Starting phenix.real_space_refine on Tue Dec 31 15:35:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qn9_14071/12_2024/7qn9_14071.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qn9_14071/12_2024/7qn9_14071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qn9_14071/12_2024/7qn9_14071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qn9_14071/12_2024/7qn9_14071.map" model { file = "/net/cci-nas-00/data/ceres_data/7qn9_14071/12_2024/7qn9_14071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qn9_14071/12_2024/7qn9_14071.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 91 5.16 5 C 10194 2.51 5 N 2533 2.21 5 O 2878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15696 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2693 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 315} Chain breaks: 1 Chain: "B" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2720 Classifications: {'peptide': 331} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "C" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2720 Classifications: {'peptide': 331} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2720 Classifications: {'peptide': 331} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "E" Number of atoms: 2579 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 321, 2569 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 308} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 321, 2569 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 308} Chain breaks: 1 bond proxies already assigned to first conformer: 2627 Chain: "L" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "M" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'HSM': 1, 'R16': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'D10': 1, 'HSM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N HSM C 501 " occ=0.70 ... (6 atoms not shown) pdb=" NE2 HSM C 501 " occ=0.70 residue: pdb=" N HSM D 502 " occ=0.70 ... (6 atoms not shown) pdb=" NE2 HSM D 502 " occ=0.70 Time building chain proxies: 11.09, per 1000 atoms: 0.71 Number of scatterers: 15696 At special positions: 0 Unit cell: (113.792, 116.48, 129.92, 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 91 16.00 O 2878 8.00 N 2533 7.00 C 10194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 164 " - pdb=" SG CYS E 178 " distance=2.03 Simple disulfide: pdb=" SG CYS L 409 " - pdb=" SG CYS L 483 " distance=2.03 Simple disulfide: pdb=" SG CYS M 409 " - pdb=" SG CYS M 483 " 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 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A 601 " - " ASN A 157 " " NAG E 501 " - " ASN E 65 " " NAG F 1 " - " ASN B 149 " " NAG G 1 " - " ASN C 149 " " NAG H 1 " - " ASN D 149 " " NAG a 1 " - " ASN A 144 " " NAG b 1 " - " ASN B 80 " " NAG c 1 " - " ASN C 80 " " NAG d 1 " - " ASN D 80 " Time building additional restraints: 4.56 Conformation dependent library (CDL) restraints added in 2.2 seconds 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3564 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 21 sheets defined 37.8% alpha, 40.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 106 through 109 removed outlier: 3.527A pdb=" N LYS A 109 " --> pdb=" O LYS A 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 106 through 109' Processing helix chain 'A' and resid 120 through 127 removed outlier: 3.620A pdb=" N THR A 125 " --> pdb=" O MET A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 263 through 275 Processing helix chain 'A' and resid 275 through 280 removed outlier: 4.277A pdb=" N TRP A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 275 through 280' Processing helix chain 'A' and resid 284 through 310 removed outlier: 3.760A pdb=" N HIS A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 348 Processing helix chain 'A' and resid 516 through 543 removed outlier: 3.682A pdb=" N ILE A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Proline residue: A 527 - end of helix removed outlier: 3.622A pdb=" N SER A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 21 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 225 through 238 removed outlier: 3.520A pdb=" N SER B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 242 Processing helix chain 'B' and resid 246 through 269 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 279 through 306 Processing helix chain 'B' and resid 420 through 447 removed outlier: 3.507A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 9 through 21 Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 84 through 91 Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 225 through 238 removed outlier: 3.520A pdb=" N SER C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 242 Processing helix chain 'C' and resid 246 through 269 Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 279 through 306 Processing helix chain 'C' and resid 420 through 447 removed outlier: 3.507A pdb=" N ILE C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'D' and resid 9 through 21 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 84 through 91 Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 177 through 181 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 225 through 238 removed outlier: 3.519A pdb=" N SER D 229 " --> pdb=" O THR D 225 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TRP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 242 Processing helix chain 'D' and resid 246 through 269 Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'D' and resid 279 through 306 Processing helix chain 'D' and resid 420 through 447 removed outlier: 3.509A pdb=" N ILE D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 45 through 50 Processing helix chain 'E' and resid 98 through 101 Processing helix chain 'E' and resid 112 through 118 removed outlier: 3.549A pdb=" N PHE E 115 " --> pdb=" O ASP E 112 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP E 117 " --> pdb=" O ARG E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 202 removed outlier: 3.762A pdb=" N GLU E 201 " --> pdb=" O GLU E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 271 Proline residue: E 257 - end of helix removed outlier: 4.262A pdb=" N SER E 268 " --> pdb=" O MET E 264 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE E 269 " --> pdb=" O SER E 265 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP E 270 " --> pdb=" O TRP E 266 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 271 " --> pdb=" O VAL E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 301 removed outlier: 3.698A pdb=" N ARG E 298 " --> pdb=" O MET E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 336 removed outlier: 4.026A pdb=" N ASP E 336 " --> pdb=" O HIS E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 451 removed outlier: 3.541A pdb=" N ALA E 433 " --> pdb=" O ILE E 429 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE E 435 " --> pdb=" O ALA E 431 " (cutoff:3.500A) Proline residue: E 436 - end of helix Processing helix chain 'L' and resid 449 through 452 Processing helix chain 'L' and resid 495 through 499 Processing helix chain 'M' and resid 449 through 452 Processing helix chain 'M' and resid 495 through 499 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 119 removed outlier: 4.654A pdb=" N PHE A 152 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR A 159 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLU A 92 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR A 94 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N PHE A 83 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASP A 96 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 79 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE A 104 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU A 73 " --> pdb=" O ILE A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 142 removed outlier: 6.773A pdb=" N SER A 169 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER A 140 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR A 167 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N SER A 142 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ARG A 165 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLU A 92 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR A 94 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N PHE A 83 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASP A 96 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 79 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE A 104 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU A 73 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N GLU A 213 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE A 78 " --> pdb=" O GLU A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 134 removed outlier: 4.272A pdb=" N SER A 192 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE A 244 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY A 228 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A 253 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU A 226 " --> pdb=" O ARG A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 83 removed outlier: 4.282A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.691A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.609A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 81 through 83 removed outlier: 4.283A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.691A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.609A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 81 through 83 removed outlier: 4.282A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.691A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL D 106 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ARG D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.609A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 72 through 79 removed outlier: 5.942A pdb=" N VAL E 72 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE E 90 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE E 78 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU E 84 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ALA E 163 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA E 129 " --> pdb=" O ALA E 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 109 through 111 removed outlier: 4.444A pdb=" N ARG E 96 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN E 65 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL E 64 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N TYR E 195 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL E 66 " --> pdb=" O TYR E 195 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 124 through 126 removed outlier: 3.996A pdb=" N SER E 218 " --> pdb=" O HIS E 242 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG E 244 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE E 216 " --> pdb=" O ARG E 244 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 2 through 7 Processing sheet with id=AB8, first strand: chain 'L' and resid 445 through 447 removed outlier: 5.818A pdb=" N PHE L 434 " --> pdb=" O ARG L 425 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG L 425 " --> pdb=" O PHE L 434 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE L 420 " --> pdb=" O LYS L 486 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR L 501 " --> pdb=" O ALA L 485 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 445 through 447 removed outlier: 5.818A pdb=" N PHE L 434 " --> pdb=" O ARG L 425 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG L 425 " --> pdb=" O PHE L 434 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE L 420 " --> pdb=" O LYS L 486 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 2 through 7 Processing sheet with id=AC2, first strand: chain 'M' and resid 445 through 447 removed outlier: 5.818A pdb=" N PHE M 434 " --> pdb=" O ARG M 425 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG M 425 " --> pdb=" O PHE M 434 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR M 501 " --> pdb=" O ALA M 485 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 445 through 447 removed outlier: 5.818A pdb=" N PHE M 434 " --> pdb=" O ARG M 425 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG M 425 " --> pdb=" O PHE M 434 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) 906 hydrogen bonds defined for protein. 2537 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: 6.06 Time building geometry restraints manager: 5.