Starting phenix.real_space_refine on Mon Sep 30 05:49:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz8_41737/09_2024/8tz8_41737_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz8_41737/09_2024/8tz8_41737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz8_41737/09_2024/8tz8_41737.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz8_41737/09_2024/8tz8_41737.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz8_41737/09_2024/8tz8_41737_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz8_41737/09_2024/8tz8_41737_trim.cif" } resolution = 3.19 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= 0.064 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 2 5.49 5 S 87 5.16 5 C 8179 2.51 5 N 1927 2.21 5 O 2130 1.98 5 H 12101 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-5461/modules/chem_data/mon_lib" Total number of atoms: 24426 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'LBN': 1, 'XMO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'XMO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'LBN': 1, 'XMO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 19 Time building chain proxies: 11.84, per 1000 atoms: 0.48 Number of scatterers: 24426 At special positions: 0 Unit cell: (131.76, 129.6, 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 2 15.00 O 2130 8.00 N 1927 7.00 C 8179 6.00 H 12101 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: 5.83 Conformation dependent library (CDL) restraints added in 1.9 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 1 sheets defined 88.0% alpha, 0.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 103 through 130 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: 4.813A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.968A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 251 removed outlier: 4.551A pdb=" N VAL A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 270 Processing helix chain 'A' and resid 272 through 282 removed outlier: 4.245A pdb=" N GLY A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 287 Processing helix chain 'A' and resid 288 through 312 removed outlier: 4.425A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 312 through 330 removed outlier: 3.690A pdb=" N VAL A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.638A pdb=" N ARG A 355 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 362 through 375 Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.544A pdb=" N TYR A 385 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 414 removed outlier: 4.222A 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 479 removed outlier: 3.816A pdb=" N SER A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'A' and resid 487 through 496 Processing helix chain 'A' and resid 496 through 503 Processing helix chain 'A' and resid 506 through 523 removed outlier: 4.272A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 removed outlier: 4.108A 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 572 through 586 removed outlier: 4.350A pdb=" N GLY A 576 " --> pdb=" O PHE A 572 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 619 removed outlier: 3.793A pdb=" N ALA A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N MET A 598 " --> pdb=" O THR A 594 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ARG A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 618 " --> pdb=" O ILE A 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 103 Processing helix chain 'B' and resid 103 through 130 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: 4.655A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 223 removed outlier: 3.681A pdb=" N LEU B 207 " --> pdb=" O GLY B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 250 removed outlier: 4.550A pdb=" N VAL B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 271 Processing helix chain 'B' and resid 272 through 282 removed outlier: 4.198A pdb=" N GLY B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 312 removed outlier: 4.588A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Proline residue: B 296 - end of helix Processing helix chain 'B' and resid 312 through 329 removed outlier: 3.630A pdb=" N TRP B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET B 325 " --> pdb=" O VAL B 321 " (cutoff:3.500A) 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: 3.764A pdb=" N THR B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 388 removed outlier: 3.736A pdb=" N LEU B 382 " --> pdb=" O ALA B 378 