Starting phenix.real_space_refine on Sat Aug 23 12:53:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c8r_45308/08_2025/9c8r_45308_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c8r_45308/08_2025/9c8r_45308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c8r_45308/08_2025/9c8r_45308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c8r_45308/08_2025/9c8r_45308.map" model { file = "/net/cci-nas-00/data/ceres_data/9c8r_45308/08_2025/9c8r_45308_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c8r_45308/08_2025/9c8r_45308_neut.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.039 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 69 5.16 5 C 7822 2.51 5 N 2074 2.21 5 O 2255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12220 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4067 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 513, 4052 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 478} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 513, 4052 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 478} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 4157 Chain: "B" Number of atoms: 4068 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 512, 4049 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 477} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 512, 4049 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 477} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 4148 Chain: "C" Number of atoms: 4085 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 519, 4071 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 484} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 519, 4071 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 484} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 4178 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALA A 191 " occ=0.82 ... (3 atoms not shown) pdb=" CB ALA A 191 " occ=0.82 residue: pdb=" N ALYS A 540 " occ=0.30 ... (16 atoms not shown) pdb=" NZ BLYS A 540 " occ=0.70 Time building chain proxies: 4.50, per 1000 atoms: 0.37 Number of scatterers: 12220 At special positions: 0 Unit cell: (126.38, 124.25, 74.55, 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 69 16.00 O 2255 8.00 N 2074 7.00 C 7822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 908.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2856 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 18 sheets defined 37.0% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 47 through 56 removed outlier: 3.515A pdb=" N TYR A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 103 through 109 Processing helix chain 'A' and resid 109 through 116 Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 137 through 154 Processing helix chain 'A' and resid 169 through 182 removed outlier: 4.178A pdb=" N ALA A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 174 " --> pdb=" O TRP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 224 through 234 Processing helix chain 'A' and resid 262 through 268 removed outlier: 3.817A pdb=" N LYS A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.628A pdb=" N PHE A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 341 Processing helix chain 'A' and resid 342 through 349 Processing helix chain 'A' and resid 365 through 375 Processing helix chain 'A' and resid 382 through 393 Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 440 through 444 Processing helix chain 'A' and resid 507 through 516 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'B' and resid 47 through 59 removed outlier: 3.600A pdb=" N TYR B 51 " --> pdb=" O ASN B 47 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 59 " --> pdb=" O TRP B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 75 removed outlier: 4.393A pdb=" N TRP B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 109 Processing helix chain 'B' and resid 109 through 114 Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 137 through 154 Processing helix chain 'B' and resid 169 through 182 removed outlier: 4.177A pdb=" N ALA B 173 " --> pdb=" O THR B 169 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B 174 " --> pdb=" O TRP B 170 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N CYS B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 224 through 234 Processing helix chain 'B' and resid 262 through 268 removed outlier: 3.826A pdb=" N LYS B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 318 removed outlier: 3.586A pdb=" N PHE B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 341 removed outlier: 3.525A pdb=" N ILE B 341 " --> pdb=" O GLY B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 348 Processing helix chain 'B' and resid 365 through 375 Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 416 through 426 Processing helix chain 'B' and resid 440 through 444 Processing helix chain 'B' and resid 507 through 516 Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 63 through 75 Processing helix chain 'C' and resid 103 through 109 Processing helix chain 'C' and resid 109 through 116 Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.520A pdb=" N SER C 132 " --> pdb=" O PRO C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 