Starting phenix.real_space_refine on Fri May 23 18:47:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz7_41736/05_2025/8tz7_41736_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz7_41736/05_2025/8tz7_41736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tz7_41736/05_2025/8tz7_41736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz7_41736/05_2025/8tz7_41736.map" model { file = "/net/cci-nas-00/data/ceres_data/8tz7_41736/05_2025/8tz7_41736_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz7_41736/05_2025/8tz7_41736_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.083 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 87 5.16 5 C 8187 2.51 5 N 1923 2.21 5 O 2139 1.98 5 H 12069 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24408 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "C" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'LBN': 1, 'XMO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 15 Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'LBN': 1, 'XMO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 15 Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'LBN': 1, 'XMO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 15 Time building chain proxies: 11.73, per 1000 atoms: 0.48 Number of scatterers: 24408 At special positions: 0 Unit cell: (128.52, 128.52, 76.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 87 16.00 P 3 15.00 O 2139 8.00 N 1923 7.00 C 8187 6.00 H 12069 1.00 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: 6.51 Conformation dependent library (CDL) restraints added in 2.2 seconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 0 sheets defined 89.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 90 through 130 removed outlier: 5.832A pdb=" N THR A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 157 Processing helix chain 'A' and resid 157 through 203 Proline residue: A 167 - end of helix removed outlier: 4.714A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.760A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE A 210 " --> pdb=" O GLN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 252 removed outlier: 4.442A pdb=" N VAL A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 277 removed outlier: 3.513A pdb=" N ALA A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 283 through 287 removed outlier: 4.404A pdb=" N THR A 286 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 293 Processing helix chain 'A' and resid 294 through 312 removed outlier: 3.831A pdb=" N VAL A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 330 Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 349 through 361 Proline residue: A 356 - end of helix Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 362 through 376 removed outlier: 3.637A pdb=" N THR A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 removed outlier: 4.058A pdb=" N GLY A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 389 " --> pdb=" O TYR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 414 removed outlier: 4.083A pdb=" N ALA A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 423 through 429 Processing helix chain 'A' and resid 437 through 481 removed outlier: 3.706A pdb=" N SER A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET A 480 " --> pdb=" O TRP A 476 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.590A pdb=" N TYR A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 503 Processing helix chain 'A' and resid 506 through 523 removed outlier: 4.274A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 removed outlier: 3.988A pdb=" N ALA A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 574 through 586 Processing helix chain 'A' and resid 589 through 596 Processing helix chain 'A' and resid 596 through 619 removed outlier: 3.548A pdb=" N LEU A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 602 " --> pdb=" O MET A 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 130 removed outlier: 5.832A pdb=" N THR B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N THR B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 157 through 203 Proline residue: B 167 - end of helix removed outlier: 4.714A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 223 removed outlier: 3.761A pdb=" N LEU B 207 " --> pdb=" O GLY B 203 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 252 removed outlier: 4.441A pdb=" N VAL B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 277 removed outlier: 3.514A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 283 through 287 removed outlier: 4.403A pdb=" N THR B 286 " --> pdb=" O GLU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 293 Processing helix chain 'B' and resid 294 through 312 removed outlier: 3.832A pdb=" N VAL B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 330 Processing helix chain 'B' and resid 332 through 342 Processing helix chain 'B' and resid 349 through 361 Proline residue: B 356 - end of helix Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 362 through 376 removed