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 414 removed outlier: 4.195A 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 448 Processing helix chain 'B' and resid 449 through 479 Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.621A pdb=" N TYR B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 504 removed outlier: 3.597A pdb=" N ALA B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY B 504 " --> pdb=" O ALA B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 523 removed outlier: 4.125A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 542 removed outlier: 3.931A 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 574 through 586 removed outlier: 3.613A pdb=" N VAL B 578 " --> pdb=" O SER B 574 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 584 " --> pdb=" O GLY B 580 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET B 585 " --> pdb=" O GLY B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 596 removed outlier: 3.616A pdb=" N THR B 594 " --> pdb=" O LYS B 590 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 596 " --> pdb=" O ASP B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 619 Processing helix chain 'C' and resid 91 through 103 Processing helix chain 'C' and resid 103 through 130 Processing helix chain 'C' and resid 130 through 157 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 157 through 198 Proline residue: C 167 - end of helix removed outlier: 4.430A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 203 through 223 removed outlier: 3.871A pdb=" N LEU C 207 " --> pdb=" O GLY C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 252 removed outlier: 3.709A pdb=" N GLY C 238 " --> pdb=" O PRO C 234 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 271 through 281 removed outlier: 4.020A pdb=" N ALA C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL C 280 " --> pdb=" O GLY C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 287 Processing helix chain 'C' and resid 288 through 312 removed outlier: 4.220A pdb=" N LEU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Proline residue: C 296 - end of helix Processing helix chain 'C' and resid 312 through 330 removed outlier: 3.855A pdb=" N VAL C 324 " --> pdb=" O LYS C 320 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET C 325 " --> pdb=" O VAL C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 342 Processing helix chain 'C' and resid 349 through 361 removed outlier: 3.573A pdb=" N ARG C 355 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Proline residue: C 356 - end of helix Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 362 through 375 removed outlier: 3.828A pdb=" N GLY C 373 " --> pdb=" O ILE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 388 removed outlier: 3.965A pdb=" N GLY C 383 " --> pdb=" O GLY C 379 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 414 Proline residue: C 404 - end of helix removed outlier: 3.850A pdb=" N LEU C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 429 Processing helix chain 'C' and resid 437 through 449 removed outlier: 3.908A pdb=" N SER C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 480 removed outlier: 3.816A pdb=" N MET C 480 " --> pdb=" O TRP C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.573A 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: 4.173A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 542 removed outlier: 3.908A 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 573 through 586 removed outlier: 4.558A pdb=" N ILE C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 618 removed outlier: 3.600A pdb=" N THR C 594 " --> pdb=" O LYS C 590 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N MET C 598 " --> pdb=" O THR C 594 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ARG C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 600 " --> pdb=" O GLY C 596 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 546 through 547 964 hydrogen bonds defined for protein. 2850 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: 8.18 Time building geometry restraints manager: 7.