154 Processing helix chain 'C' and resid 169 through 182 removed outlier: 4.269A pdb=" N ALA C 173 " --> pdb=" O THR C 169 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 174 " --> pdb=" O TRP C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 206 Processing helix chain 'C' and resid 224 through 234 removed outlier: 3.695A pdb=" N GLN C 234 " --> pdb=" O ASP C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 267 Processing helix chain 'C' and resid 303 through 317 Processing helix chain 'C' and resid 334 through 341 Processing helix chain 'C' and resid 342 through 348 Processing helix chain 'C' and resid 365 through 375 Processing helix chain 'C' and resid 382 through 392 Processing helix chain 'C' and resid 416 through 427 Processing helix chain 'C' and resid 507 through 516 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 136 removed outlier: 6.271A pdb=" N ALA A 121 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL A 354 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE A 123 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N CYS A 328 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N PHE A 355 " --> pdb=" O CYS A 328 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG A 325 " --> pdb=" O GLN A 378 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N TYR A 380 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA A 327 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 379 " --> pdb=" O GLY A 409 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL A 411 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR A 381 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 259 through 261 removed outlier: 4.443A pdb=" N VAL A 209 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR A 213 " --> pdb=" O TYR A 165 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A 162 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL A 189 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 164 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N HIS A 186 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N TYR A 288 " --> pdb=" O HIS A 186 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ALA A 188 " --> pdb=" O TYR A 288 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE A 285 " --> pdb=" O HIS A 301 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 503 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 218 Processing sheet with id=AA6, first strand: chain 'A' and resid 471 through 474 removed outlier: 5.325A pdb=" N ASP A 527 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N ALA A 493 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 525 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA8, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA9, first strand: chain 'B' and resid 133 through 136 removed outlier: 6.294A pdb=" N ALA B 121 " --> pdb=" O THR B 352 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL B 354 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE B 123 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N CYS B 328 " --> pdb=" O ALA B 353 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N PHE B 355 " --> pdb=" O CYS B 328 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG B 325 " --> pdb=" O GLN B 378 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N TYR B 380 " --> pdb=" O ARG B 325 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA B 327 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 379 " --> pdb=" O GLY B 409 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL B 411 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR B 381 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B 408 " --> pdb=" O VAL B 435 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N THR B 437 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N SER B 410 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 259 through 261 removed outlier: 4.471A pdb=" N VAL B 209 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR B 213 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL B 162 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL B 189 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 164 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N HIS B 186 " --> pdb=" O ILE B 286 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N TYR B 288 " --> pdb=" O HIS B 186 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA B 188 " --> pdb=" O TYR B 288 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE B 285 " --> pdb=" O HIS B 301 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR B 503 " --> pdb=" O VAL B 300 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 216 through 218 Processing sheet with id=AB3, first strand: chain 'B' and resid 471 through 474 removed outlier: 5.268A pdb=" N ASP B 527 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N ALA B 493 " --> pdb=" O PHE B 525 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N PHE B 525 " --> pdb=" O ALA B 493 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY B 528 " --> pdb=" O LYS B 540 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AB5, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AB6, first