outlier: 3.637A pdb=" N THR B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 389 removed outlier: 4.059A pdb=" N GLY B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B 389 " --> pdb=" O TYR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 414 removed outlier: 4.083A pdb=" N ALA B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 423 through 429 Processing helix chain 'B' and resid 437 through 481 removed outlier: 3.706A pdb=" N SER B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET B 480 " --> pdb=" O TRP B 476 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.589A pdb=" N TYR B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 506 through 523 removed outlier: 4.274A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 542 removed outlier: 3.988A pdb=" N ALA B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 574 through 586 Processing helix chain 'B' and resid 589 through 596 Processing helix chain 'B' and resid 596 through 619 removed outlier: 3.548A pdb=" N LEU B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 602 " --> pdb=" O MET B 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 130 removed outlier: 5.833A pdb=" N THR C 105 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 157 Processing helix chain 'C' and resid 157 through 203 Proline residue: C 167 - end of helix removed outlier: 4.713A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 223 removed outlier: 3.761A pdb=" N LEU C 207 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER C 209 " --> pdb=" O GLN C 205 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE C 210 " --> pdb=" O GLN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 252 removed outlier: 4.441A pdb=" N VAL C 235 " --> pdb=" O TYR C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 277 removed outlier: 3.513A pdb=" N ALA C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP C 260 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER C 273 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 283 through 287 removed outlier: 4.404A pdb=" N THR C 286 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 294 through 312 removed outlier: 3.831A pdb=" N VAL C 298 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 330 Processing helix chain 'C' and resid 332 through 342 Processing helix chain 'C' and resid 349 through 361 Proline residue: C 356 - end of helix Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 362 through 376 removed outlier: 3.636A pdb=" N THR C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 389 removed outlier: 4.059A pdb=" N GLY C 383 " --> pdb=" O GLY C 379 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY C 389 " --> pdb=" O TYR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 414 removed outlier: 4.084A pdb=" N ALA C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'C' and resid 423 through 429 Processing helix chain 'C' and resid 437 through 481 removed outlier: 3.706A pdb=" N SER C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET C 480 " --> pdb=" O TRP C 476 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.590A pdb=" N TYR C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 503 Processing helix chain 'C' and resid 506 through 523 removed outlier: 4.274A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 542 removed outlier: 3.988A pdb=" N ALA C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 566 Processing helix chain 'C' and resid 571 through 573 No H-bonds generated for 'chain 'C' and resid 571 through 573' Processing helix chain 'C' and resid 574 through 586 Processing helix chain 'C' and resid 589 through 596 Processing helix chain 'C' and resid 596 through 619 removed outlier: 3.548A pdb=" N LEU C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 602 " --> pdb=" O MET C 598 " (cutoff:3.500A) 967 hydrogen bonds defined for protein. 2856 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: 9.06 Time building geometry restraints manager: 7.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12051 1.03 - 1.23: 31 1.23 - 1.42: 5345 1.42 - 1.62: 7149 1.62 - 1.81: 165 Bond restraints: 24741 Sorted by residual: bond pdb=" C11 XMO B 801 " pdb=" O12 XMO B 801 " ideal model delta sigma weight residual 1.398 1.683 -0.285 2.00e-02 2.50e+03 2.02e+02 bond pdb=" C11 XMO A 801 " pdb=" O12 XMO A 801 " ideal model delta sigma weight residual 1.398 1.682 -0.284 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C11 XMO C 801 " pdb=" O12 XMO C 801 " ideal model delta sigma weight residual 1.398 1.681 -0.283 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C10 XMO B 801 " pdb=" C11 XMO B 801 " ideal model delta sigma weight residual 1.534 1.291 0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C10 XMO A 801 " pdb=" C11 XMO A 801 " ideal model delta sigma weight residual 1.534 1.291 0.243 2.00e-02 2.50e+03 1.47e+02 ... (remaining 24736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 44413 3.18 - 6.35: 129 6.35 - 9.53: 11 9.53 - 12.71: 3 12.71 - 15.89: 3 Bond angle restraints: 44559 Sorted