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 12083 1.01 - 1.21: 28 1.21 - 1.41: 5215 1.41 - 1.61: 7272 1.61 - 1.81: 163 Bond restraints: 24761 Sorted by residual: bond pdb=" C11 XMO A 801 " pdb=" O12 XMO A 801 " ideal model delta sigma weight residual 1.398 1.681 -0.283 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 1.677 -0.279 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C11 XMO B 801 " pdb=" O12 XMO B 801 " ideal model delta sigma weight residual 1.398 1.676 -0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" C10 XMO C 801 " pdb=" C11 XMO C 801 " ideal model delta sigma weight residual 1.534 1.289 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C10 XMO B 801 " pdb=" C11 XMO B 801 " ideal model delta sigma weight residual 1.534 1.289 0.245 2.00e-02 2.50e+03 1.49e+02 ... (remaining 24756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 44504 3.22 - 6.44: 97 6.44 - 9.66: 10 9.66 - 12.88: 2 12.88 - 16.11: 2 Bond angle restraints: 44615 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 93.45 109.56 -16.11 3.00e+00 1.11e-01 2.88e+01 angle pdb=" O1 LBN A 802 " pdb=" P1 LBN A 802 " pdb=" O2 LBN A 802 " ideal model delta sigma weight residual 93.45 109.49 -16.04 3.00e+00 1.11e-01 2.86e+01 angle pdb=" O3 LBN C 802 " pdb=" P1 LBN C 802 " pdb=" O4 LBN C 802 " ideal model delta sigma weight residual 119.36 109.56 9.80 3.00e+00 1.11e-01 1.07e+01 angle pdb=" O3 LBN A 802 " pdb=" P1 LBN A 802 " pdb=" O4 LBN A 802 " ideal model delta sigma weight residual 119.36 109.64 9.72 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C02 XMO B 801 " pdb=" C04 XMO B 801 " pdb=" O06 XMO B 801 " ideal model delta sigma weight residual 111.45 120.15 -8.70 3.00e+00 1.11e-01 8.40e+00 ... (remaining 44610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.98: 11444 32.98 - 65.96: 362 65.96 - 98.94: 15 98.94 - 131.92: 4 131.92 - 164.89: 4 Dihedral angle restraints: 11829 sinusoidal: 6099 harmonic: 5730 Sorted by residual: dihedral pdb=" C01 XMO C 801 " pdb=" C02 XMO C 801 " pdb=" C04 XMO C 801 " pdb=" O06 XMO C 801 " ideal model delta sinusoidal sigma weight residual 296.92 132.03 164.89 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C01 XMO C 801 " pdb=" C02 XMO C 801 " pdb=" C04 XMO C 801 " pdb=" O05 XMO C 801 " ideal model delta sinusoidal sigma weight residual 116.78 -47.37 164.15 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C01 XMO B 801 " pdb=" C02 XMO B 801 " pdb=" C04 XMO B 801 " pdb=" O06 XMO B 801 " ideal model delta sinusoidal sigma weight residual 296.92 148.56 148.36 1 3.00e+01 1.11e-03 1.97e+01 ... (remaining 11826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1873 0.074 - 0.148: 114 0.148 - 0.222: 1 0.222 - 0.296: 0 0.296 - 0.369: 3 Chirality restraints: 1991 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 2.37 0.37 2.00e-01 2.50e+01 3.41e+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 2.38 0.36 2.00e-01 2.50e+01 3.26e+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 2.42 0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 1988 not shown) Planarity restraints: 3631 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 290 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C PHE C 290 " 0.033 2.00e-02 2.50e+03 pdb=" O PHE C 290 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA C 291 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 599 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" C ARG A 599 " 0.032 2.00e-02 2.50e+03 pdb=" O ARG A 599 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA A 600 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 608 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C CYS A 608 " -0.031 2.00e-02 2.50e+03 pdb=" O CYS A 608 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE A 609 " 0.010 2.00e-02 2.50e+03 ... (remaining 3628 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 901 2.18 - 2.79: 46951 2.79 - 3.39: 67449 3.39 - 4.00: 83999 4.00 - 4.60: 133737 Nonbonded interactions: 333037 Sorted by model distance: nonbonded pdb=" OE1 GLN A 206 " pdb=" H GLN A 206 " model vdw 1.580 2.450 nonbonded pdb=" O SER A 451 " pdb="HD22 ASN A 455 " model vdw 1.588 2.450 nonbonded pdb=" H ARG A 436 " pdb=" OE1 GLU A 440 " model vdw 1.593 2.450 nonbonded pdb=" OE1 GLU A 525 " pdb=" H GLU A 525 " model vdw 1.597 2.450 nonbonded pdb=" O LEU C 248 " pdb=" HG1 THR C 252 " model vdw 1.608 2.450 ... (remaining 333032 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 90 through 104 or (resid 105 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 106 or (resid 107 thro \ ugh 110 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 111 through 113 or (resid 114 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 115 through 176 or (resid 17 \ 7 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 178 through 420 or (resid 421 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 