ( 102) hydrogen bonds : bond 0.03213 ( 686) hydrogen bonds : angle 5.53786 ( 1887) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 221 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8052 (mm) REVERT: A 145 ARG cc_start: 0.8500 (ttp-110) cc_final: 0.8163 (ttp-110) REVERT: A 177 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8142 (mm-30) REVERT: A 204 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8459 (ttm110) REVERT: A 359 GLU cc_start: 0.8015 (mp0) cc_final: 0.7693 (pm20) REVERT: A 365 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8183 (mmm) REVERT: A 399 GLN cc_start: 0.8379 (tt0) cc_final: 0.8153 (tp-100) REVERT: A 403 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8259 (pt0) REVERT: B 48 LEU cc_start: 0.8735 (tt) cc_final: 0.8525 (mt) REVERT: B 51 LEU cc_start: 0.8296 (tt) cc_final: 0.8059 (mm) REVERT: B 145 ARG cc_start: 0.9052 (ttm110) cc_final: 0.8755 (mtp85) REVERT: B 356 LYS cc_start: 0.8347 (mtpp) cc_final: 0.8043 (mttm) REVERT: B 359 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: B 365 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8463 (mmm) REVERT: B 380 LYS cc_start: 0.8304 (ttmm) cc_final: 0.8004 (ttpt) REVERT: B 418 GLU cc_start: 0.8045 (pt0) cc_final: 0.7626 (pt0) REVERT: B 438 GLN cc_start: 0.8715 (mm110) cc_final: 0.8291 (mm-40) REVERT: B 449 THR cc_start: 0.8931 (p) cc_final: 0.8666 (t) REVERT: C 50 PHE cc_start: 0.7302 (t80) cc_final: 0.7051 (t80) REVERT: C 129 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7933 (mmm) REVERT: C 148 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8937 (mptp) REVERT: C 177 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8198 (mt-10) REVERT: C 359 GLU cc_start: 0.8644 (mp0) cc_final: 0.8431 (mp0) REVERT: E 14 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8681 (m-30) REVERT: E 22 ASP cc_start: 0.9017 (m-30) cc_final: 0.8738 (m-30) REVERT: E 100 CYS cc_start: 0.7421 (OUTLIER) cc_final: 0.6936 (t) REVERT: E 112 LYS cc_start: 0.9125 (mmmm) cc_final: 0.8858 (mmmt) REVERT: G 103 THR cc_start: 0.9361 (m) cc_final: 0.9081 (p) REVERT: H 2 ILE cc_start: 0.9096 (tp) cc_final: 0.8664 (tt) REVERT: H 9 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8331 (mm-30) REVERT: I 36 VAL cc_start: 0.8885 (p) cc_final: 0.8617 (m) REVERT: I 46 GLN cc_start: 0.8163 (tt0) cc_final: 0.7955 (tt0) REVERT: I 55 LYS cc_start: 0.8500 (ttmm) cc_final: 0.8187 (tppp) REVERT: I 117 ARG cc_start: 0.8654 (mtp180) cc_final: 0.8063 (mtp180) outliers start: 49 outliers final: 21 residues processed: 246 average time/residue: 0.5107 time to fit residues: 137.8181 Evaluate side-chains 233 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 11 CYS Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain G residue 49 CYS Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 59 HIS Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 76 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 96 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 49 optimal weight: 0.0050 chunk 118 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN D 15 GLN G 46 GLN G 88 ASN G 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.082236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.064482 restraints weight = 27408.006| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.68 r_work: 0.2744 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14671 Z= 0.121 Angle : 0.562 11.637 19872 Z= 0.279 Chirality : 0.040 0.278 2103 Planarity : 0.003 0.037 2597 Dihedral : 4.402 26.854 1962 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.54 % Allowed : 16.91 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.20), residues: 1757 helix: 1.94 (0.21), residues: 599 sheet: -0.15 (0.27), residues: 303 loop : 0.76 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 41 TYR 0.012 0.001 TYR G 66 PHE 0.025 0.001 PHE A 442 TRP 0.014 0.001 TRP A 46 HIS 0.005 0.001 HIS H 59 Details of bonding type rmsd covalent geometry : bond 0.00285 (14620) covalent geometry : angle 0.55184 (19770) SS BOND : bond 0.00234 ( 51) SS BOND : angle 1.56336 ( 102) hydrogen bonds : bond 0.03246 ( 686) hydrogen bonds : angle 5.47251 ( 1887) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 215 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8043 (mm) REVERT: A 84 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8842 (tt0) REVERT: A 132 GLU cc_start: 0.8446 (pm20) cc_final: 0.8243 (pt0) REVERT: A 145 ARG cc_start: 0.8493 (ttp-110) cc_final: 0.8154 (ttp-110) REVERT: A 177 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8078 (mm-30) REVERT: A 204 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8470 (ttm110) REVERT: A 356 LYS cc_start: 0.8683 (mttt) cc_final: 0.8402 (mtpm) REVERT: A 359 GLU cc_start: 0.8009 (mp0) cc_final: 0.7688 (pm20) REVERT: A 365 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8149 (mmm) REVERT: A 399 GLN cc_start: 0.8343 (tt0) cc_final: 0.8104 (tp-100) REVERT: A 403 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8241 (pt0) REVERT: A 418 GLU cc_start: 0.8450 (pt0) cc_final: 0.7698 (pm20) REVERT: B 48 LEU cc_start: 0.8733 (tt) cc_final: 0.8505 (mt) REVERT: B 51 LEU cc_start: 0.8248 (tt) cc_final: 0.8029 (mm) REVERT: B 356 LYS cc_start: 0.8322 (mtpp) cc_final: 0.7990 (mttm) REVERT: B 359 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7784 (mt-10) REVERT: B 365 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8415 (mmm) REVERT: B 380 LYS cc_start: 0.8210 (ttmm) cc_final: 0.7924 (ttpt) REVERT: B 418 GLU cc_start: 0.7983 (pt0) cc_final: 0.7558 (pt0) REVERT: B 438 GLN cc_start: 0.8676 (mm110) cc_final: 0.8237 (mm-40) REVERT: B 449 THR cc_start: 0.8902 (p) cc_final: 0.8648 (t) REVERT: C 50 PHE cc_start: 0.7246 (t80) cc_final: 0.7031 (t80) REVERT: C 129 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7994 (mmm) REVERT: C 148 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8967 (mptp) REVERT: C 177 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8168 (mt-10) REVERT: C 359 GLU cc_start: 0.8616 (mp0) cc_final: 0.8371 (mp0) REVERT: D 53 GLU cc_start: 0.8296 (tt0) cc_final: 0.7680 (tm-30) REVERT: E 22 ASP cc_start: 0.9020 (m-30) cc_final: 0.8719 (m-30) REVERT: E 100 CYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6820 (t) REVERT: E 112 LYS cc_start: 0.9118 (mmmm) cc_final: 0.8850 (mmmt) REVERT: G 103 THR cc_start: 0.9346 (m) cc_final: 0.9066 (p) REVERT: H 2 ILE cc_start: 0.9068 (tp) cc_final: 0.8625 (tt) REVERT: H 9 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8317 (mm-30) REVERT: H 15 GLN cc_start: 0.8342 (mt0) cc_final: 0.8091 (mt0) REVERT: I 36 VAL cc_start: 0.8808 (p) cc_final: 0.8605 (m) REVERT: I 55 LYS cc_start: 0.8460 (ttmm) cc_final: 0.8142 (tppp) REVERT: I 85 LYS cc_start: 0.8485 (tppt) cc_final: 0.8268 (tppt) REVERT: I 117 ARG cc_start: 0.8700 (mtp180) cc_final: 0.8105 (mtp180) outliers start: 40 outliers final: 15 residues processed: 238 average time/residue: 0.5251 time to fit residues: 136.9524 Evaluate side-chains 229 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 11 CYS Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 59 