by residual: angle pdb=" O1 LBN C 802 " pdb=" P1 LBN C 802 " pdb=" O2 LBN C 802 " ideal model delta sigma weight residual 93.45 109.34 -15.89 3.00e+00 1.11e-01 2.80e+01 angle pdb=" O1 LBN B 802 " pdb=" P1 LBN B 802 " pdb=" O2 LBN B 802 " ideal model delta sigma weight residual 93.45 109.32 -15.87 3.00e+00 1.11e-01 2.80e+01 angle pdb=" O1 LBN A 802 " pdb=" P1 LBN A 802 " pdb=" O2 LBN A 802 " ideal model delta sigma weight residual 93.45 109.30 -15.85 3.00e+00 1.11e-01 2.79e+01 angle pdb=" N ASP A 548 " pdb=" CA ASP A 548 " pdb=" C ASP A 548 " ideal model delta sigma weight residual 108.19 103.85 4.34 1.29e+00 6.01e-01 1.13e+01 angle pdb=" N ASP B 548 " pdb=" CA ASP B 548 " pdb=" C ASP B 548 " ideal model delta sigma weight residual 108.19 103.89 4.30 1.29e+00 6.01e-01 1.11e+01 ... (remaining 44554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.60: 11314 26.60 - 53.21: 406 53.21 - 79.81: 106 79.81 - 106.41: 6 106.41 - 133.02: 3 Dihedral angle restraints: 11835 sinusoidal: 6105 harmonic: 5730 Sorted by residual: dihedral pdb=" O5 LBN A 802 " pdb=" C2 LBN A 802 " pdb=" C3 LBN A 802 " pdb=" O7 LBN A 802 " ideal model delta sinusoidal sigma weight residual 62.67 -164.31 -133.02 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" O5 LBN C 802 " pdb=" C2 LBN C 802 " pdb=" C3 LBN C 802 " pdb=" O7 LBN C 802 " ideal model delta sinusoidal sigma weight residual 62.67 -164.35 -132.98 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" O5 LBN B 802 " pdb=" C2 LBN B 802 " pdb=" C3 LBN B 802 " pdb=" O7 LBN B 802 " ideal model delta sinusoidal sigma weight residual 62.67 -164.36 -132.97 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 11832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1756 0.067 - 0.134: 230 0.134 - 0.202: 0 0.202 - 0.269: 0 0.269 - 0.336: 3 Chirality restraints: 1989 Sorted by residual: chirality pdb=" C10 XMO B 801 " pdb=" C09 XMO B 801 " pdb=" C11 XMO B 801 " pdb=" O22 XMO B 801 " both_signs ideal model delta sigma weight residual False 2.74 2.40 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C10 XMO C 801 " pdb=" C09 XMO C 801 " pdb=" C11 XMO C 801 " pdb=" O22 XMO C 801 " both_signs ideal model delta sigma weight residual False 2.74 2.40 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" C10 XMO A 801 " pdb=" C09 XMO A 801 " pdb=" C11 XMO A 801 " pdb=" O22 XMO A 801 " both_signs ideal model delta sigma weight residual False 2.74 2.41 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 1986 not shown) Planarity restraints: 3633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 295 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO C 296 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 296 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 296 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 295 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO A 296 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 296 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 296 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 295 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO B 296 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 296 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 296 " 0.024 5.00e-02 4.00e+02 ... (remaining 3630 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 486 2.13 - 2.75: 42845 2.75 - 3.36: 69920 3.36 - 3.98: 86051 3.98 - 4.60: 139144 Nonbonded interactions: 338446 Sorted by model distance: nonbonded pdb=" O LEU A 248 " pdb=" HG1 THR A 252 " model vdw 1.511 2.450 nonbonded pdb=" O LEU B 248 " pdb=" HG1 THR B 252 " model vdw 1.513 2.450 nonbonded pdb=" O LEU C 248 " pdb=" HG1 THR C 252 " model vdw 1.513 2.450 nonbonded pdb=" O LEU C 195 " pdb=" HG1 THR C 199 " model vdw 1.559 2.450 nonbonded pdb=" O LEU B 195 " pdb=" HG1 THR B 199 " model vdw 1.560 2.450 ... (remaining 338441 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.420 Extract box with map and model: 0.940 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 51.200 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.100 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:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 : 0.010 0.285 12672 Z= 0.487 Angle : 0.682 15.886 17241 Z= 0.330 Chirality : 0.040 0.336 1989 Planarity : 0.003 0.044 2091 Dihedral : 12.773 133.018 4365 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.48 % Allowed : 3.12 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.50 (0.21), residues: 1593 helix: 2.94 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -0.75 (0.30), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 316 HIS 0.002 0.001 HIS A 394 PHE 0.015 0.001 PHE B 488 TYR 0.007 0.001 TYR B 519 ARG 0.002 0.000 ARG A 539 Details of bonding type rmsd hydrogen bonds : bond 0.14689 ( 967) hydrogen bonds : angle 5.14034 ( 2856) covalent geometry : bond 0.00978 (12672) covalent geometry : angle 0.68238 (17241) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 241 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 235 