strand: chain 'C' and resid 133 through 136 removed outlier: 6.251A pdb=" N ALA C 121 " --> pdb=" O THR C 352 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL C 354 " --> pdb=" O ALA C 121 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE C 123 " --> pdb=" O VAL C 354 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N CYS C 328 " --> pdb=" O ALA C 353 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N PHE C 355 " --> pdb=" O CYS C 328 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG C 325 " --> pdb=" O GLN C 378 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N TYR C 380 " --> pdb=" O ARG C 325 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA C 327 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU C 379 " --> pdb=" O GLY C 409 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL C 411 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR C 381 " --> pdb=" O VAL C 411 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 4.549A pdb=" N VAL C 209 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR C 213 " --> pdb=" O TYR C 165 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N HIS C 186 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N TYR C 288 " --> pdb=" O HIS C 186 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ALA C 188 " --> pdb=" O TYR C 288 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N HIS C 301 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE C 286 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL C 299 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR C 503 " --> pdb=" O VAL C 300 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 216 through 218 Processing sheet with id=AB9, first strand: chain 'C' and resid 471 through 474 removed outlier: 5.124A pdb=" N ASP C 527 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N ALA C 493 " --> pdb=" O PHE C 525 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE C 525 " --> pdb=" O ALA C 493 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY C 541 " --> pdb=" O GLY C 528 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA C 530 " --> pdb=" O ILE C 539 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ILE C 539 " --> pdb=" O ALA C 530 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1267 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: 1.69 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3937 1.34 - 1.46: 3122 1.46 - 1.58: 5431 1.58 - 1.70: 0 1.70 - 1.82: 105 Bond restraints: 12595 Sorted by residual: bond pdb=" N VAL B 397 " pdb=" CA VAL B 397 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.06e-02 8.90e+03 1.24e+01 bond pdb=" N ASN B 399 " pdb=" CA ASN B 399 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.10e-02 8.26e+03 7.86e+00 bond pdb=" N HIS B 400 " pdb=" CA HIS B 400 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.23e-02 6.61e+03 7.41e+00 bond pdb=" N LYS B 398 " pdb=" CA LYS B 398 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.21e-02 6.83e+03 6.77e+00 bond pdb=" N GLU B 394 " pdb=" CA GLU B 394 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.16e-02 7.43e+03 5.90e+00 ... (remaining 12590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 16851 1.73 - 3.46: 281 3.46 - 5.18: 31 5.18 - 6.91: 4 6.91 - 8.64: 1 Bond angle restraints: 17168 Sorted by residual: angle pdb=" N ASP B 395 " pdb=" CA ASP B 395 " pdb=" C ASP B 395 " ideal model delta sigma weight residual 112.88 107.72 5.16 1.29e+00 6.01e-01 1.60e+01 angle pdb=" N HIS B 396 " pdb=" CA HIS B 396 " pdb=" C HIS B 396 " ideal model delta sigma weight residual 113.72 108.76 4.96 1.30e+00 5.92e-01 1.46e+01 angle pdb=" N VAL B 397 " pdb=" CA VAL B 397 " pdb=" C VAL B 397 " ideal model delta sigma weight residual 112.12 109.61 2.51 8.40e-01 1.42e+00 8.96e+00 angle pdb=" CB MET B 33 " pdb=" CG MET B 33 " pdb=" SD MET B 33 " ideal model delta sigma weight residual 112.70 121.34 -8.64 3.00e+00 1.11e-01 8.29e+00 angle pdb=" C HIS B 400 " pdb=" CA HIS B 400 " pdb=" CB HIS B 400 " ideal model delta sigma weight residual 109.33 114.81 -5.48 1.97e+00 2.58e-01 7.74e+00 ... (remaining 17163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 6638 17.78 - 35.55: 555 35.55 - 53.33: 158 53.33 - 71.10: 27 71.10 - 88.88: 19 Dihedral angle restraints: 7397 sinusoidal: 2904 harmonic: 4493 Sorted by residual: dihedral pdb=" CA LEU C 109 " pdb=" C LEU C 109 " pdb=" N ASP C 110 " pdb=" CA ASP C 110 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LEU A 109 " pdb=" C LEU A 109 " pdb=" N ASP A 110 " pdb=" CA ASP A 110 " ideal model delta harmonic sigma weight residual -180.00 -162.56 -17.44 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CB GLU A 49 " pdb=" CG GLU A 49 " pdb=" CD GLU A 49 " pdb=" OE1 GLU A 49 " ideal model delta sinusoidal sigma weight residual 0.00 88.88 -88.88 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 7394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1342 0.045 - 0.089: 312 0.089 - 0.134: 137 0.134 - 0.178: 3 0.178 - 0.223: 2 Chirality restraints: 1796 Sorted by residual: chirality pdb=" CB VAL B 397 " pdb=" CA VAL B 397 " pdb=" CG1 VAL B 397 " pdb=" CG2 VAL B 397 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA VAL B 397 " pdb=" N VAL B 397 " pdb=" C VAL B 397 " pdb=" CB VAL B 397 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE C 286 " pdb=" N ILE C 286 " pdb=" C ILE C 286 " pdb=" CB ILE C 286 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 1793 not shown) Planarity restraints: 2222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 416 " -0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO B 417 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 417 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 417 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 30 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO C 31 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 31 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 31 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 363 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO B 364 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 364 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 364 " -0.023 5.00e-02 4.00e+02 ... (remaining 2219 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1686 2.76 - 3.29: 10998 3.29 - 3.83: 21497 3.83 - 4.36: 26361 4.36 - 4.90: 44395 Nonbonded interactions: 104937 Sorted by model distance: nonbonded pdb=" OE2 GLU A 442 " pdb=" OH TYR A 515 " model vdw 2.220 3.040 nonbonded pdb=" NZ LYS C 297 " pdb=" OH TYR C 515 " model vdw 2.221 3.120 nonbonded pdb=" OG SER B 63 " pdb=" NH2 ARG B 85 " model vdw 2.265 3.120 nonbonded pdb=" OE2 GLU B 442 " pdb=" OH TYR B 515 " model vdw 2.273 3.040 nonbonded pdb=" O HIS A 400 " pdb=" NZ LYS A 429 " model vdw 2.293 3.120 ... (remaining 104932 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 61 or (resid 62 and (name N or nam \ e CA or name C or name O or name CB )) or resid 63 through 220 or (resid 221 and \ (name N or name CA or name C or name O or name CB )) or resid 222 through 226 o \ r resid 228 through 290 or (resid 295 and (name N or name CA or name C or name O \ or name CB )) or resid 296 through 324 or resid 326 through 372 or resid 374 th \ rough 383 or resid 385 through 420 or resid 422 through 494 or (resid 495 and (n \ ame N or name CA or name C or name O or name CB )) or resid 496 through 508 or ( \ resid 509 and (name N or name CA or name C or name O or name CB )) or resid 510 \ through 539 or resid 541)) selection = (chain 'B' and (resid 26 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 226 or resid 228 through 250 or (r \ esid 251 and (name N or name CA or name C or name O or name CB )) or resid 252 t \ hrough 290 or (resid 295 and (name N or name CA or name C or name O or name CB ) \ ) or resid 296 through 324 or resid 326 through 372 or resid 374 through 383 or \ resid 385 through 420 or resid 422 through 482 or (resid 483 and (name N or name \ CA or name C or name O or name CB )) or resid 484 through 494 or (resid 495 and \ (name N or name CA or name C or name O or name CB )) or resid 496 through 508 o \ r (resid 509 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 10 through 539 or resid 541)) selection = (chain 'C' and (resid 26 through 220 or (resid 221 and (name N or name CA or nam \ e C or name O or name CB )) or resid 222 through 226 or resid 228 through 290 or \ resid 295 through 324 or resid 326 through 372 or resid 374 through 383 or resi \ d 385 through 420 or resid 422 through 539 or resid 541)) } 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=0.07 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.260 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 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 0.037 12595 Z= 0.144 Angle : 0.552 8.640 17168 Z= 0.317 Chirality : 0.045 0.223 1796 Planarity : 0.005 0.044 2222 Dihedral : 15.123 88.878 4541 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.95 % Allowed : 13.68 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.21), residues: 1542 helix: 0.56 (0.23), residues: 512 sheet: -0.73 (0.36), residues: 192 loop : -0.15 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 494 TYR 0.018 0.001 TYR B 340 PHE 0.008 0.001 PHE C 355 TRP 0.019 0.001 TRP B 262 HIS 0.003 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00265 (12595) covalent geometry : angle 0.55184 (17168) hydrogen bonds : bond 0.16167 ( 456) hydrogen bonds : angle 6.82237 ( 1267) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.8034 (ttt-90) cc_final: 0.7733 (mtp180) REVERT: A 440 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8760 (ptm) REVERT: B 206 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8115 (mt-10) REVERT: B 315 LYS cc_start: 0.8723 (tttt) cc_final: 0.8439 (tttp) REVERT: B 394 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7337 (pt0) REVERT: B 403 SER cc_start: 0.8278 (p) cc_final: 0.7776 (t) REVERT: C 53 LYS cc_start: 0.7720 (tttp) cc_final: 0.7140 (tttm) REVERT: C 221 LYS cc_start: 0.7759 (mttm) cc_final: 0.7074 (mtpt) REVERT: C 254 MET cc_start: 0.9271 (tpt) cc_final: 0.8913 (tpt) outliers start: 11 outliers final: 5 residues processed: 142 average time/residue: 0.5888 time to fit residues: 89.9931 Evaluate side-chains 130 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 474 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS A 116 ASN A 421 HIS