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4782 1.34 - 1.46: 4108 1.46 - 1.58: 7050 1.58 - 1.69: 0 1.69 - 1.81: 159 Bond restraints: 16099 Sorted by residual: bond pdb=" C1 BMA a 3 " pdb=" C2 BMA a 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 MAN F 5 " pdb=" O5 MAN F 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C1 MAN F 4 " pdb=" O5 MAN F 4 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.06e+00 bond pdb=" C1 MAN H 5 " pdb=" O5 MAN H 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C1 MAN G 5 " pdb=" O5 MAN G 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.04e+00 ... (remaining 16094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 20799 1.28 - 2.55: 808 2.55 - 3.83: 193 3.83 - 5.11: 48 5.11 - 6.39: 24 Bond angle restraints: 21872 Sorted by residual: angle pdb=" C TYR B 304 " pdb=" N ILE B 305 " pdb=" CA ILE B 305 " ideal model delta sigma weight residual 121.85 116.69 5.16 1.19e+00 7.06e-01 1.88e+01 angle pdb=" C TYR C 304 " pdb=" N ILE C 305 " pdb=" CA ILE C 305 " ideal model delta sigma weight residual 121.85 116.71 5.14 1.19e+00 7.06e-01 1.87e+01 angle pdb=" C TYR D 304 " pdb=" N ILE D 305 " pdb=" CA ILE D 305 " ideal model delta sigma weight residual 121.85 116.71 5.14 1.19e+00 7.06e-01 1.86e+01 angle pdb=" C HIS B 267 " pdb=" N LEU B 268 " pdb=" CA LEU B 268 " ideal model delta sigma weight residual 120.38 125.22 -4.84 1.37e+00 5.33e-01 1.25e+01 angle pdb=" C HIS D 267 " pdb=" N LEU D 268 " pdb=" CA LEU D 268 " ideal model delta sigma weight residual 120.38 125.20 -4.82 1.37e+00 5.33e-01 1.24e+01 ... (remaining 21867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 9339 21.75 - 43.49: 325 43.49 - 65.24: 35 65.24 - 86.99: 35 86.99 - 108.73: 19 Dihedral angle restraints: 9753 sinusoidal: 4188 harmonic: 5565 Sorted by residual: dihedral pdb=" CA SER B 46 " pdb=" C SER B 46 " pdb=" N ILE B 47 " pdb=" CA ILE B 47 " ideal model delta harmonic sigma weight residual 180.00 154.79 25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA SER D 46 " pdb=" C SER D 46 " pdb=" N ILE D 47 " pdb=" CA ILE D 47 " ideal model delta harmonic sigma weight residual 180.00 154.84 25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA SER C 46 " pdb=" C SER C 46 " pdb=" N ILE C 47 " pdb=" CA ILE C 47 " ideal model delta harmonic sigma weight residual 180.00 154.88 25.12 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 9750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2091 0.058 - 0.116: 374 0.116 - 0.174: 33 0.174 - 0.231: 7 0.231 - 0.289: 5 Chirality restraints: 2510 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.63e+01 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.51e+01 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.52e+01 ... (remaining 2507 not shown) Planarity restraints: 2691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 157 " 0.007 2.00e-02 2.50e+03 1.53e-02 4.68e+00 pdb=" CG TYR C 157 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR C 157 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR C 157 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 157 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR C 157 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 157 " -0.020 2.00e-02 2.50e+03 pdb=" OH TYR C 157 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 157 " -0.007 2.00e-02 2.50e+03 1.53e-02 4.66e+00 pdb=" CG TYR B 157 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B 157 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR B 157 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 157 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR B 157 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 157 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR B 157 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 157 " 0.006 2.00e-02 2.50e+03 1.52e-02 4.61e+00 pdb=" CG TYR D 157 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR D 157 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR D 157 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR D 157 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR D 157 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 157 " -0.021 2.00e-02 2.50e+03 pdb=" OH TYR D 157 " 0.022 2.00e-02 2.50e+03 ... (remaining 2688 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 417 2.71 - 3.26: 15527 3.26 - 3.81: 26302 3.81 - 4.35: 33906 4.35 - 4.90: 56253 Nonbonded interactions: 132405 Sorted by model distance: nonbonded pdb=" O TRP M 440 " pdb=" NH1 ARG M 459 " model vdw 2.164 3.120 nonbonded pdb=" O TRP L 440 " pdb=" NH1 ARG L 459 " model vdw 2.165 3.120 nonbonded pdb=" OG1 THR E 215 " pdb=" OD1 ASN E 246 " model vdw 2.224 3.040 nonbonded pdb=" O VAL A 290 " pdb=" OG1 THR A 294 " model vdw 2.257 3.040 nonbonded pdb=" O SER A 305 " pdb=" ND1 HIS A 308 " model vdw 2.267 3.120 ... (remaining 132400 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 'B' and resid 8 through 447) selection = (chain 'C' and resid 8 through 447) selection = (chain 'D' and resid 8 through 447) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'b' selection = chain 'c' selection = chain 'd' } 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=0.50 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: 2.120 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: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 40.150 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 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: 0.020 Load rotamer database and sin/cos tables:14.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 : 0.003 0.034 16099 Z= 0.201 Angle : 0.636 6.387 21872 Z= 0.335 Chirality : 0.046 0.289 2510 Planarity : 0.005 0.058 2682 Dihedral : 13.258 108.734 6168 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.48 % Allowed : 3.60 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.19), residues: 1863 helix: 0.70 (0.20), residues: 573 sheet: 0.37 (0.24), residues: 453 loop : 0.33 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 440 HIS 0.004 0.001 HIS D 267 PHE 0.017 0.001 PHE D 306 TYR 0.022 0.004 TYR B 157 ARG 0.014 0.002 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 427 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 TRP cc_start: 0.7080 (m-10) cc_final: 0.6471 (m100) REVERT: B 13 LYS cc_start: 0.9000 (tttt) cc_final: 0.8686 (ttpp) REVERT: B 215 LYS cc_start: 0.9016 (tttt) cc_final: 0.8781 (ttmm) REVERT: B 298 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8568 (tm-30) REVERT: B 306 PHE cc_start: 0.7427 (t80) cc_final: 0.7067 (t80) REVERT: C 9 MET cc_start: 0.8505 (mtp) cc_final: 0.8185 (mtt) REVERT: C 90 GLN cc_start: 0.8970 (mp10) cc_final: 0.8271 (mp10) REVERT: C 230 ILE cc_start: 0.9663 (mt) cc_final: 0.9431 (mp) REVERT: D 13 LYS cc_start: 0.9103 (tttt) cc_final: 0.8671 (tmmt) REVERT: D 190 GLU cc_start: 0.8018 (tt0) cc_final: 0.7741 (tt0) REVERT: D 214 LEU