HIS Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 62 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 132 optimal weight: 0.0050 chunk 87 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN D 15 GLN G 46 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.082488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.064665 restraints weight = 27519.446| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.70 r_work: 0.2753 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14671 Z= 0.117 Angle : 0.564 12.280 19872 Z= 0.278 Chirality : 0.040 0.223 2103 Planarity : 0.003 0.052 2597 Dihedral : 4.373 25.420 1962 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.48 % Allowed : 17.42 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.20), residues: 1757 helix: 1.96 (0.22), residues: 592 sheet: -0.10 (0.27), residues: 303 loop : 0.75 (0.23), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 145 TYR 0.015 0.001 TYR G 66 PHE 0.013 0.001 PHE A 442 TRP 0.012 0.001 TRP A 46 HIS 0.004 0.001 HIS I 57 Details of bonding type rmsd covalent geometry : bond 0.00277 (14620) covalent geometry : angle 0.55537 (19770) SS BOND : bond 0.00229 ( 51) SS BOND : angle 1.47208 ( 102) hydrogen bonds : bond 0.03138 ( 686) hydrogen bonds : angle 5.40022 ( 1887) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8090 (mm) REVERT: A 66 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7605 (mp10) REVERT: A 84 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8849 (tt0) REVERT: A 145 ARG cc_start: 0.8472 (ttp-110) cc_final: 0.8131 (ttp-110) REVERT: A 177 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8136 (mm-30) REVERT: A 204 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8510 (ttm110) REVERT: A 356 LYS cc_start: 0.8747 (mttt) cc_final: 0.8497 (mtpm) REVERT: A 359 GLU cc_start: 0.8057 (mp0) cc_final: 0.7742 (pm20) REVERT: A 365 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8218 (mmm) REVERT: A 399 GLN cc_start: 0.8392 (tt0) cc_final: 0.8136 (tp-100) REVERT: A 403 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8321 (pt0) REVERT: A 418 GLU cc_start: 0.8513 (pt0) cc_final: 0.7766 (pm20) REVERT: B 48 LEU cc_start: 0.8742 (tt) cc_final: 0.8513 (mt) REVERT: B 51 LEU cc_start: 0.8292 (tt) cc_final: 0.8087 (mm) REVERT: B 129 MET cc_start: 0.8465 (tpp) cc_final: 0.8021 (tpp) REVERT: B 145 ARG cc_start: 0.9071 (ttm110) cc_final: 0.8790 (mtp85) REVERT: B 356 LYS cc_start: 0.8317 (mtpp) cc_final: 0.8007 (mttm) REVERT: B 359 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: B 380 LYS cc_start: 0.8295 (ttmm) cc_final: 0.8019 (ttpt) REVERT: B 418 GLU cc_start: 0.8045 (pt0) cc_final: 0.7617 (pt0) REVERT: B 438 GLN cc_start: 0.8677 (mm110) cc_final: 0.8257 (mm-40) REVERT: C 50 PHE cc_start: 0.7327 (t80) cc_final: 0.7082 (t80) REVERT: C 63 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7885 (tm-30) REVERT: C 129 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.8059 (mmm) REVERT: C 148 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8983 (mptp) REVERT: C 177 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8309 (mt-10) REVERT: C 359 GLU cc_start: 0.8633 (mp0) cc_final: 0.8326 (pm20) REVERT: D 53 GLU cc_start: 0.8363 (tt0) cc_final: 0.7774 (tm-30) REVERT: E 22 ASP cc_start: 0.9032 (m-30) cc_final: 0.8736 (m-30) REVERT: E 100 CYS cc_start: 0.7421 (OUTLIER) cc_final: 0.6883 (t) REVERT: E 112 LYS cc_start: 0.9135 (mmmm) cc_final: 0.8881 (mmmt) REVERT: F 27 ASN cc_start: 0.8257 (t0) cc_final: 0.7921 (t0) REVERT: G 103 THR cc_start: 0.9343 (m) cc_final: 0.9056 (p) REVERT: G 112 LYS cc_start: 0.9082 (mptm) cc_final: 0.8849 (mptt) REVERT: H 2 ILE cc_start: 0.9106 (tp) cc_final: 0.8657 (tt) REVERT: H 9 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8352 (mm-30) REVERT: H 15 GLN cc_start: 0.8440 (mt0) cc_final: 0.8194 (mt0) REVERT: I 52 GLU cc_start: 0.8648 (tp30) cc_final: 0.7750 (tp30) REVERT: I 55 LYS cc_start: 0.8477 (ttmm) cc_final: 0.8195 (tppp) REVERT: I 56 VAL cc_start: 0.9314 (p) cc_final: 0.8483 (m) REVERT: I 117 ARG cc_start: 0.8705 (mtp180) cc_final: 0.8127 (mtp180) outliers start: 39 outliers final: 18 residues processed: 238 average time/residue: 0.5453 time to fit residues: 141.9836 Evaluate side-chains 230 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 11 CYS Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 59 HIS Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 40 ASP Chi-restraints excluded: chain I residue 62 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 83 optimal weight: 0.0060 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN C 329 HIS D 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.082672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.064625 restraints weight = 27146.726| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.73 r_work: 0.2743 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14671 Z= 0.126 Angle : 0.570 12.912 19872 Z= 0.278 Chirality : 0.041 0.236 2103 Planarity : 0.003 0.053 2597 Dihedral : 4.350 24.811 1962 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.42 % Allowed : 17.48 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.21), residues: 1757 helix: 2.00 (0.22), residues: 601 sheet: -0.09 (0.28), residues: 303 loop : 0.76 (0.23), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 145 TYR 0.015 0.001 TYR G 66 PHE 0.012 0.001 PHE F 6 TRP 0.016 0.001 TRP A 46 HIS 0.005 0.001 HIS H 59 Details of bonding type rmsd covalent geometry : bond 0.00299 (14620) covalent geometry : angle 0.56307 (19770) SS BOND : bond 0.00218 ( 51) SS BOND : angle 1.32567 ( 102) hydrogen bonds : bond 0.03120 ( 686) hydrogen bonds : angle 5.37475 ( 1887) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8144 (mm) REVERT: A 66 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7654 (mp10) REVERT: A 84 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8897 (tt0) REVERT: A 145 ARG cc_start: 0.8414 (ttp-110) cc_final: 0.8129 (ttp-110) REVERT: A 177 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8195 (mm-30) REVERT: A 204 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8524 (ttm110) REVERT: A 356 LYS cc_start: 0.8787 (mttt) cc_final: 0.8530 (mtpm) REVERT: A 359 GLU cc_start: 0.8096 (mp0) cc_final: 0.7795 (pm20) REVERT: A 365 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8260 (mmm) REVERT: A 399 GLN cc_start: 0.8440 (tt0) cc_final: 0.8201 (tp-100) REVERT: A 418 GLU cc_start: 0.8546 (pt0) cc_final: 0.7785 (pm20) REVERT: B 48 LEU cc_start: 0.8790 (tt) cc_final: 0.8503 (mt) REVERT: B 51 LEU cc_start: 0.8274 (tt) cc_final: 0.8071 (mm) REVERT: B 145 ARG cc_start: 0.9071 (ttm110) cc_final: 0.8789 (mtp85) REVERT: B 356 LYS cc_start: 0.8367 (mtpp) cc_final: 0.8045 (mttm) REVERT: B 359 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8017 (mt-10) REVERT: B 380 LYS cc_start: 0.8351 (ttmm) cc_final: 0.8065 (ttpt) REVERT: B 418 GLU cc_start: 0.8102 (pt0) cc_final: 0.7681 (pt0) REVERT: B 438 GLN cc_start: 0.8673 (mm110) cc_final: 0.8255 (mm-40) REVERT: C 50 PHE cc_start: 0.7428 (t80) cc_final: 0.7143 (t80) REVERT: C 63 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7903 (tm-30) REVERT: C 129 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8041 (mmm) REVERT: C 148 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.9000 (mptp) REVERT: C 177 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8289 (mt-10) REVERT: C 359 GLU cc_start: 0.8665 (mp0) cc_final: 0.8342 (pm20) REVERT: D 53 GLU cc_start: 0.8435 (tt0) cc_final: 0.7827 (tm-30) REVERT: E 14 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8691 (m-30) REVERT: E 22 ASP cc_start: 0.9058 (m-30) cc_final: 0.8760 (m-30) REVERT: E 100 CYS cc_start: 0.7486 (OUTLIER) cc_final: 0.6955 (t) REVERT: E 112 LYS cc_start: 0.9145 (mmmm) cc_final: 0.8894 (mmmt) REVERT: F 27 ASN cc_start: 0.8334 (t0) cc_final: 0.8001 (t0) REVERT: G 103 THR cc_start: 0.9321 (m) cc_final: 0.9032 (p) REVERT: H 2 ILE cc_start: 0.9164 (tp) cc_final: 0.8740 (tt) REVERT: H 9 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8385 (mm-30) REVERT: H 15 GLN cc_start: 0.8495 (mt0) cc_final: 0.8250 (mt0) REVERT: I 52 GLU cc_start: 0.8651 (tp30) cc_final: 0.7750 (tp30) REVERT: I 55 LYS cc_start: 0.8494 (ttmm) cc_final: 0.8235 (tppt) REVERT: I 56 VAL cc_start: 0.9342 (p) cc_final: 0.8561 (m) REVERT: I 85 LYS cc_start: 0.8587 (tppt) cc_final: 0.8367 (tppt) REVERT: I 117 ARG cc_start: 0.8738 (mtp180) cc_final: 0.8175 (mtp180) outliers start: 38 outliers final: 16 residues processed: 236 average time/residue: 0.5194 time to fit residues: 134.3815 Evaluate side-chains 228 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 11 CYS Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 59 HIS Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 76 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 13 optimal weight: 0.2980 chunk 68 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN G 46 GLN I 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.082593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.064468 restraints weight = 27265.145| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.75 r_work: 0.2732 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14671 Z= 0.126 Angle : 0.575 14.019 19872 Z= 0.281 Chirality : 0.041 0.208 2103 Planarity : 0.003 0.049 2597 Dihedral : 4.339 24.347 1962 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.84 % Allowed : 18.31 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.21), residues: 1757 helix: 2.13 (0.22), residues: 589 sheet: -0.01 (0.27), residues: 311 loop : 0.72 (0.23), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 145 TYR 0.016 0.001 TYR G 66 PHE 0.014 0.001 PHE B 442 TRP 0.014 0.001 TRP A 46 HIS 0.004 0.001 HIS H 59 Details of bonding type rmsd covalent geometry : bond 0.00298 (14620) covalent geometry : angle 0.56873 (19770) SS BOND : bond 0.00216 ( 51) SS BOND : angle 1.28493 ( 102) hydrogen bonds : bond 0.03125 ( 686) hydrogen bonds : angle 5.34443 ( 1887) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8120 (mm) REVERT: A 66 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7579 (mp10) REVERT: A 84 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8871 (tt0) REVERT: A 145 ARG cc_start: 0.8430 (ttp-110) cc_final: 0.8150 (ttp-110) REVERT: A 148 LYS cc_start: 0.9100 (mptt) cc_final: 0.8820 (mmmm) REVERT: A 177 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8177 (mm-30) REVERT: A 204 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8532 (ttm110) REVERT: A 327 MET cc_start: 0.8353 (mtp) cc_final: 0.7898 (mmm) REVERT: A 356 LYS cc_start: 0.8767 (mttt) cc_final: 0.8512 (mtpm) REVERT: A 359 GLU cc_start: 0.8123 (mp0) cc_final: 