B 116 ASN C 116 ASN C 421 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.115313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.083564 restraints weight = 33991.123| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 3.55 r_work: 0.2445 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2433 r_free = 0.2433 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2433 r_free = 0.2433 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.0600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12595 Z= 0.122 Angle : 0.517 6.603 17168 Z= 0.271 Chirality : 0.046 0.160 1796 Planarity : 0.005 0.044 2222 Dihedral : 4.651 50.736 1735 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.58 % Allowed : 12.81 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.21), residues: 1542 helix: 0.82 (0.23), residues: 521 sheet: -0.87 (0.33), residues: 213 loop : -0.14 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 390 TYR 0.019 0.001 TYR B 340 PHE 0.009 0.001 PHE C 355 TRP 0.019 0.001 TRP B 262 HIS 0.004 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00290 (12595) covalent geometry : angle 0.51747 (17168) hydrogen bonds : bond 0.04386 ( 456) hydrogen bonds : angle 5.24916 ( 1267) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.8096 (ttt-90) cc_final: 0.7879 (ttp80) REVERT: B 206 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8105 (mt-10) REVERT: B 403 SER cc_start: 0.8386 (p) cc_final: 0.8177 (p) REVERT: C 221 LYS cc_start: 0.7995 (mttm) cc_final: 0.7351 (mtpt) REVERT: C 254 MET cc_start: 0.9294 (tpt) cc_final: 0.9049 (tpt) REVERT: C 386 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7314 (mt) outliers start: 18 outliers final: 11 residues processed: 146 average time/residue: 0.5775 time to fit residues: 91.2714 Evaluate side-chains 138 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 126 optimal weight: 0.0000 chunk 106 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN B 116 ASN C 116 ASN C 421 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.116721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.084530 restraints weight = 32520.301| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 3.22 r_work: 0.2472 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2467 r_free = 0.2467 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2467 r_free = 0.2467 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12595 Z= 0.100 Angle : 0.482 5.616 17168 Z= 0.251 Chirality : 0.045 0.151 1796 Planarity : 0.004 0.041 2222 Dihedral : 4.103 25.388 1725 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.66 % Allowed : 12.96 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.22), residues: 1542 helix: 0.99 (0.23), residues: 521 sheet: -0.86 (0.33), residues: 220 loop : -0.13 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 390 TYR 0.016 0.001 TYR B 340 PHE 0.010 0.001 PHE A 176 TRP 0.017 0.001 TRP B 262 HIS 0.002 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00227 (12595) covalent geometry : angle 0.48190 (17168) hydrogen bonds : bond 0.03762 ( 456) hydrogen bonds : angle 4.98914 ( 1267) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 ARG cc_start: 0.8139 (ttt-90) cc_final: 0.7875 (ttp80) REVERT: B 206 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7989 (mt-10) REVERT: B 315 LYS cc_start: 0.8871 (tttt) cc_final: 0.8614 (tttp) REVERT: B 403 SER cc_start: 0.8418 (p) cc_final: 0.8123 (p) REVERT: C 221 LYS cc_start: 0.7983 (mttm) cc_final: 0.7333 (mtpt) REVERT: C 254 MET cc_start: 0.9301 (tpt) cc_final: 0.9050 (tpt) REVERT: C 401 ASP cc_start: 0.7659 (t0) cc_final: 0.7453 (t0) outliers start: 19 outliers final: 11 residues processed: 142 average time/residue: 0.6300 time to fit residues: 96.4792 Evaluate side-chains 138 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 474 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 136 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 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 116 ASN B 116 ASN C 116 ASN C 421 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.115920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.085861 restraints weight = 44853.272| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 4.50 r_work: 0.2487 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2415 r_free = 0.2415 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2415 r_free = 0.2415 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12595 Z= 0.105 Angle : 0.483 5.023 17168 Z= 0.251 Chirality : 0.045 0.152 1796 Planarity : 0.004 0.041 2222 Dihedral : 4.083 23.792 1725 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.98 % Allowed : 12.89 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.22), residues: 1542 helix: 1.05 (0.23), residues: 521 sheet: -0.83 (0.33), residues: 220 loop : -0.10 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 390 TYR 0.017 0.001 TYR B 340 PHE 0.012 0.001 PHE A 426 TRP 0.017 0.001 TRP A 262 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00246 (12595) covalent geometry : angle 0.48271 (17168) hydrogen bonds : bond 0.03701 ( 456) hydrogen bonds : angle 4.87112 ( 1267) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 ARG cc_start: 0.8245 (ttt-90) cc_final: 