422 through 435 or (resid 436 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 437 through 622 or resid 801)) selection = (chain 'B' and (resid 90 through 162 or (resid 163 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 164 through 433 or (re \ sid 434 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 435 through 609 or (resid 610 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 611 through 622 or resid 801 \ )) selection = (chain 'C' and (resid 90 through 162 or (resid 163 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 164 through 433 or (re \ sid 434 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 435 through 609 or (resid 610 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 611 through 622 or resid 801 \ )) } 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: 1.660 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: 0.430 Extract box with map and model: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 48.720 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.070 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 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 0.283 12660 Z= 0.614 Angle : 0.622 16.106 17229 Z= 0.301 Chirality : 0.039 0.369 1991 Planarity : 0.004 0.039 2089 Dihedral : 13.771 164.894 4351 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: 2.71 (0.21), residues: 1593 helix: 2.31 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -0.55 (0.31), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.002 0.001 HIS A 288 PHE 0.018 0.001 PHE C 413 TYR 0.009 0.001 TYR A 357 ARG 0.002 0.000 ARG B 319 *********************** 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 TYR 109 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 LEU 610 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 302 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 TRP cc_start: 0.6533 (m100) cc_final: 0.6121 (m100) REVERT: A 264 LYS cc_start: 0.7884 (mttt) cc_final: 0.7602 (mtpt) REVERT: A 345 ILE cc_start: 0.8286 (mm) cc_final: 0.8057 (mp) REVERT: A 350 SER cc_start: 0.8346 (t) cc_final: 0.8088 (t) REVERT: A 497 MET cc_start: 0.7602 (tmm) cc_final: 0.7320 (tmm) REVERT: B 370 MET cc_start: 0.7987 (mtm) cc_final: 0.7731 (mtp) REVERT: B 458 VAL cc_start: 0.8301 (t) cc_final: 0.8020 (t) REVERT: B 585 MET cc_start: 0.8711 (mtt) cc_final: 0.8457 (mtt) REVERT: C 242 GLN cc_start: 0.8341 (mt0) cc_final: 0.8117 (mt0) REVERT: C 357 TYR cc_start: 0.8340 (m-80) cc_final: 0.8100 (m-80) REVERT: C 370 MET cc_start: 0.8805 (mtm) cc_final: 0.8569 (mtm) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.4809 time to fit residues: 213.4313 Evaluate side-chains 220 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12660 Z= 0.172 Angle : 0.477 5.317 17229 Z= 0.252 Chirality : 0.035 0.138 1991 Planarity : 0.003 0.046 2089 Dihedral : 10.217 165.530 1827 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.36 % Allowed : 7.98 % Favored : 90.66 % 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: 3.26 (0.21), residues: 1593 helix: 2.64 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : -0.35 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 184 HIS 0.002 0.001 HIS A 132 PHE 0.016 0.001 PHE C 413 TYR 0.011 0.001 TYR A 357 ARG 0.004 0.000 ARG B 589 *********************** 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 TYR 109 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 LEU 610 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 238 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 221 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 TRP cc_start: 0.6601 (m100) cc_final: 0.6092 (m100) REVERT: A 264 LYS cc_start: 0.7948 (mttt) cc_final: 0.7696 (mtpt) REVERT: A 342 ASN cc_start: 0.8766 (t0) cc_final: 0.8565 (m-40) REVERT: A 428 MET cc_start: 0.8075 (mmt) cc_final: 0.7758 (mmt) REVERT: A 497 MET cc_start: 0.7474 (tmm) cc_final: 0.7184 (tmm) REVERT: B 158 GLU cc_start: 0.7278 (pm20) cc_final: 0.6980 (pm20) REVERT: B 202 LEU cc_start: 0.8743 (mp) cc_final: 0.8500 (mt) REVERT: B 242 GLN cc_start: 0.8285 (mt0) cc_final: 0.7949 (mt0) REVERT: B 370 MET cc_start: 0.7844 (mtm) cc_final: 0.7519 (mtp) REVERT: B 458 VAL cc_start: 0.8320 (t) cc_final: 0.8023 (t) REVERT: B 485 GLN cc_start: 0.8353 (mp10) cc_final: 0.8130 (mp10) REVERT: B 503 MET cc_start: 0.9035 (mtp) cc_final: 0.8708 (mtp) REVERT: B 598 MET cc_start: 0.7503 (tpt) cc_final: 0.7149 (tpt) REVERT: C 219 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7742 (mp) REVERT: C 357 TYR cc_start: 0.8350 (m-80) cc_final: 0.8107 (m-80) outliers start: 17 outliers final: 10 residues processed: 229 average time/residue: 0.4646 time to fit residues: 163.1026 Evaluate side-chains 217 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 206 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 458 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12660 Z= 0.185 Angle : 0.453 5.057 17229 Z= 0.239 Chirality : 0.035 0.151 1991 Planarity : 0.003 0.045 2089 Dihedral : 8.565 119.811 1827 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.36 % Allowed : 8.22 % Favored : 90.42 % 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: 3.34 (0.21), residues: 1593 helix: 2.71 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -0.44 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 316 HIS 0.003 0.000 HIS A 288 PHE 0.017 0.001 PHE C 413 TYR 0.011 0.001 TYR B 231 ARG 0.002 0.000 ARG B 355 *********************** 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 TYR 109 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 LEU 610 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 223 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 206 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 TRP cc_start: 0.6643 (m100) cc_final: 0.6078 (m100) REVERT: A 264 LYS cc_start: 0.7930 (mttt) cc_final: 0.7684 (mtpt) REVERT: A 342 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8581 (m-40) REVERT: A 428 MET cc_start: 0.8077 (mmt) cc_final: 0.7681 (mmt) REVERT: A 430 MET cc_start: 0.8067 (mtt) cc_final: 0.7853 (mtt) REVERT: A 480 MET cc_start: 0.8183 (mmt) cc_final: 0.7698 (mmt) REVERT: A 497 MET cc_start: 0.7645 (tmm) cc_final: 0.7409 (tmm) REVERT: B 157 TYR cc_start: 0.7492 (m-10) cc_final: 0.7273 (m-80) REVERT: B 158 GLU cc_start: 0.7365 (pm20) cc_final: 0.7006 (pm20) REVERT: B 370 MET cc_start: 0.7885 (mtm) cc_final: 0.7535 (mtp) REVERT: B 444 GLN cc_start: 0.6911 (mm-40) cc_final: 0.6702 (tt0) REVERT: B 458 VAL cc_start: 0.8335 (t) cc_final: 0.8046 (t) REVERT: B 598 MET cc_start: 0.7499 (tpt) cc_final: 0.7033 (tpt) REVERT: C 219 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7830 (mp) REVERT: C 257 MET cc_start: 0.6872 (ptt) cc_final: 0.6492 (ptp) REVERT: C 357 TYR cc_start: 0.8325 (m-80) cc_final: 0.8106 (m-80) outliers start: 17 outliers final: 10 residues processed: 216 average time/residue: 0.4407 time to fit residues: 146.5066 Evaluate side-chains 204 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 75 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12660 Z= 0.234 Angle : 0.472 5.115 17229 Z= 0.252 Chirality : 0.036 0.205 1991 Planarity : 0.004 0.046 2089 Dihedral : 8.050 93.640 1827 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.28 % Allowed : 9.10 % Favored : 89.62 % 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: 3.18 (0.21), residues: 1593 helix: 2.62 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.52 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 181 HIS 0.003 0.001 HIS A 288 PHE 0.020 0.001 PHE C 413 TYR 0.011 0.001 TYR A 357 ARG 0.003 0.000 ARG B 251 *********************** 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 TYR 109 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 LEU 610 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 215 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 199 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7960 (mttt) cc_final: 0.7680 (mtpt) REVERT: A 428 MET cc_start: 0.8161 (mmt) cc_final: 0.7734 (mmt) REVERT: B 158 GLU cc_start: 0.7534 (pm20) cc_final: 0.6891 (pm20) REVERT: B 370 MET cc_start: 0.7929 (mtm) cc_final: 0.7632 (mtp) REVERT: B 503 MET cc_start: 0.9026 (mtp) cc_final: 0.8646 (mtp) REVERT: B 598 MET cc_start: 0.7581 (tpt) cc_final: 0.7075 (tpt) REVERT: C 219 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7901 (mp) REVERT: C 257 MET cc_start: 0.6953 (ptt) cc_final: 0.6580 (ptp) outliers start: 16 outliers final: 12 residues processed: 210 average time/residue: 0.4397 time to fit residues: 140.6074 Evaluate side-chains 203 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 190 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 78 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12660 Z= 0.282 Angle : 0.489 5.180 17229 Z= 0.265 Chirality : 0.036 0.150 1991 Planarity : 0.004 0.048 2089 Dihedral : 8.101 96.293 1827 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.28 % Allowed : 10.69 % Favored : 88.03 % 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: 