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.6891 (tp) cc_final: 0.6669 (mt) REVERT: A 307 MET cc_start: 0.8471 (mtm) cc_final: 0.8098 (mtp) REVERT: A 497 MET cc_start: 0.7792 (tmt) cc_final: 0.6777 (tmt) REVERT: A 598 MET cc_start: 0.8202 (tpp) cc_final: 0.7635 (tpt) REVERT: B 307 MET cc_start: 0.8419 (mtm) cc_final: 0.8215 (mtp) REVERT: B 329 MET cc_start: 0.8462 (mtp) cc_final: 0.8238 (mtm) REVERT: C 329 MET cc_start: 0.8538 (mtp) cc_final: 0.8160 (mtm) REVERT: C 344 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7910 (p90) REVERT: C 430 MET cc_start: 0.8057 (mtt) cc_final: 0.7540 (mtt) REVERT: C 497 MET cc_start: 0.7517 (tmt) cc_final: 0.7170 (tmt) outliers start: 6 outliers final: 2 residues processed: 239 average time/residue: 1.5647 time to fit residues: 427.5458 Evaluate side-chains 175 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 172 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain C residue 344 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.5980 chunk 120 optimal weight: 0.5980 chunk 66 optimal weight: 0.0770 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN C 423 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.166844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.134152 restraints weight = 35788.995| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.26 r_work: 0.3045 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12672 Z= 0.125 Angle : 0.480 4.620 17241 Z= 0.256 Chirality : 0.036 0.126 1989 Planarity : 0.003 0.040 2091 Dihedral : 9.148 140.857 1860 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.36 % Allowed : 9.86 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.21), residues: 1593 helix: 2.78 (0.14), residues: 1323 sheet: None (None), residues: 0 loop : -0.98 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 323 HIS 0.004 0.001 HIS B 288 PHE 0.013 0.001 PHE A 523 TYR 0.006 0.001 TYR A 309 ARG 0.003 0.000 ARG C 539 Details of bonding type rmsd hydrogen bonds : bond 0.04791 ( 967) hydrogen bonds : angle 4.25344 ( 2856) covalent geometry : bond 0.00248 (12672) covalent geometry : angle 0.47992 (17241) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.6605 (tp) cc_final: 0.6315 (mp) REVERT: A 307 MET cc_start: 0.8538 (mtm) cc_final: 0.8222 (mtp) REVERT: A 497 MET cc_start: 0.8191 (tmt) cc_final: 0.7190 (tmt) REVERT: A 583 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8194 (t) REVERT: A 598 MET cc_start: 0.8375 (tpp) cc_final: 0.7856 (tpt) REVERT: B 205 GLN cc_start: 0.7674 (mp10) cc_final: 0.7034 (mt0) REVERT: B 482 ASP cc_start: 0.8263 (t0) cc_final: 0.7978 (m-30) REVERT: B 497 MET cc_start: 0.8215 (tmt) cc_final: 0.7382 (tmt) REVERT: B 620 ASN cc_start: 0.8122 (p0) cc_final: 0.7853 (t0) REVERT: C 129 MET cc_start: 0.7149 (mtp) cc_final: 0.6825 (mtp) REVERT: C 329 MET cc_start: 0.8885 (mtp) cc_final: 0.8464 (mtm) REVERT: C 344 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.8006 (p90) REVERT: C 497 MET cc_start: 0.8056 (tmt) cc_final: 0.7521 (tmt) REVERT: C 583 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.8096 (t) outliers start: 17 outliers final: 5 residues processed: 188 average time/residue: 1.4461 time to fit residues: 315.1884 Evaluate side-chains 158 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 344 PHE Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 155 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 HIS B 508 GLN C 426 ASN C 508 GLN C 571 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.140936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.103812 restraints weight = 36615.071| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.50 r_work: 0.2852 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12672 Z= 0.180 Angle : 0.514 4.554 17241 Z= 0.280 Chirality : 0.037 0.115 1989 Planarity : 0.004 0.049 2091 Dihedral : 9.156 144.825 1860 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.84 % Allowed : 12.18 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.21), residues: 1593 helix: 2.42 (0.14), residues: 1326 sheet: None (None), residues: 0 loop : -1.14 (0.33), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 323 HIS 0.004 0.001 HIS B 226 PHE 0.018 0.002 PHE B 413 TYR 0.009 0.001 TYR C 494 ARG 0.003 0.001 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.06223 ( 967) hydrogen bonds : angle 4.27627 ( 2856) covalent geometry : bond 0.00415 (12672) covalent geometry : angle 0.51354 (17241) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 1.696 Fit side-chains REVERT: A 248 LEU cc_start: 0.6824 (tp) cc_final: 0.6447 (mp) REVERT: A 307 MET cc_start: 0.8546 (mtm) cc_final: 0.8214 (mtp) REVERT: A 430 MET cc_start: 0.8457 (mtt) cc_final: 0.8231 (mtt) REVERT: A 497 MET cc_start: 0.8212 (tmt) cc_final: 0.7198 (tmt) REVERT: A 583 THR cc_start: 0.8239 (OUTLIER) cc_final: 0.8029 (t) REVERT: A 598 MET cc_start: 0.8516 (tpp) cc_final: 0.8035 (tpt) REVERT: A 620 ASN cc_start: 0.7949 (p0) cc_final: 0.7564 (t0) REVERT: B 205 GLN cc_start: 0.7790 (mp10) cc_final: 0.6991 (mt0) REVERT: B 257 MET cc_start: 0.7460 (mmm) cc_final: 0.7151 (mtm) REVERT: B 284 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7327 (mtpp) REVERT: B 482 ASP cc_start: 0.8282 (t0) cc_final: 0.7883 (m-30) REVERT: B 583 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8166 (t) REVERT: B 620 ASN cc_start: 0.8154 (p0) cc_final: 0.7853 (t0) REVERT: C 189 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7401 (tm) REVERT: C 329 MET cc_start: 0.8814 (mtp) cc_final: 0.8528 (mtm) REVERT: C 344 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.8324 (p90) REVERT: C 470 MET cc_start: 0.8400 (ttm) cc_final: 0.8159 (ttm) REVERT: C 480 MET cc_start: 0.7834 (mmm) cc_final: 0.7569 (mtt) outliers start: 23 outliers final: 13 residues processed: 194 average time/residue: 1.7372 time to fit residues: 382.1527 Evaluate side-chains 182 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 344 PHE Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 447 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 65 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN B 315 GLN B 394 HIS B 508 GLN C 394 HIS C 508 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.153199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.124928 restraints weight = 37003.379| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.18 r_work: 0.2865 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12672 Z= 0.197 Angle : 0.521 4.798 17241 Z= 0.281 Chirality : 0.037 0.117 1989 Planarity : 0.004 0.057 2091 Dihedral : 9.109 145.028 1860 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.56 % Allowed : 14.10 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.21), residues: 1593 helix: 2.14 (0.14), residues: 1335 sheet: None (None), residues: 0 loop : -1.23 (0.32), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 184 HIS 0.004 0.001 HIS C 226 PHE 0.016 0.002 PHE A 413 TYR 0.010 0.001 TYR C 494 ARG 0.003 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.06215 ( 967) hydrogen bonds : angle 4.33246 ( 2856) covalent geometry : bond 0.00464 (12672) covalent geometry : angle 0.52080 (17241) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 1.967 Fit side-chains revert: symmetry clash REVERT: A 248 LEU cc_start: 0.7324 (tp) cc_final: 0.6938 (mp) REVERT: A 307 MET cc_start: 0.8618 (mtm) cc_final: 0.8341 (mtp) REVERT: A 344 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8307 (p90) REVERT: A 477 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7936 (tp) REVERT: A 497 MET cc_start: 0.8256 (tmt) cc_final: 0.7312 (tmt) REVERT: A 598 MET cc_start: 0.8639 (tpp) cc_final: 0.8118 (tpt) REVERT: B 205 GLN cc_start: 0.7926 (mp10) cc_final: 0.7234 (mt0) REVERT: B 257 MET cc_start: 0.7702 (mmm) cc_final: 0.7437 (mtm) REVERT: B 284 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7515 (mtpp) REVERT: B 482 ASP cc_start: 0.8424 (t0) cc_final: 0.7891 (m-30) REVERT: B 620 ASN cc_start: 0.8188 (p0) cc_final: 0.7905 (t0) REVERT: C 189 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7755 (tm) REVERT: C 329 MET cc_start: 0.8840 (mtp) cc_final: 0.8598 (mtm) REVERT: C 418 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6795 (pt0) REVERT: C 470 MET cc_start: 0.8442 (ttm) cc_final: 0.8173 (ttm) REVERT: C 497 MET cc_start: 0.8186 (tmt) cc_final: 0.7124 (tmt) REVERT: C 583 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8189 (t) outliers start: 32 outliers final: 12 residues processed: 190 average time/residue: 1.7693 time to fit residues: 382.0602 Evaluate side-chains 184 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 100 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN B 508 GLN C 508 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.155395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.125224 restraints weight = 36538.945| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.21 r_work: 0.2903 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12672 Z= 0.133 Angle : 0.455 4.423 17241 Z= 0.244 Chirality : 0.035 0.112 1989 Planarity : 0.004 0.052 2091 Dihedral : 8.529 141.956 1856 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.76 % Allowed : 14.98 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.21), residues: 1593 helix: 2.37 (0.15), residues: 1329 sheet: None (None), residues: 0 loop : -1.41 (0.31), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 323 HIS 0.002 0.001 HIS B 226 PHE 0.012 0.001 PHE C 413 TYR 0.006 0.001 TYR B 309 ARG 0.001 0.000 ARG C 355 Details of bonding type rmsd hydrogen bonds : bond 0.05206 ( 967) hydrogen bonds : angle 4.12543 ( 2856) covalent geometry : bond 0.00291 (12672) covalent geometry : angle 0.45475 (17241) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 1.820 Fit side-chains revert: symmetry clash REVERT: A 248 LEU cc_start: 0.7168 (tp) cc_final: 0.6804 (mp) REVERT: A 307 MET cc_start: 0.8551 (mtm) cc_final: 0.8335 (mtp) REVERT: A 344 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8358 (p90) REVERT: A 497 MET cc_start: 0.8237 (tmt) cc_final: 0.7291 (tmt) REVERT: A 598 MET cc_start: 0.8689 (tpp) cc_final: 0.8163 (tpt) REVERT: B 205 GLN cc_start: 0.7902 (mp10) cc_final: 0.7228 (mt0) REVERT: B 257 MET cc_start: 0.7574 (mmm) cc_final: 0.7309 (mtm) REVERT: B 329 MET cc_start: 0.8900 (mtp) cc_final: 0.8538 (mtp) REVERT: B 482 ASP cc_start: 0.8467 (t0) cc_final: 0.8041 (m-30) REVERT: B 583 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8419 (t) REVERT: C 189 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7795 (tm) REVERT: C 470 MET cc_start: 0.8426 (ttm) cc_final: 0.8169 (ttm) REVERT: C 583 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8312 (t) outliers start: 22 outliers final: 9 residues processed: 182 average time/residue: 1.7557 time to fit residues: 362.8375 Evaluate side-chains 179 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 588 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 6 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.152620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.117814 restraints weight = 36642.144| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.36 r_work: 0.2833 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12672 Z= 0.185 Angle : 0.503 4.586 17241 Z= 0.270 Chirality : 0.037 0.116 1989 Planarity : 0.004 0.056 2091 Dihedral : 8.683 144.663 1856 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.08 % Allowed : 15.54 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.21), residues: 1593 helix: 2.20 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -1.17 (0.30), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 178 HIS 0.004 0.001 HIS B 226 PHE 0.014 0.002 PHE B 413 TYR 0.008 0.001 TYR C 119 ARG 0.002 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.06088 ( 967) hydrogen bonds : angle 4.23954 ( 2856) covalent geometry : bond 0.00434 (12672) covalent geometry : angle 0.50343 (17241) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 1.791 Fit side-chains revert: symmetry clash REVERT: A 248 LEU cc_start: 0.7092 (tp) cc_final: 0.6705 (mp) REVERT: A 307 MET cc_start: 0.8566 (mtm) cc_final: 0.8361 (mtp) REVERT: A 344 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8290 (p90) REVERT: A 497 MET cc_start: 0.8211 (tmt) cc_final: 0.7241 (tmt) REVERT: A 598 MET cc_start: 0.8674 (tpp) cc_final: 0.8197 (tpt) REVERT: B 189 LEU cc_start: 0.7838 (tm) cc_final: 0.7605 (tt) REVERT: B 205 GLN cc_start: 0.7902 (mp10) cc_final: 0.7159 (mt0) REVERT: B 257 MET cc_start: 0.7624 (mmm) cc_final: 0.7370 (mtm) REVERT: B 284 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7394 (mtpp) REVERT: B 329 MET cc_start: 0.8940 (mtp) cc_final: 0.8617 (mtp) REVERT: B 482 ASP cc_start: 0.8324 (t0) cc_final: 0.7871 (m-30) REVERT: B 583 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8278 (t) REVERT: B 620 ASN cc_start: 0.8064 (p0) cc_final: 0.7729 (t0) REVERT: C 189 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7653 (tm) REVERT: C 284 LYS cc_start: 0.8419 (mttm) cc_final: 0.8128 (mtpp) REVERT: C 329 MET cc_start: 0.8796 (mtp) cc_final: 0.8547 (mtm) REVERT: C 470 MET cc_start: 0.8439 (ttm) cc_final: 0.8182 (ttm) REVERT: C 497 MET cc_start: 0.8180 (tmt) cc_final: 0.7130 (tmt) REVERT: C 583 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8117 (t) outliers start: 26 outliers final: 15 residues processed: 183 average time/residue: 1.7585 time to fit residues: 364.4694 Evaluate side-chains 186 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 588 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 111 optimal weight: 0.4980 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.154492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.118934 restraints weight = 36447.687| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.43 r_work: 0.2847 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12672 Z= 0.139 Angle : 0.460 4.440 17241 Z= 0.245 Chirality : 0.035 0.112 1989 Planarity : 0.004 0.053 2091 Dihedral : 8.485 141.434 1856 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.60 % Allowed : 16.11 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.21), residues: 1593 helix: 2.34 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -1.16 (0.30), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 178 HIS 0.003 0.001 HIS C 226 PHE 0.013 0.001 PHE C 413 TYR 0.005 0.001 TYR C 119 ARG 0.001 0.000 ARG C 557 Details of bonding type rmsd hydrogen bonds : bond 0.05275 ( 967) hydrogen bonds : angle 4.11267 ( 2856) covalent geometry : bond 0.00309 (12672) covalent geometry : angle 0.45967 (17241) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.7019 (tp) cc_final: 0.6670 (mp) REVERT: A 307 MET cc_start: 0.8492 (mtm) cc_final: 0.8263 (mtp) REVERT: A 497 MET cc_start: 0.8235 (tmt) cc_final: 0.7256 (tmt) REVERT: A 598 MET cc_start: 0.8708 (tpp) cc_final: 0.8233 (tpt) REVERT: B 189 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7595 (tt) REVERT: B 205 GLN cc_start: 0.7888 (mp10) cc_final: 0.7097 (mt0) REVERT: B 257 MET cc_start: 0.7516 (mmm) cc_final: 0.7246 (mtm) REVERT: B 284 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7310 (mtpp) REVERT: B 329 MET cc_start: 0.8945 (mtp) cc_final: 0.8647 (mtp) REVERT: B 482 ASP cc_start: 0.8345 (t0) cc_final: 0.7892 (m-30) REVERT: B 583 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8265 (t) REVERT: B 620 ASN cc_start: 0.8014 (p0) cc_final: 0.7678 (t0) REVERT: C 189 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7637 (tm) REVERT: C 284 LYS cc_start: 0.8396 (mttm) cc_final: 0.8124 (mtpp) REVERT: C 329 MET cc_start: 0.8797 (mtp) cc_final: 0.8560 (mtm) REVERT: C 470 MET cc_start: 0.8461 (ttm) cc_final: 0.8226 (ttm) REVERT: C 497 MET cc_start: 0.8189 (tmt) cc_final: 0.7104 (tmt) REVERT: C 583 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8166 (t) outliers start: 20 outliers final: 11 residues processed: 180 average time/residue: 1.7904 time to fit residues: 364.5740 Evaluate side-chains 182 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 588 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 116 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 86 optimal weight: 0.0030 chunk 146 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.136151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.099266 restraints weight = 37025.205| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.46 r_work: 0.2869 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12672 Z= 0.120 Angle : 0.441 4.394 17241 Z= 0.234 Chirality : 0.034 0.110 1989 Planarity : 0.004 0.051 2091 Dihedral : 8.270 139.110 1854 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.84 % Allowed : 16.03 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.21), residues: 1593 helix: 2.48 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -1.12 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 178 HIS 0.002 0.001 HIS C 226 PHE 0.010 0.001 PHE C 413 TYR 0.004 0.001 TYR B 309 ARG 0.001 0.000 ARG A 589 Details of bonding type rmsd hydrogen bonds : bond 0.04840 ( 967) hydrogen bonds : angle 4.00300 ( 2856) covalent geometry : bond 0.00258 (12672) covalent geometry : angle 0.44129 (17241) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.6935 (tp) cc_final: 0.6597 (mp) REVERT: A 307 MET cc_start: 0.8489 (mtm) cc_final: 0.8255 (mtp) REVERT: A 344 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.8284 (p90) REVERT: A 497 MET cc_start: 0.8227 (tmt) cc_final: 0.7229 (tmt) REVERT: A 598 MET cc_start: 0.8729 (tpp) cc_final: 0.8265 (tpt) REVERT: B 189 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7569 (tt) REVERT: B 205 GLN cc_start: 0.7854 (mp10) cc_final: 0.7070 (mt0) REVERT: B 257 MET cc_start: 0.7402 (mmm) cc_final: 0.7145 (mtm) REVERT: B 284 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7316 (mtpp) REVERT: B 482 ASP cc_start: 0.8343 (t0) cc_final: 0.7888 (m-30) REVERT: B 583 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8254 (t) REVERT: B 620 ASN cc_start: 0.7996 (p0) cc_final: 0.7626 (t0) REVERT: C 189 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7626 (tm) REVERT: C 284 LYS cc_start: 0.8374 (mttm) cc_final: 0.8116 (mtpp) REVERT: C 329 MET cc_start: 0.8791 (mtp) cc_final: 0.8550 (mtm) REVERT: C 418 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6648 (pt0) REVERT: C 470 MET cc_start: 0.8454 (ttm) cc_final: 0.8226 (ttm) REVERT: C 583 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8126 (t) outliers start: 23 outliers final: 12 residues processed: 184 average time/residue: 1.7638 time to fit residues: 369.3304 Evaluate side-chains 188 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 588 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 114 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 GLN B 347 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.133384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.096241 restraints weight = 37502.173| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.47 r_work: 0.2824 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12672 Z= 0.172 Angle : 0.489 4.509 17241 Z= 0.262 Chirality : 0.036 0.114 1989 Planarity : 0.004 0.055 2091 Dihedral : 8.524 142.405 1854 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.76 % Allowed : 16.27 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.21), residues: 1593 helix: 2.28 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -1.15 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 178 HIS 0.003 0.001 HIS C 226 PHE 0.014 0.001 PHE B 413 TYR 0.007 0.001 TYR C 119 ARG 0.002 0.000 ARG C 557 Details of bonding type rmsd hydrogen bonds : bond 0.05834 ( 967) hydrogen bonds : angle 4.15129 ( 2856) covalent geometry : bond 0.00402 (12672) covalent geometry : angle 0.48936 (17241) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.7089 (tp) cc_final: 0.6736 (mp) REVERT: A 307 MET cc_start: 0.8587 (mtm) cc_final: 0.8374 (mtp) REVERT: A 344 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8273 (p90) REVERT: A 497 MET cc_start: 0.8254 (tmt) cc_final: 0.7271 (tmt) REVERT: A 598 MET cc_start: 0.8721 (tpp) cc_final: 0.8235 (tpt) REVERT: B 189 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7622 (tt) REVERT: B 205 GLN cc_start: 0.7940 (mp10) cc_final: 