0.7952 (ttp80) REVERT: B 206 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7990 (mt-10) REVERT: B 315 LYS cc_start: 0.8976 (tttt) cc_final: 0.8731 (tttp) REVERT: B 403 SER cc_start: 0.8404 (p) cc_final: 0.7824 (t) REVERT: B 488 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7942 (tt0) REVERT: C 221 LYS cc_start: 0.8032 (mttm) cc_final: 0.7374 (mtpt) REVERT: C 254 MET cc_start: 0.9334 (tpt) cc_final: 0.9065 (tpt) outliers start: 22 outliers final: 15 residues processed: 163 average time/residue: 0.5732 time to fit residues: 100.9110 Evaluate side-chains 151 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 474 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 127 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 82 optimal weight: 0.0670 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN B 116 ASN C 116 ASN C 421 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.111928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.080630 restraints weight = 35174.311| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 3.69 r_work: 0.2400 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2382 r_free = 0.2382 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2382 r_free = 0.2382 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12595 Z= 0.167 Angle : 0.545 5.579 17168 Z= 0.284 Chirality : 0.048 0.173 1796 Planarity : 0.005 0.043 2222 Dihedral : 4.314 27.186 1725 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.98 % Allowed : 13.12 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.21), residues: 1542 helix: 0.92 (0.23), residues: 521 sheet: -0.91 (0.33), residues: 213 loop : -0.17 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 325 TYR 0.021 0.002 TYR B 340 PHE 0.011 0.002 PHE A 176 TRP 0.021 0.002 TRP A 262 HIS 0.006 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00414 (12595) covalent geometry : angle 0.54492 (17168) hydrogen bonds : bond 0.04637 ( 456) hydrogen bonds : angle 5.04837 ( 1267) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.7915 (mmtt) cc_final: 0.7116 (mtpt) REVERT: A 403 SER cc_start: 0.8401 (p) cc_final: 0.7922 (t) REVERT: B 206 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8111 (mt-10) REVERT: B 403 SER cc_start: 0.8366 (p) cc_final: 0.7748 (t) REVERT: B 488 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7898 (tt0) REVERT: C 221 LYS cc_start: 0.7953 (mttm) cc_final: 0.7278 (mtpt) REVERT: C 254 MET cc_start: 0.9315 (tpt) cc_final: 0.8992 (tpt) REVERT: C 540 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8259 (mptp) outliers start: 23 outliers final: 13 residues processed: 154 average time/residue: 0.5419 time to fit residues: 90.2162 Evaluate side-chains 145 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 540 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN B 116 ASN C 116 ASN C 421 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.111549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.080260 restraints weight = 36326.161| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 3.81 r_work: 0.2392 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2383 r_free = 0.2383 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2383 r_free = 0.2383 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12595 Z= 0.178 Angle : 0.553 6.111 17168 Z= 0.288 Chirality : 0.048 0.170 1796 Planarity : 0.005 0.043 2222 Dihedral : 4.402 29.050 1725 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.13 % Allowed : 13.60 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.21), residues: 1542 helix: 0.86 (0.23), residues: 521 sheet: -0.96 (0.33), residues: 212 loop : -0.23 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 531 TYR 0.021 0.002 TYR B 340 PHE 0.012 0.002 PHE A 176 TRP 0.023 0.002 TRP A 262 HIS 0.006 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00444 (12595) covalent geometry : angle 0.55281 (17168) hydrogen bonds : bond 0.04640 ( 456) hydrogen bonds : angle 5.06995 ( 1267) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 ARG cc_start: 0.8183 (ttt-90) cc_final: 0.7867 (ttp80) REVERT: A 403 SER cc_start: 0.8435 (p) cc_final: 0.7951 (t) REVERT: B 206 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8091 (mt-10) REVERT: B 403 SER cc_start: 0.8353 (p) cc_final: 0.7725 (t) REVERT: B 488 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7917 (tt0) REVERT: C 221 LYS cc_start: 0.7936 (mttm) cc_final: 0.7241 (mtpt) REVERT: C 254 MET cc_start: 0.9319 (tpt) cc_final: 0.8995 (tpt) REVERT: C 540 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8243 (mptp) outliers start: 24 outliers final: 12 residues processed: 153 average time/residue: 0.5315 time to fit residues: 87.8350 Evaluate side-chains 139 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 540 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 41 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN B 116 ASN C 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.114631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.083539 restraints weight = 38173.518| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 4.08 r_work: 0.2423 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2409 r_free = 0.2409 