cc_start: 0.8965 (mt) cc_final: 0.8748 (mt) REVERT: D 215 LYS cc_start: 0.8822 (tttt) cc_final: 0.8133 (ttmm) REVERT: D 223 LEU cc_start: 0.9025 (mt) cc_final: 0.8235 (tp) REVERT: D 230 ILE cc_start: 0.9604 (mt) cc_final: 0.9399 (mp) REVERT: D 306 PHE cc_start: 0.7580 (t80) cc_final: 0.7085 (t80) REVERT: D 433 PHE cc_start: 0.8640 (t80) cc_final: 0.8415 (t80) REVERT: E 203 ILE cc_start: 0.8721 (pp) cc_final: 0.8493 (pp) REVERT: E 250 TYR cc_start: 0.7105 (p90) cc_final: 0.6874 (p90) REVERT: E 334 ASN cc_start: 0.8913 (m-40) cc_final: 0.8631 (m110) REVERT: L 3 GLN cc_start: 0.8303 (mp10) cc_final: 0.6900 (mp10) REVERT: L 468 LEU cc_start: 0.8918 (tp) cc_final: 0.8582 (tt) REVERT: L 472 ASN cc_start: 0.8462 (t0) cc_final: 0.7939 (t0) REVERT: M 468 LEU cc_start: 0.8661 (tp) cc_final: 0.8450 (tp) REVERT: M 472 ASN cc_start: 0.8723 (t0) cc_final: 0.7843 (t0) REVERT: M 482 TYR cc_start: 0.8582 (m-80) cc_final: 0.8359 (m-80) outliers start: 8 outliers final: 3 residues processed: 431 average time/residue: 1.5038 time to fit residues: 706.1509 Evaluate side-chains 254 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 251 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain L residue 459 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 79 optimal weight: 0.0970 chunk 48 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 147 optimal weight: 0.0020 chunk 57 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 overall best weight: 2.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 149 ASN A 345 ASN B 243 ASN B 267 HIS D 90 GLN D 185 GLN D 267 HIS E 77 HIS ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN E 233 GLN E 240 HIS ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 504 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16099 Z= 0.298 Angle : 0.677 13.587 21872 Z= 0.356 Chirality : 0.046 0.165 2510 Planarity : 0.005 0.064 2682 Dihedral : 8.935 77.685 2673 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.18 % Allowed : 14.05 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.20), residues: 1863 helix: 1.71 (0.21), residues: 576 sheet: 0.38 (0.23), residues: 488 loop : 0.75 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 315 HIS 0.009 0.001 HIS E 77 PHE 0.026 0.002 PHE B 293 TYR 0.025 0.002 TYR B 299 ARG 0.008 0.001 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 274 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8423 (mtm) cc_final: 0.8065 (mmm) REVERT: A 260 MET cc_start: 0.8209 (tpp) cc_final: 0.8008 (tpp) REVERT: A 321 TRP cc_start: 0.7170 (m-10) cc_final: 0.6538 (m100) REVERT: B 13 LYS cc_start: 0.8947 (tttt) cc_final: 0.8627 (ttpp) REVERT: B 52 GLU cc_start: 0.8507 (mp0) cc_final: 0.8265 (mp0) REVERT: B 70 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8749 (mtpp) REVERT: B 215 LYS cc_start: 0.9054 (tttt) cc_final: 0.8828 (ttmm) REVERT: B 269 ARG cc_start: 0.8364 (ptm160) cc_final: 0.8085 (ptm160) REVERT: B 298 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8783 (tm-30) REVERT: B 306 PHE cc_start: 0.7831 (t80) cc_final: 0.7276 (t80) REVERT: C 9 MET cc_start: 0.8572 (mtp) cc_final: 0.8233 (mtt) REVERT: C 90 GLN cc_start: 0.8971 (mp10) cc_final: 0.8217 (mp10) REVERT: C 230 ILE cc_start: 0.9608 (mt) cc_final: 0.9396 (mp) REVERT: C 286 MET cc_start: 0.8489 (mmp) cc_final: 0.8217 (mmm) REVERT: C 302 VAL cc_start: 0.9349 (t) cc_final: 0.9140 (t) REVERT: C 440 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8939 (tp) REVERT: D 13 LYS cc_start: 0.9323 (tttt) cc_final: 0.8684 (tmmt) REVERT: D 21 LYS cc_start: 0.8323 (mmmm) cc_final: 0.7954 (mmmm) REVERT: D 147 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7277 (mm-30) REVERT: D 215 LYS cc_start: 0.8888 (tttt) cc_final: 0.8481 (ttmm) REVERT: D 243 ASN cc_start: 0.8114 (t0) cc_final: 0.7733 (t0) REVERT: D 306 PHE cc_start: 0.7565 (t80) cc_final: 0.7083 (t80) REVERT: D 433 PHE cc_start: 0.8723 (t80) cc_final: 0.8504 (t80) REVERT: E 118 LYS cc_start: 0.8936 (mmtm) cc_final: 0.8235 (mppt) REVERT: E 435 PHE cc_start: 0.8719 (m-80) cc_final: 0.8459 (m-80) REVERT: L 3 GLN cc_start: 0.8166 (mp10) cc_final: 0.7497 (mp10) REVERT: L 472 ASN cc_start: 0.8731 (t0) cc_final: 0.8262 (t0) REVERT: M 11 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7199 (tm) REVERT: M 452 LYS cc_start: 0.8814 (ttmm) cc_final: 0.8577 (ttmm) REVERT: M 472 ASN cc_start: 0.8856 (t0) cc_final: 0.8287 (t0) REVERT: M 473 LEU cc_start: 0.9400 (mt) cc_final: 0.9123 (mm) REVERT: M 474 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8404 (mmmt) outliers start: 53 outliers final: 12 residues processed: 301 average time/residue: 1.5852 time to fit residues: 519.5714 Evaluate side-chains 248 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 233 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 11 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 0.0670 chunk 142 optimal weight: 0.9980 chunk 116 optimal weight: 0.0050 chunk 47 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 152 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 overall best weight: 0.7934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN B 243 ASN B 267 HIS C 267 HIS ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN E 227 ASN E 253 GLN L 1 GLN L 3 GLN L 472 ASN L 504 GLN M 3 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16099 Z= 0.182 Angle : 0.606 10.397 21872 Z= 0.313 Chirality : 0.044 0.207 2510 Planarity : 0.004 0.035 2682 Dihedral : 7.278 70.027 2666 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.28 % Allowed : 15.07 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.20), residues: 1863 helix: 1.78 (0.21), residues: 569 sheet: 0.49 (0.23), residues: 498 loop : 0.78 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 315 HIS 0.005 0.001 HIS A 308 PHE 0.017 0.002 PHE B 306 TYR 0.024 0.001 TYR B 299 ARG 0.007 0.000 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 261 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8398 (mtm) cc_final: 0.8086 (mmm) REVERT: A 321 TRP cc_start: 0.7153 (m-10) cc_final: 0.6489 (m100) REVERT: B 13 LYS cc_start: 0.9024 (tttt) cc_final: 0.8671 (ttpp) REVERT: B 89 ASP cc_start: 0.8431 (m-30) cc_final: 0.8042 (m-30) REVERT: B 215 LYS cc_start: 0.9024 (tttt) cc_final: 0.8785 (ttmm) REVERT: B 269 ARG cc_start: 0.8491 (ptm160) cc_final: 0.7703 (ttm-80) REVERT: B 274 LYS cc_start: 0.8818 (ttmm) cc_final: 0.8561 (tmtp) REVERT: B 306 PHE cc_start: 0.7775 (t80) cc_final: 0.7487 (t80) REVERT: C 9 MET cc_start: 