0.7825 (pm20) REVERT: A 399 GLN cc_start: 0.8488 (tt0) cc_final: 0.8203 (tp-100) REVERT: A 418 GLU cc_start: 0.8505 (pt0) cc_final: 0.7760 (pm20) REVERT: B 48 LEU cc_start: 0.8767 (tt) cc_final: 0.8495 (mt) REVERT: B 129 MET cc_start: 0.8420 (tpp) cc_final: 0.8142 (tpp) REVERT: B 145 ARG cc_start: 0.9082 (ttm110) cc_final: 0.8809 (mtp85) REVERT: B 356 LYS cc_start: 0.8350 (mtpp) cc_final: 0.8023 (mttm) REVERT: B 359 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: B 380 LYS cc_start: 0.8307 (ttmm) cc_final: 0.8022 (ttpt) REVERT: B 418 GLU cc_start: 0.8088 (pt0) cc_final: 0.7678 (pt0) REVERT: B 438 GLN cc_start: 0.8689 (mm110) cc_final: 0.8274 (mm-40) REVERT: C 50 PHE cc_start: 0.7505 (t80) cc_final: 0.7248 (t80) REVERT: C 129 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8077 (mmm) REVERT: C 148 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.9006 (mptp) REVERT: C 177 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8266 (mt-10) REVERT: C 359 GLU cc_start: 0.8684 (mp0) cc_final: 0.8326 (pm20) REVERT: D 53 GLU cc_start: 0.8422 (tt0) cc_final: 0.7809 (tm-30) REVERT: E 22 ASP cc_start: 0.9051 (m-30) cc_final: 0.8762 (m-30) REVERT: E 100 CYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6955 (t) REVERT: E 112 LYS cc_start: 0.9139 (mmmm) cc_final: 0.8898 (mmmt) REVERT: F 27 ASN cc_start: 0.8339 (t0) cc_final: 0.8004 (t0) REVERT: G 103 THR cc_start: 0.9293 (m) cc_final: 0.8993 (p) REVERT: H 2 ILE cc_start: 0.9153 (tp) cc_final: 0.8718 (tt) REVERT: H 9 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8375 (mm-30) REVERT: I 52 GLU cc_start: 0.8630 (tp30) cc_final: 0.7738 (tp30) REVERT: I 55 LYS cc_start: 0.8468 (ttmm) cc_final: 0.8215 (tppt) REVERT: I 56 VAL cc_start: 0.9339 (p) cc_final: 0.8560 (m) REVERT: I 85 LYS cc_start: 0.8596 (tppt) cc_final: 0.8385 (tppt) REVERT: I 117 ARG cc_start: 0.8756 (mtp180) cc_final: 0.8216 (mtp180) outliers start: 29 outliers final: 14 residues processed: 226 average time/residue: 0.5202 time to fit residues: 128.7501 Evaluate side-chains 224 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain G residue 11 CYS Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 59 HIS Chi-restraints excluded: chain I residue 32 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 103 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN C 329 HIS D 15 GLN H 15 GLN I 48 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.082499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.064456 restraints weight = 27186.314| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.76 r_work: 0.2740 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14671 Z= 0.129 Angle : 0.568 13.535 19872 Z= 0.278 Chirality : 0.040 0.201 2103 Planarity : 0.003 0.047 2597 Dihedral : 4.325 24.075 1962 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.97 % Allowed : 18.18 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.21), residues: 1757 helix: 2.16 (0.22), residues: 589 sheet: -0.00 (0.27), residues: 311 loop : 0.70 (0.23), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 145 TYR 0.017 0.001 TYR G 66 PHE 0.015 0.001 PHE B 442 TRP 0.013 0.001 TRP A 46 HIS 0.003 0.001 HIS H 59 Details of bonding type rmsd covalent geometry : bond 0.00306 (14620) covalent geometry : angle 0.56189 (19770) SS BOND : bond 0.00215 ( 51) SS BOND : angle 1.25700 ( 102) hydrogen bonds : bond 0.03099 ( 686) hydrogen bonds : angle 5.32651 ( 1887) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4618.85 seconds wall clock time: 79 minutes 26.10 seconds (4766.10 seconds total)