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2409 r_free = 0.2409 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12595 Z= 0.109 Angle : 0.495 5.800 17168 Z= 0.257 Chirality : 0.045 0.153 1796 Planarity : 0.004 0.041 2222 Dihedral : 4.220 25.728 1725 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.74 % Allowed : 14.15 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.22), residues: 1542 helix: 1.01 (0.23), residues: 521 sheet: -0.92 (0.33), residues: 213 loop : -0.15 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 390 TYR 0.016 0.001 TYR B 340 PHE 0.009 0.001 PHE A 176 TRP 0.019 0.001 TRP A 262 HIS 0.003 0.001 HIS C 186 Details of bonding type rmsd covalent geometry : bond 0.00255 (12595) covalent geometry : angle 0.49497 (17168) hydrogen bonds : bond 0.03768 ( 456) hydrogen bonds : angle 4.89713 ( 1267) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.7837 (mmtt) cc_final: 0.7013 (mtpt) REVERT: A 403 SER cc_start: 0.8404 (p) cc_final: 0.7930 (t) REVERT: B 206 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7923 (mt-10) REVERT: B 403 SER cc_start: 0.8215 (p) cc_final: 0.7643 (t) REVERT: B 488 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7949 (tt0) REVERT: C 221 LYS cc_start: 0.7921 (mttm) cc_final: 0.7225 (mtpt) REVERT: C 254 MET cc_start: 0.9331 (tpt) cc_final: 0.9047 (tpt) outliers start: 19 outliers final: 12 residues processed: 146 average time/residue: 0.5650 time to fit residues: 89.6153 Evaluate side-chains 144 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 474 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 69 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 0.4980 chunk 82 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN B 116 ASN C 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.115176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.083755 restraints weight = 34559.733| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.54 r_work: 0.2449 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2434 r_free = 0.2434 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2434 r_free = 0.2434 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12595 Z= 0.103 Angle : 0.484 6.318 17168 Z= 0.251 Chirality : 0.045 0.150 1796 Planarity : 0.004 0.041 2222 Dihedral : 4.096 21.989 1725 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.58 % Allowed : 14.31 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.22), residues: 1542 helix: 1.10 (0.23), residues: 521 sheet: -0.83 (0.34), residues: 213 loop : -0.12 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 494 TYR 0.015 0.001 TYR B 340 PHE 0.009 0.001 PHE A 176 TRP 0.018 0.001 TRP B 262 HIS 0.003 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00241 (12595) covalent geometry : angle 0.48445 (17168) hydrogen bonds : bond 0.03578 ( 456) hydrogen bonds : angle 4.78777 ( 1267) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7856 (tttm) cc_final: 0.7632 (tttp) REVERT: A 206 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8011 (mt-10) REVERT: A 221 LYS cc_start: 0.7885 (mmtt) cc_final: 0.7051 (mtpt) REVERT: A 390 ARG cc_start: 0.8144 (ttt-90) cc_final: 0.7846 (ttp80) REVERT: A 403 SER cc_start: 0.8433 (p) cc_final: 0.7953 (t) REVERT: B 206 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7935 (mt-10) REVERT: B 315 LYS cc_start: 0.8930 (tttt) cc_final: 0.8694 (tttp) REVERT: B 395 ASP cc_start: 0.8004 (m-30) cc_final: 0.7788 (m-30) REVERT: B 403 SER cc_start: 0.8223 (p) cc_final: 0.7642 (t) REVERT: B 488 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7971 (tt0) REVERT: C 221 LYS cc_start: 0.7967 (mttm) cc_final: 0.7281 (mtpt) REVERT: C 254 MET cc_start: 0.9347 (tpt) cc_final: 0.9071 (tpt) REVERT: C 537 MET cc_start: 0.8830 (mmm) cc_final: 0.8590 (tpp) outliers start: 17 outliers final: 11 residues processed: 146 average time/residue: 0.6011 time to fit residues: 94.6409 Evaluate side-chains 143 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 474 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 126 optimal weight: 0.4980 chunk 140 optimal weight: 10.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN B 116 ASN C 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.114140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.084511 restraints weight = 45338.674| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 4.75 r_work: 0.2377 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2359 r_free = 0.2359 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2359 r_free = 0.2359 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12595 Z= 0.129 Angle : 0.507 5.754 17168 Z= 0.263 Chirality : 0.046 0.158 1796 Planarity : 0.005 0.042 2222 Dihedral : 4.110 19.522 1724 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.42 % Allowed : 14.55 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.22), residues: 1542 helix: 1.06 (0.23), residues: 521 sheet: -0.86 (0.34), residues: 213 loop : -0.15 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 494 TYR 0.017 0.001 TYR B 340 PHE 0.010 0.001 PHE A 176 TRP 0.019 0.001 TRP B 262 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00316 (12595) covalent geometry : angle 0.50747 (17168) hydrogen bonds : bond 0.03922 ( 