0.8533 (mtp) cc_final: 0.8313 (ttm) REVERT: C 90 GLN cc_start: 0.8946 (mp10) cc_final: 0.8178 (mp10) REVERT: C 230 ILE cc_start: 0.9636 (mt) cc_final: 0.9353 (mp) REVERT: D 13 LYS cc_start: 0.9332 (tttt) cc_final: 0.8595 (tmmt) REVERT: D 21 LYS cc_start: 0.8421 (mmmm) cc_final: 0.7979 (mmmm) REVERT: D 147 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7392 (mm-30) REVERT: D 215 LYS cc_start: 0.8904 (tttt) cc_final: 0.8424 (tttp) REVERT: D 227 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8288 (tpt) REVERT: D 243 ASN cc_start: 0.8171 (t0) cc_final: 0.7664 (t0) REVERT: D 433 PHE cc_start: 0.8715 (t80) cc_final: 0.8482 (t80) REVERT: E 118 LYS cc_start: 0.9045 (mmtm) cc_final: 0.8674 (mmtp) REVERT: E 142 LYS cc_start: 0.8981 (mtmt) cc_final: 0.8734 (mtmm) REVERT: E 224 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6118 (tm-30) REVERT: E 233 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7419 (tp-100) REVERT: L 3 GLN cc_start: 0.8321 (mp-120) cc_final: 0.7593 (mp10) REVERT: L 472 ASN cc_start: 0.8773 (t0) cc_final: 0.8412 (t0) REVERT: M 11 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7015 (tm) REVERT: M 469 GLU cc_start: 0.7519 (mp0) cc_final: 0.7055 (mp0) REVERT: M 472 ASN cc_start: 0.8958 (t0) cc_final: 0.8435 (t0) REVERT: M 473 LEU cc_start: 0.9404 (mt) cc_final: 0.8888 (mm) REVERT: M 474 LYS cc_start: 0.8720 (mmmt) cc_final: 0.8497 (mmmt) REVERT: M 504 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8452 (pm20) outliers start: 38 outliers final: 10 residues processed: 281 average time/residue: 1.5075 time to fit residues: 464.3864 Evaluate side-chains 246 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 231 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 504 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 181 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 162 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN C 267 HIS ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 GLN ** L 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16099 Z= 0.218 Angle : 0.616 13.200 21872 Z= 0.315 Chirality : 0.044 0.219 2510 Planarity : 0.004 0.060 2682 Dihedral : 6.650 65.679 2666 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.40 % Allowed : 15.37 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.20), residues: 1863 helix: 1.78 (0.21), residues: 569 sheet: 0.59 (0.23), residues: 503 loop : 0.75 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 440 HIS 0.007 0.001 HIS C 267 PHE 0.019 0.001 PHE C 293 TYR 0.025 0.001 TYR B 299 ARG 0.008 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 244 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8415 (mtm) cc_final: 0.8147 (mmm) REVERT: A 321 TRP cc_start: 0.7148 (m-10) cc_final: 0.6472 (m100) REVERT: A 345 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8084 (m-40) REVERT: B 13 LYS cc_start: 0.9076 (tttt) cc_final: 0.8744 (ttpp) REVERT: B 18 LYS cc_start: 0.9150 (pttp) cc_final: 0.8901 (pptt) REVERT: B 215 LYS cc_start: 0.9032 (tttt) cc_final: 0.8786 (ttmm) REVERT: B 269 ARG cc_start: 0.8473 (ptm160) cc_final: 0.8226 (ttm-80) REVERT: B 278 VAL cc_start: 0.8327 (t) cc_final: 0.8091 (p) REVERT: C 9 MET cc_start: 0.8532 (mtp) cc_final: 0.8311 (ttm) REVERT: C 90 GLN cc_start: 0.8948 (mp10) cc_final: 0.8164 (mp10) REVERT: C 230 ILE cc_start: 0.9583 (mt) cc_final: 0.9178 (mp) REVERT: C 424 ASP cc_start: 0.8998 (m-30) cc_final: 0.8701 (m-30) REVERT: D 13 LYS cc_start: 0.9278 (tttt) cc_final: 0.8644 (tmmt) REVERT: D 21 LYS cc_start: 0.8501 (mmmm) cc_final: 0.8255 (mmmm) REVERT: D 147 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7333 (mm-30) REVERT: D 215 LYS cc_start: 0.8887 (tttt) cc_final: 0.8506 (ttmm) REVERT: D 227 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8295 (tpt) REVERT: D 243 ASN cc_start: 0.8152 (t0) cc_final: 0.7612 (t0) REVERT: D 433 PHE cc_start: 0.8731 (t80) cc_final: 0.8481 (t80) REVERT: E 118 LYS cc_start: 0.9011 (mmtm) cc_final: 0.8330 (mppt) REVERT: E 142 LYS cc_start: 0.8979 (mtmt) cc_final: 0.8733 (mtmm) REVERT: E 213 GLN cc_start: 0.8315 (tt0) cc_final: 0.8062 (tt0) REVERT: E 224 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6322 (tm-30) REVERT: E 250 TYR cc_start: 0.7084 (p90) cc_final: 0.6118 (p90) REVERT: L 3 GLN cc_start: 0.8348 (mp-120) cc_final: 0.7916 (mp10) REVERT: L 472 ASN cc_start: 0.8760 (t0) cc_final: 0.7570 (t0) REVERT: L 474 LYS cc_start: 0.8804 (mptm) cc_final: 0.8410 (mptt) REVERT: M 11 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7084 (tm) REVERT: M 460 ASP cc_start: 0.7650 (p0) cc_final: 0.6534 (p0) REVERT: M 469 GLU cc_start: 0.7655 (mp0) cc_final: 0.7164 (mp0) REVERT: M 472 ASN cc_start: 0.8986 (t0) cc_final: 0.8496 (t0) REVERT: M 504 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8438 (pm20) outliers start: 40 outliers final: 11 residues processed: 271 average time/residue: 1.4585 time to fit residues: 432.7268 Evaluate side-chains 252 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 504 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16099 Z= 0.282 Angle : 0.621 9.694 21872 Z= 0.320 Chirality : 0.044 0.219 2510 Planarity : 0.003 0.027 2682 Dihedral : 6.362 62.535 2666 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.34 % Allowed : 16.21 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.20), residues: 1863 helix: 1.73 (0.21), residues: 570 sheet: 0.65 (0.23), residues: 503 loop : 0.66 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 440 HIS 0.004 0.001 HIS A 308 PHE 0.018 0.002 PHE D 306 TYR 0.027 0.002 TYR B 299 ARG 0.005 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8433 (mtm) cc_final: 0.8097 (mmm) REVERT: A 262 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8744 (mt0) REVERT: A 321 TRP cc_start: 0.7174 (m-10) cc_final: 0.6508 (m100) REVERT: B 13 LYS cc_start: 0.9118 (tttt) cc_final: 0.8742 (ttpp) REVERT: B 18 LYS cc_start: 0.9161 (pttp) cc_final: 0.8905 (pptt) REVERT: B 215 LYS cc_start: 0.9062 (tttt) cc_final: 0.8782 (ttmm) REVERT: B 269 ARG cc_start: 0.8489 (ptm160) cc_final: 0.8085 (ttm-80) REVERT: B 297 LEU cc_start: 0.9364 (tp) cc_final: 0.9141 (mm) REVERT: C 9 MET cc_start: 0.8534 (mtp) cc_final: 0.8314 (ttm) REVERT: C 90 GLN cc_start: 0.8944 (mp10) cc_final: 0.8113 (mp10) REVERT: C 102 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8499 (mtmt) REVERT: C 424 ASP cc_start: 0.9005 (m-30) cc_final: 0.8693 (m-30) REVERT: D 9 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.8007 (tpt) REVERT: D 13 LYS cc_start: 0.9268 (tttt) cc_final: 0.8642 (tmmt) REVERT: D 21 LYS cc_start: 0.8556 (mmmm) cc_final: 0.8319 (mmmm) REVERT: D 147 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7219 (mm-30) REVERT: D 215 LYS cc_start: 0.8941 (tttt) cc_final: 0.8450 (ttmm) REVERT: D 243 ASN cc_start: 0.8179 (t0) cc_final: 0.7592 (t0) REVERT: D 433 PHE cc_start: 0.8744 (t80) cc_final: 0.8527 (t80) REVERT: E 118 LYS cc_start: 0.9092 (mmtm) cc_final: 0.8477 (mppt) REVERT: E 142 LYS cc_start: 0.8973 (mtmt) cc_final: 0.8735 (mtmm) REVERT: E 213 GLN cc_start: 0.8436 (tt0) cc_final: 0.8180 (tt0) REVERT: E 224 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6135 (tm-30) REVERT: E 226 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6558 (ppp) REVERT: L 3 GLN cc_start: 0.8440 (mp-120) cc_final: 0.7970 (mp10) REVERT: L 472 ASN cc_start: 0.8811 (t0) cc_final: 0.8491 (t0) REVERT: M 11 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7132 (tm) REVERT: M 460 ASP cc_start: 0.7478 (p0) cc_final: 0.7175 (p0) REVERT: M 467 TYR cc_start: 0.8293 (m-80) cc_final: 0.8016 (m-80) REVERT: M 469 GLU cc_start: 0.7812 (mp0) cc_final: 0.7284 (mp0) REVERT: M 472 ASN cc_start: 0.9050 (t0) cc_final: 0.8613 (t0) outliers start: 39 outliers final: 14 residues processed: 269 average time/residue: 1.6039 time to fit residues: 471.1366 Evaluate side-chains 251 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 232 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 460 ASP Chi-restraints excluded: chain M residue 11 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 106 optimal weight: 0.4980 chunk 44 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 150 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 345 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN E 253 GLN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 472 ASN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16099 Z= 0.197 Angle : 0.615 12.613 21872 Z= 0.314 Chirality : 0.044 0.226 2510 Planarity : 0.003 0.037 2682 Dihedral : 6.022 57.593 2666 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.28 % Allowed : 16.45 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.20), residues: 1863 helix: 1.79 (0.21), residues: 570 sheet: 0.70 (0.23), residues: 503 loop : 0.67 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 440 HIS 0.004 0.001 HIS A 308 PHE 0.021 0.001 PHE M 455 TYR 0.026 0.001 TYR B 299 ARG 0.012 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 259 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8289 (mtm) cc_final: 0.8050 (mmm) REVERT: A 181 MET cc_start: 0.8432 (mtm) cc_final: 0.8153 (pmm) REVERT: A 262 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8815 (mt0) REVERT: A 267 CYS cc_start: 0.8866 (m) cc_final: 0.8536 (m) REVERT: A 321 TRP cc_start: 0.7150 (m-10) cc_final: 0.6494 (m100) REVERT: B 13 LYS cc_start: 0.9051 (tttt) cc_final: 0.8709 (ttpp) REVERT: B 70 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8857 (mmtm) REVERT: B 215 LYS cc_start: 0.9033 (tttt) cc_final: 0.8751 (ttmm) REVERT: B 306 PHE cc_start: 0.7500 (t80) cc_final: 0.7285 (t80) REVERT: C 9 MET cc_start: 0.8543 (mtp) cc_final: 0.8307 (ttm) REVERT: C 90 GLN cc_start: 0.8927 (mp10) cc_final: 0.8107 (mp10) REVERT: C 102 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8398 (mtmt) REVERT: C 424 ASP cc_start: 0.8925 (m-30) cc_final: 0.8620 (m-30) REVERT: D 13 LYS cc_start: 0.9260 (tttt) cc_final: 0.8630 (tmmt) REVERT: D 21 LYS cc_start: 0.8586 (mmmm) cc_final: 0.8328 (mmmm) REVERT: D 147 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7382 (mm-30) REVERT: D 215 LYS cc_start: 0.8916 (tttt) cc_final: 0.8438 (ttmm) REVERT: D 243 ASN cc_start: 0.8175 (t0) cc_final: 0.7694 (t0) REVERT: D 433 PHE cc_start: 0.8737 (t80) cc_final: 0.8489 (t80) REVERT: E 118 LYS cc_start: 0.9139 (mmtm) cc_final: 0.8504 (mppt) REVERT: E 142 LYS cc_start: 0.8941 (mtmt) cc_final: 0.8713 (mtmm) REVERT: E 213 GLN cc_start: 0.8374 (tt0) cc_final: 0.8113 (tt0) REVERT: E 224 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6558 (tm-30) REVERT: E 313 TYR cc_start: 0.9317 (t80) cc_final: 0.9006 (t80) REVERT: L 3 GLN cc_start: 0.8511 (mp-120) cc_final: 0.8004 (mp10) REVERT: L 430 LYS cc_start: 0.8743 (mppt) cc_final: 0.8458 (mptt) REVERT: L 472 ASN cc_start: 0.8817 (t0) cc_final: 0.8483 (t0) REVERT: M 11 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7202 (tm) REVERT: M 467 TYR cc_start: 0.8296 (m-80) cc_final: 0.8074 (m-80) REVERT: M 469 GLU cc_start: 0.7836 (mp0) cc_final: 0.7366 (mp0) outliers start: 38 outliers final: 15 residues processed: 281 average time/residue: 1.4446 time to fit residues: 444.7697 Evaluate side-chains 248 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 229 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain M residue 11 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 181 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN D 224 GLN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN E 253 GLN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16099 Z= 0.194 Angle : 0.626 9.001 21872 Z= 0.320 Chirality : 0.044 0.231 2510 Planarity : 0.003 0.062 2682 Dihedral : 5.832 54.813 2666 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.34 % Allowed : 17.53 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.20), residues: 1863 helix: 1.75 (0.21), residues: 570 sheet: 0.72 (0.23), residues: 500 loop : 0.65 (0.24), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 440 HIS 0.005 0.001 HIS A 184 PHE 0.022 0.002 PHE D 306 TYR 0.037 0.002 TYR D 220 ARG 0.012 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 241 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8297 (mtm) cc_final: 0.8002 (mmm) REVERT: A 181 MET cc_start: 0.8480 (mtm) cc_final: 0.8206 (pmm) REVERT: A 267 CYS cc_start: 0.8836 (m) cc_final: 0.8508 (m) REVERT: A 282 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8581 (ptpp) REVERT: A 321 TRP cc_start: 0.7160 (m-10) cc_final: 0.6524 (m100) REVERT: B 49 MET cc_start: 0.7980 (ttp) cc_final: 0.7454 (tmm) REVERT: B 70 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8910 (mmtm) REVERT: C 9 MET cc_start: 0.8537 (mtp) cc_final: 0.8298 (ttm) REVERT: C 90 GLN cc_start: 0.8924 (mp10) cc_final: 0.8103 (mp10) REVERT: C 424 ASP cc_start: 0.8878 (m-30) cc_final: 0.8569 (m-30) REVERT: D 13 LYS cc_start: 0.9263 (tttt) cc_final: 0.8616 (tmmt) REVERT: D 21 LYS cc_start: 0.8598 (mmmm) cc_final: 0.8347 (mmmm) REVERT: D 147 