0.7162 (mt0) REVERT: B 257 MET cc_start: 0.7627 (mmm) cc_final: 0.7362 (mtm) REVERT: B 284 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7316 (mtpp) REVERT: B 482 ASP cc_start: 0.8348 (t0) cc_final: 0.7894 (m-30) REVERT: B 497 MET cc_start: 0.8339 (tmt) cc_final: 0.7467 (tmt) REVERT: B 583 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8275 (t) REVERT: B 620 ASN cc_start: 0.8086 (p0) cc_final: 0.7666 (t0) REVERT: C 189 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7642 (tm) REVERT: C 284 LYS cc_start: 0.8381 (mttm) cc_final: 0.8116 (mtpp) REVERT: C 329 MET cc_start: 0.8813 (mtp) cc_final: 0.8582 (mtm) REVERT: C 418 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6705 (pt0) REVERT: C 470 MET cc_start: 0.8482 (ttm) cc_final: 0.8248 (ttm) REVERT: C 497 MET cc_start: 0.8153 (tmt) cc_final: 0.7090 (tmt) REVERT: C 583 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8176 (t) outliers start: 22 outliers final: 12 residues processed: 181 average time/residue: 1.8205 time to fit residues: 372.0438 Evaluate side-chains 187 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 588 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 90 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 110 optimal weight: 0.0370 chunk 157 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.137892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.101230 restraints weight = 36882.139| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.45 r_work: 0.2888 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12672 Z= 0.108 Angle : 0.434 4.481 17241 Z= 0.228 Chirality : 0.034 0.108 1989 Planarity : 0.004 0.050 2091 Dihedral : 8.093 137.090 1854 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.44 % Allowed : 16.67 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.22), residues: 1593 helix: 2.54 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -1.08 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 178 HIS 0.002 0.001 HIS C 226 PHE 0.008 0.001 PHE B 413 TYR 0.004 0.001 TYR B 216 ARG 0.001 0.000 ARG A 589 Details of bonding type rmsd hydrogen bonds : bond 0.04501 ( 967) hydrogen bonds : angle 3.95743 ( 2856) covalent geometry : bond 0.00226 (12672) covalent geometry : angle 0.43360 (17241) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 1.707 Fit side-chains revert: symmetry clash REVERT: A 248 LEU cc_start: 0.6904 (tp) cc_final: 0.6593 (mp) REVERT: A 307 MET cc_start: 0.8495 (mtm) cc_final: 0.8270 (mtp) REVERT: A 344 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8295 (p90) REVERT: A 497 MET cc_start: 0.8230 (tmt) cc_final: 0.7231 (tmt) REVERT: A 598 MET cc_start: 0.8704 (tpp) cc_final: 0.8223 (tpt) REVERT: B 189 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7598 (tt) REVERT: B 205 GLN cc_start: 0.7869 (mp10) cc_final: 0.7085 (mt0) REVERT: B 257 MET cc_start: 0.7372 (mmm) cc_final: 0.7149 (mtm) REVERT: B 284 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7324 (mtpp) REVERT: B 482 ASP cc_start: 0.8355 (t0) cc_final: 0.7927 (m-30) REVERT: B 583 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8253 (t) REVERT: B 620 ASN cc_start: 0.8043 (p0) cc_final: 0.7623 (t0) REVERT: C 189 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7656 (tm) REVERT: C 284 LYS cc_start: 0.8308 (mttm) cc_final: 0.8052 (mtpp) REVERT: C 329 MET cc_start: 0.8794 (mtp) cc_final: 0.8559 (mtm) REVERT: C 418 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6630 (pt0) REVERT: C 470 MET cc_start: 0.8431 (ttm) cc_final: 0.8229 (ttm) REVERT: C 497 MET cc_start: 0.8141 (tmt) cc_final: 0.7017 (tmt) REVERT: C 583 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.8136 (t) outliers start: 18 outliers final: 9 residues processed: 180 average time/residue: 1.8001 time to fit residues: 365.9729 Evaluate side-chains 183 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 588 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 68 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.137263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.100525 restraints weight = 37046.659| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.46 r_work: 0.2872 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12672 Z= 0.134 Angle : 0.457 4.544 17241 Z= 0.242 Chirality : 0.035 0.112 1989 Planarity : 0.004 0.052 2091 Dihedral : 8.113 138.047 1854 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.20 % Allowed : 17.55 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.21), residues: 1593 helix: 2.48 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -1.01 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 178 HIS 0.002 0.001 HIS B 226 PHE 0.013 0.001 PHE C 413 TYR 0.005 0.001 TYR B 119 ARG 0.001 0.000 ARG C 557 Details of bonding type rmsd hydrogen bonds : bond 0.05074 ( 967) hydrogen bonds : angle 4.01206 ( 2856) covalent geometry : bond 0.00298 (12672) covalent geometry : angle 0.45726 (17241) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13204.24 seconds wall clock time: 226 minutes 42.55 seconds (13602.55 seconds total)