2.96 (0.21), residues: 1593 helix: 2.46 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : -0.49 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 150 HIS 0.004 0.001 HIS A 288 PHE 0.018 0.001 PHE B 413 TYR 0.013 0.001 TYR A 357 ARG 0.002 0.000 ARG A 436 *********************** 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 TYR 109 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 LEU 610 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 207 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 191 time to evaluate : 1.793 Fit side-chains revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8044 (mttt) cc_final: 0.7754 (mtpt) REVERT: B 158 GLU cc_start: 0.7609 (pm20) cc_final: 0.6863 (pm20) REVERT: B 370 MET cc_start: 0.8034 (mtm) cc_final: 0.7603 (mtp) REVERT: B 503 MET cc_start: 0.9042 (mtp) cc_final: 0.8654 (mtp) REVERT: B 598 MET cc_start: 0.7679 (tpt) cc_final: 0.7187 (tpt) REVERT: C 219 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7928 (mp) REVERT: C 257 MET cc_start: 0.6921 (ptt) cc_final: 0.6550 (ptp) outliers start: 16 outliers final: 11 residues processed: 203 average time/residue: 0.4247 time to fit residues: 132.5475 Evaluate side-chains 196 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 184 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 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 160 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12660 Z= 0.287 Angle : 0.493 5.495 17229 Z= 0.266 Chirality : 0.036 0.152 1991 Planarity : 0.004 0.050 2089 Dihedral : 7.824 91.675 1827 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.12 % Allowed : 11.73 % Favored : 87.15 % 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: 2.35 (0.14), residues: 1310 sheet: None (None), residues: 0 loop : -0.51 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 178 HIS 0.004 0.001 HIS A 288 PHE 0.018 0.001 PHE C 413 TYR 0.013 0.001 TYR A 357 ARG 0.002 0.000 ARG A 436 *********************** 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 TYR 109 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 LEU 610 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 209 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 195 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8060 (mttt) cc_final: 0.7774 (mtpt) REVERT: A 421 LYS cc_start: 0.8072 (mttm) cc_final: 0.7859 (mtpt) REVERT: A 428 MET cc_start: 0.8198 (mmt) cc_final: 0.7769 (mmt) REVERT: B 112 TRP cc_start: 0.6233 (t60) cc_final: 0.5732 (t-100) REVERT: B 158 GLU cc_start: 0.7801 (pm20) cc_final: 0.7105 (pm20) REVERT: B 370 MET cc_start: 0.8065 (mtm) cc_final: 0.7623 (mtp) REVERT: B 503 MET cc_start: 0.9014 (mtp) cc_final: 0.8630 (mtp) REVERT: B 598 MET cc_start: 0.7676 (tpt) cc_final: 0.7189 (tpt) REVERT: C 219 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7979 (mp) REVERT: C 257 MET cc_start: 0.6935 (ptt) cc_final: 0.6579 (ptp) REVERT: C 413 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8359 (t80) outliers start: 14 outliers final: 12 residues processed: 206 average time/residue: 0.4362 time to fit residues: 137.8321 Evaluate side-chains 205 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 191 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12660 Z= 0.200 Angle : 0.458 5.070 17229 Z= 0.244 Chirality : 0.035 0.139 1991 Planarity : 0.004 0.050 2089 Dihedral : 7.476 82.586 1827 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.04 % Allowed : 12.69 % Favored : 86.27 % 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: 3.04 (0.21), residues: 1593 helix: 2.52 (0.15), residues: 1311 sheet: None (None), residues: 0 loop : -0.50 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 184 HIS 0.003 0.001 HIS A 288 PHE 0.013 0.001 PHE C 413 TYR 0.011 0.001 TYR A 357 ARG 0.001 0.000 ARG A 355 *********************** 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 TYR 109 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 LEU 610 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 212 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 199 time to evaluate : 1.702 Fit side-chains revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7968 (mttt) cc_final: 0.7688 (mtpt) REVERT: A 421 LYS cc_start: 0.8053 (mttm) cc_final: 0.7811 (mtpt) REVERT: A 428 MET cc_start: 0.8139 (mmt) cc_final: 0.7698 (mmt) REVERT: A 562 SER cc_start: 0.8482 (m) cc_final: 0.8251 (m) REVERT: B 112 TRP cc_start: 0.6202 (t60) cc_final: 0.5738 (t-100) REVERT: B 158 GLU cc_start: 