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7408 (mm-30) REVERT: D 215 LYS cc_start: 0.8916 (tttt) cc_final: 0.8449 (tttp) REVERT: D 243 ASN cc_start: 0.8181 (t0) cc_final: 0.7646 (t0) REVERT: D 433 PHE cc_start: 0.8734 (t80) cc_final: 0.8486 (t80) REVERT: E 82 ASN cc_start: 0.8966 (m-40) cc_final: 0.8762 (m-40) REVERT: E 118 LYS cc_start: 0.9134 (mmtm) cc_final: 0.8504 (mppt) REVERT: E 142 LYS cc_start: 0.8921 (mtmt) cc_final: 0.8689 (mtmm) REVERT: E 213 GLN cc_start: 0.8371 (tt0) cc_final: 0.8146 (tt0) REVERT: E 224 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6437 (tm-30) REVERT: E 253 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7793 (pp30) REVERT: E 313 TYR cc_start: 0.9310 (t80) cc_final: 0.9020 (t80) REVERT: L 3 GLN cc_start: 0.8499 (mp-120) cc_final: 0.7995 (mp10) REVERT: L 430 LYS cc_start: 0.8734 (mppt) cc_final: 0.8509 (mptt) REVERT: L 472 ASN cc_start: 0.8853 (t0) cc_final: 0.8541 (t0) REVERT: M 11 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7352 (tm) REVERT: M 454 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7544 (ttp80) REVERT: M 459 ARG cc_start: 0.8041 (pmt170) cc_final: 0.7682 (pmt-80) REVERT: M 469 GLU cc_start: 0.8091 (mp0) cc_final: 0.7416 (mp0) REVERT: M 472 ASN cc_start: 0.9218 (t0) cc_final: 0.8856 (t0) outliers start: 39 outliers final: 12 residues processed: 267 average time/residue: 1.4411 time to fit residues: 421.0115 Evaluate side-chains 249 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 231 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 454 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 0.0070 chunk 115 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 142 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN E 253 GLN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16099 Z= 0.217 Angle : 0.646 12.486 21872 Z= 0.327 Chirality : 0.044 0.231 2510 Planarity : 0.003 0.053 2682 Dihedral : 5.707 52.707 2666 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.98 % Allowed : 18.01 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.20), residues: 1863 helix: 1.77 (0.21), residues: 570 sheet: 0.69 (0.24), residues: 497 loop : 0.62 (0.24), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 440 HIS 0.002 0.001 HIS A 308 PHE 0.027 0.002 PHE C 293 TYR 0.033 0.002 TYR D 220 ARG 0.012 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 251 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ILE cc_start: 0.9265 (mt) cc_final: 0.9025 (mp) REVERT: A 175 ARG cc_start: 0.7816 (mmm160) cc_final: 0.7551 (tpt170) REVERT: A 181 MET cc_start: 0.8516 (mtm) cc_final: 0.8248 (pmm) REVERT: A 267 CYS cc_start: 0.8824 (m) cc_final: 0.8496 (m) REVERT: A 307 ARG cc_start: 0.8686 (ttm110) cc_final: 0.7800 (mtt90) REVERT: A 321 TRP cc_start: 0.7171 (m-10) cc_final: 0.6460 (m100) REVERT: B 49 MET cc_start: 0.7983 (ttp) cc_final: 0.7331 (pp-130) REVERT: B 190 GLU cc_start: 0.8044 (tt0) cc_final: 0.7587 (pt0) REVERT: B 269 ARG cc_start: 0.8311 (ttm-80) cc_final: 0.8083 (ttt90) REVERT: C 9 MET cc_start: 0.8529 (mtp) cc_final: 0.8307 (ttm) REVERT: C 84 ASP cc_start: 0.8084 (t70) cc_final: 0.7739 (t70) REVERT: C 90 GLN cc_start: 0.8910 (mp10) cc_final: 0.8055 (mp10) REVERT: C 297 LEU cc_start: 0.9351 (mp) cc_final: 0.9071 (mp) REVERT: C 424 ASP cc_start: 0.8820 (m-30) cc_final: 0.8531 (m-30) REVERT: D 13 LYS cc_start: 0.9263 (tttt) cc_final: 0.8617 (tmmt) REVERT: D 21 LYS cc_start: 0.8617 (mmmm) cc_final: 0.8360 (mmmm) REVERT: D 147 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7323 (mm-30) REVERT: D 215 LYS cc_start: 0.8914 (tttt) cc_final: 0.8586 (tttp) REVERT: D 243 ASN cc_start: 0.8228 (t0) cc_final: 0.7758 (t0) REVERT: D 433 PHE cc_start: 0.8738 (t80) cc_final: 0.8489 (t80) REVERT: E 82 ASN cc_start: 0.8974 (m-40) cc_final: 0.8755 (m-40) REVERT: E 118 LYS cc_start: 0.9151 (mmtm) cc_final: 0.8951 (mppt) REVERT: E 142 LYS cc_start: 0.8917 (mtmt) cc_final: 0.8684 (mtmm) REVERT: E 213 GLN cc_start: 0.8419 (tt0) cc_final: 0.8146 (tt0) REVERT: E 224 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6456 (tm-30) REVERT: E 253 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7852 (pp30) REVERT: E 313 TYR cc_start: 0.9302 (t80) cc_final: 0.8965 (t80) REVERT: L 3 GLN cc_start: 0.8508 (mp-120) cc_final: 0.8014 (mp10) REVERT: L 472 ASN cc_start: 0.8928 (t0) cc_final: 0.8649 (t0) REVERT: M 11 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7419 (tm) REVERT: M 454 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7423 (ttp80) REVERT: M 463 LYS cc_start: 0.9270 (ptpp) cc_final: 0.8992 (pmtt) REVERT: M 469 GLU cc_start: 0.8120 (mp0) cc_final: 0.7443 (mp0) REVERT: M 472 ASN cc_start: 0.9205 (t0) cc_final: 0.8779 (t0) outliers start: 33 outliers final: 13 residues processed: 270 average time/residue: 1.4689 time to fit residues: 435.7405 Evaluate side-chains 249 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 232 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 474 LYS Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 454 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 168 optimal weight: 0.4980 chunk 101 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 132 optimal weight: 0.2980 chunk 51 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN D 224 GLN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 GLN L 3 GLN M 3 GLN M 461 ASN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16099 Z= 0.191 Angle : 0.659 11.255 21872 Z= 0.334 Chirality : 0.044 0.232 2510 Planarity : 0.003 0.053 2682 Dihedral : 5.522 49.743 2666 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.56 % Allowed : 18.85 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.20), residues: 1863 helix: 1.75 (0.21), residues: 570 sheet: 0.72 (0.24), residues: 495 loop : 0.62 (0.24), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 440 HIS 0.002 0.000 HIS E 240 PHE 0.024 0.001 PHE C 293 TYR 0.028 0.002 TYR D 220 ARG 0.011 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 255 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ILE cc_start: 0.9250 (mt) cc_final: 0.9011 (mp) REVERT: A 181 MET cc_start: 0.8533 (mtm) cc_final: 0.8295 (pmm) REVERT: A 267 CYS cc_start: 0.8782 (m) cc_final: 0.8475 (m) REVERT: A 282 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8572 (ptpp) REVERT: A 307 ARG cc_start: 0.8713 (ttm110) cc_final: 0.7836 (mtt90) REVERT: A 321 TRP cc_start: 0.7176 (m-10) cc_final: 0.6481 (m100) REVERT: B 49 MET cc_start: 0.7979 (ttp) cc_final: 