456) hydrogen bonds : angle 4.84773 ( 1267) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7875 (tttm) cc_final: 0.7658 (tttp) REVERT: A 206 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8103 (mt-10) REVERT: A 221 LYS cc_start: 0.7930 (mmtt) cc_final: 0.7122 (mtpt) REVERT: A 390 ARG cc_start: 0.8187 (ttt-90) cc_final: 0.7878 (ttp80) REVERT: A 403 SER cc_start: 0.8458 (p) cc_final: 0.8001 (t) REVERT: B 206 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8029 (mt-10) REVERT: B 315 LYS cc_start: 0.8982 (tttt) cc_final: 0.8751 (tttp) REVERT: B 395 ASP cc_start: 0.8006 (m-30) cc_final: 0.7788 (m-30) REVERT: B 403 SER cc_start: 0.8202 (p) cc_final: 0.7684 (t) REVERT: B 488 GLU cc_start: 0.8282 (tm-30) cc_final: 0.8027 (tt0) REVERT: C 221 LYS cc_start: 0.8000 (mttm) cc_final: 0.7306 (mtpt) REVERT: C 254 MET cc_start: 0.9354 (tpt) cc_final: 0.9070 (tpt) REVERT: C 537 MET cc_start: 0.8889 (mmm) cc_final: 0.8643 (tpp) outliers start: 15 outliers final: 9 residues processed: 145 average time/residue: 0.5517 time to fit residues: 86.3845 Evaluate side-chains 141 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 474 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 93 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN B 116 ASN C 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.115513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.084645 restraints weight = 39131.889| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 4.08 r_work: 0.2434 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2416 r_free = 0.2416 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2416 r_free = 0.2416 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12595 Z= 0.104 Angle : 0.487 5.701 17168 Z= 0.252 Chirality : 0.045 0.150 1796 Planarity : 0.004 0.041 2222 Dihedral : 4.056 19.370 1724 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.34 % Allowed : 14.70 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.22), residues: 1542 helix: 1.11 (0.23), residues: 521 sheet: -0.81 (0.34), residues: 213 loop : -0.11 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 494 TYR 0.015 0.001 TYR B 340 PHE 0.009 0.001 PHE A 176 TRP 0.018 0.001 TRP B 262 HIS 0.003 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00247 (12595) covalent geometry : angle 0.48701 (17168) hydrogen bonds : bond 0.03586 ( 456) hydrogen bonds : angle 4.77508 ( 1267) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.6745 (mp0) cc_final: 0.6459 (tp30) REVERT: A 53 LYS cc_start: 0.7840 (tttm) cc_final: 0.7619 (tttp) REVERT: A 206 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7986 (mt-10) REVERT: A 221 LYS cc_start: 0.7868 (mmtt) cc_final: 0.7047 (mtpt) REVERT: A 390 ARG cc_start: 0.8131 (ttt-90) cc_final: 0.7822 (ttp80) REVERT: A 403 SER cc_start: 0.8407 (p) cc_final: 0.7945 (t) REVERT: B 206 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7926 (mt-10) REVERT: B 315 LYS cc_start: 0.8921 (tttt) cc_final: 0.8687 (tttp) REVERT: B 395 ASP cc_start: 0.8000 (m-30) cc_final: 0.7788 (m-30) REVERT: B 403 SER cc_start: 0.8144 (p) cc_final: 0.7638 (t) REVERT: B 488 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7974 (tt0) REVERT: C 221 LYS cc_start: 0.7948 (mttm) cc_final: 0.7250 (mtpt) REVERT: C 254 MET cc_start: 0.9345 (tpt) cc_final: 0.9068 (tpt) REVERT: C 403 SER cc_start: 0.8156 (p) cc_final: 0.7638 (t) REVERT: C 537 MET cc_start: 0.8821 (mmm) cc_final: 0.8582 (tpp) outliers start: 14 outliers final: 12 residues processed: 146 average time/residue: 0.5634 time to fit residues: 88.8585 Evaluate side-chains 143 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 474 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 94 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 104 optimal weight: 0.0010 chunk 130 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 122 optimal weight: 0.0030 chunk 45 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN B 116 ASN C 116 ASN C 424 ASN C 430 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.115691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.087079 restraints weight = 46857.718| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 5.04 r_work: 0.2403 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2388 r_free = 0.2388 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2388 r_free = 0.2388 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12595 Z= 0.099 Angle : 0.488 5.956 17168 Z= 0.252 Chirality : 0.045 0.148 1796 Planarity : 0.004 0.041 2222 Dihedral : 4.053 19.288 1724 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.42 % Allowed : 14.70 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.22), residues: 1542 helix: 1.14 (0.23), residues: 521 sheet: -0.86 (0.33), residues: 220 loop : -0.11 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 494 TYR 0.015 0.001 TYR B 340 PHE 0.009 0.001 PHE A 176 TRP 0.017 0.001 TRP B 262 HIS 0.002 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00229 (12595) covalent geometry : angle 0.48769 (17168) hydrogen bonds : bond 0.03503 ( 456) hydrogen bonds : angle 4.75726 ( 1267) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3445.73 seconds wall clock time: 59 minutes 28.03 seconds (3568.03 seconds total)