0.7412 (pp-130) REVERT: B 147 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7975 (tm-30) REVERT: B 190 GLU cc_start: 0.7983 (tt0) cc_final: 0.7570 (pt0) REVERT: B 306 PHE cc_start: 0.7324 (t80) cc_final: 0.7118 (t80) REVERT: C 9 MET cc_start: 0.8520 (mtp) cc_final: 0.8285 (ttm) REVERT: C 84 ASP cc_start: 0.8071 (t70) cc_final: 0.7720 (t70) REVERT: C 90 GLN cc_start: 0.8909 (mp10) cc_final: 0.8053 (mp10) REVERT: C 190 GLU cc_start: 0.8439 (tt0) cc_final: 0.8167 (tt0) REVERT: C 297 LEU cc_start: 0.9360 (mp) cc_final: 0.9084 (mp) REVERT: C 424 ASP cc_start: 0.8749 (m-30) cc_final: 0.8456 (m-30) REVERT: D 13 LYS cc_start: 0.9262 (tttt) cc_final: 0.8614 (tmmt) REVERT: D 147 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7307 (mm-30) REVERT: D 215 LYS cc_start: 0.8873 (tttt) cc_final: 0.8571 (tttp) REVERT: D 243 ASN cc_start: 0.8214 (t0) cc_final: 0.7731 (t0) REVERT: D 433 PHE cc_start: 0.8730 (t80) cc_final: 0.8483 (t80) REVERT: E 82 ASN cc_start: 0.8904 (m-40) cc_final: 0.8683 (m-40) REVERT: E 142 LYS cc_start: 0.8896 (mtmt) cc_final: 0.8684 (mtmm) REVERT: E 213 GLN cc_start: 0.8387 (tt0) cc_final: 0.8124 (tt0) REVERT: E 253 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7915 (pp30) REVERT: E 313 TYR cc_start: 0.9300 (t80) cc_final: 0.8917 (t80) REVERT: E 334 ASN cc_start: 0.8879 (m-40) cc_final: 0.8579 (m110) REVERT: L 3 GLN cc_start: 0.8491 (mp10) cc_final: 0.8109 (mp10) REVERT: L 472 ASN cc_start: 0.9001 (t0) cc_final: 0.8736 (t0) REVERT: M 11 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7498 (tm) REVERT: M 454 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7375 (ttp80) REVERT: M 469 GLU cc_start: 0.8177 (mp0) cc_final: 0.7481 (mp0) REVERT: M 472 ASN cc_start: 0.9226 (t0) cc_final: 0.8830 (t0) outliers start: 26 outliers final: 12 residues processed: 273 average time/residue: 1.4271 time to fit residues: 427.1682 Evaluate side-chains 257 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 241 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 474 LYS Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 454 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN B 224 GLN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 GLN L 3 GLN M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 16099 Z= 0.260 Angle : 0.695 11.889 21872 Z= 0.352 Chirality : 0.045 0.298 2510 Planarity : 0.003 0.050 2682 Dihedral : 5.541 48.967 2666 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.44 % Allowed : 18.97 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.20), residues: 1863 helix: 1.73 (0.21), residues: 570 sheet: 0.69 (0.24), residues: 501 loop : 0.57 (0.24), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 440 HIS 0.003 0.001 HIS D 267 PHE 0.023 0.002 PHE C 293 TYR 0.026 0.002 TYR D 299 ARG 0.011 0.000 ARG A 307 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 252 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8031 (pt0) cc_final: 0.7633 (pt0) REVERT: A 160 ILE cc_start: 0.9261 (mt) cc_final: 0.9021 (mp) REVERT: A 181 MET cc_start: 0.8508 (mtm) cc_final: 0.8277 (pmm) REVERT: A 267 CYS cc_start: 0.8802 (m) cc_final: 0.8486 (m) REVERT: A 282 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8584 (ptpp) REVERT: A 321 TRP cc_start: 0.7173 (m-10) cc_final: 0.6488 (m100) REVERT: B 49 MET cc_start: 0.7997 (ttp) cc_final: 0.7444 (pp-130) REVERT: B 147 GLU cc_start: 0.8253 (tm-30) cc_final: 0.8000 (tm-30) REVERT: B 190 GLU cc_start: 0.8014 (tt0) cc_final: 0.7522 (pt0) REVERT: C 9 MET cc_start: 0.8513 (mtp) cc_final: 0.8259 (ttm) REVERT: C 84 ASP cc_start: 0.8089 (t70) cc_final: 0.7734 (t70) REVERT: C 90 GLN cc_start: 0.8896 (mp10) cc_final: 0.8030 (mp10) REVERT: C 297 LEU cc_start: 0.9371 (mp) cc_final: 0.9122 (mp) REVERT: C 424 ASP cc_start: 0.8739 (m-30) cc_final: 0.8440 (m-30) REVERT: D 13 LYS cc_start: 0.9260 (tttt) cc_final: 0.8618 (tmmt) REVERT: D 21 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8333 (mtmm) REVERT: D 147 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7295 (mm-30) REVERT: D 190 GLU cc_start: 0.8140 (tt0) cc_final: 0.7822 (tt0) REVERT: D 215 LYS cc_start: 0.8910 (tttt) cc_final: 0.8591 (tttp) REVERT: D 243 ASN cc_start: 0.8238 (t0) cc_final: 0.7786 (t0) REVERT: D 433 PHE cc_start: 0.8728 (t80) cc_final: 0.8492 (t80) REVERT: E 82 ASN cc_start: 0.8830 (m-40) cc_final: 0.8580 (m-40) REVERT: E 142 LYS cc_start: 0.8910 (mtmt) cc_final: 0.8688 (mtmm) REVERT: E 213 GLN cc_start: 0.8428 (tt0) cc_final: 0.8187 (tt0) REVERT: E 313 TYR cc_start: 0.9307 (t80) cc_final: 0.8964 (t80) REVERT: E 334 ASN cc_start: 0.8913 (m-40) cc_final: 0.8600 (m110) REVERT: E 443 ASN cc_start: 0.9002 (m-40) cc_final: 0.8647 (m-40) REVERT: L 3 GLN cc_start: 0.8571 (mp-120) cc_final: 0.8063 (mp10) REVERT: L 472 ASN cc_start: 0.9037 (t0) cc_final: 0.8795 (t0) REVERT: M 11 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7558 (tm) REVERT: M 463 LYS cc_start: 0.9386 (pmtt) cc_final: 0.9169 (pmtt) REVERT: M 469 GLU cc_start: 0.8206 (mp0) cc_final: 0.7490 (mp0) REVERT: M 472 ASN cc_start: 0.9218 (t0) cc_final: 0.8891 (t0) outliers start: 24 outliers final: 16 residues processed: 264 average time/residue: 1.4601 time to fit residues: 422.2934 Evaluate side-chains 259 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 241 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 474 LYS Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 455 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 8.9990 chunk 137 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 GLN M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.083983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.061822 restraints weight = 52368.375| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.72 r_work: 0.2801 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16099 Z= 0.223 Angle : 0.692 11.728 21872 Z= 0.350 Chirality : 0.045 0.331 2510 Planarity : 0.004 0.059 2682 Dihedral : 5.412 46.202 2666 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.50 % Allowed : 19.27 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.20), residues: 1863 helix: 1.71 (0.21), residues: 570 sheet: 0.72 (0.24), residues: 494 loop : 0.53 (0.24), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 315 HIS 0.002 0.001 HIS D 267 PHE 0.023 0.002 PHE C 293 TYR 0.036 0.002 TYR E 250 ARG 0.015 0.000 ARG A 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7070.64 seconds wall clock time: 127 minutes 30.76 seconds (7650.76 seconds total)