0.7858 (pm20) cc_final: 0.7155 (pm20) REVERT: B 370 MET cc_start: 0.8003 (mtm) cc_final: 0.7730 (mtp) REVERT: B 598 MET cc_start: 0.7556 (tpt) cc_final: 0.7033 (tpt) REVERT: C 219 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.8012 (mp) REVERT: C 257 MET cc_start: 0.6929 (ptt) cc_final: 0.6575 (ptp) REVERT: C 485 GLN cc_start: 0.8576 (mp10) cc_final: 0.8314 (mp10) outliers start: 13 outliers final: 11 residues processed: 210 average time/residue: 0.4402 time to fit residues: 142.0947 Evaluate side-chains 203 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 191 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12660 Z= 0.174 Angle : 0.444 5.012 17229 Z= 0.235 Chirality : 0.034 0.133 1991 Planarity : 0.003 0.048 2089 Dihedral : 7.311 79.620 1827 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.96 % Allowed : 12.61 % Favored : 86.43 % 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: 3.21 (0.21), residues: 1593 helix: 2.64 (0.15), residues: 1309 sheet: None (None), residues: 0 loop : -0.45 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 184 HIS 0.002 0.000 HIS A 288 PHE 0.013 0.001 PHE C 413 TYR 0.010 0.001 TYR A 357 ARG 0.001 0.000 ARG B 589 *********************** 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 TYR 109 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 LEU 610 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 211 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 199 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7974 (mttt) cc_final: 0.7713 (mtpt) REVERT: A 421 LYS cc_start: 0.8055 (mttm) cc_final: 0.7835 (mtpt) REVERT: A 428 MET cc_start: 0.8201 (mmt) cc_final: 0.7698 (mmt) REVERT: A 613 CYS cc_start: 0.7106 (m) cc_final: 0.6758 (m) REVERT: B 112 TRP cc_start: 0.6177 (t60) cc_final: 0.5800 (t-100) REVERT: B 158 GLU cc_start: 0.7874 (pm20) cc_final: 0.7153 (pm20) REVERT: B 370 MET cc_start: 0.7955 (mtm) cc_final: 0.7660 (mtp) REVERT: B 503 MET cc_start: 0.8946 (mtp) cc_final: 0.8603 (mtp) REVERT: B 598 MET cc_start: 0.7532 (tpt) cc_final: 0.7039 (tpt) REVERT: C 257 MET cc_start: 0.7060 (ptt) cc_final: 0.6714 (ptp) REVERT: C 413 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8387 (t80) REVERT: C 485 GLN cc_start: 0.8464 (mp10) cc_final: 0.8230 (mp10) outliers start: 12 outliers final: 10 residues processed: 210 average time/residue: 0.4675 time to fit residues: 151.7040 Evaluate side-chains 205 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 194 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 112 optimal weight: 0.0030 chunk 43 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12660 Z= 0.142 Angle : 0.426 5.155 17229 Z= 0.223 Chirality : 0.034 0.130 1991 Planarity : 0.003 0.048 2089 Dihedral : 7.077 77.822 1827 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.72 % Allowed : 13.09 % Favored : 86.19 % 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: 3.51 (0.22), residues: 1593 helix: 2.85 (0.15), residues: 1311 sheet: None (None), residues: 0 loop : -0.41 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 184 HIS 0.002 0.000 HIS A 288 PHE 0.009 0.001 PHE C 413 TYR 0.009 0.001 TYR A 357 ARG 0.001 0.000 ARG A 355 *********************** 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 TYR 109 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 LEU 610 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 fitting. rotamer outliers: 9 poor density : 193 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7962 (mttt) cc_final: 0.7708 (mtpt) REVERT: A 421 LYS cc_start: 0.8050 (mttm) cc_final: 0.7841 (mtpt) REVERT: A 428 MET cc_start: 0.8200 (mmt) cc_final: 0.7655 (mmt) REVERT: A 613 CYS cc_start: 0.6999 (m) cc_final: 0.6672 (m) REVERT: B 112 TRP cc_start: 0.6152 (t60) cc_final: 0.5947 (t-100) REVERT: B 370 MET cc_start: 0.7880 (mtm) cc_final: 0.7564 (mtp) REVERT: B 458 VAL cc_start: 0.8365 (t) cc_final: 0.8074 (t) REVERT: B 598 MET cc_start: 0.7459 (tpt) cc_final: 0.6991 (tpt) REVERT: C 257 MET cc_start: 0.7015 (ptt) cc_final: 0.6661 (ptp) REVERT: C 485 GLN cc_start: 0.8318 (mp10) cc_final: 0.8083 (mp10) outliers start: 9 outliers final: 8 residues processed: 201 average time/residue: 0.4601 time to fit residues: 142.6522 Evaluate side-chains 196 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 188 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 145 optimal weight: 0.0870 chunk 126 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12660 Z= 0.169 Angle : 0.441 5.459 17229 Z= 0.231 Chirality : 0.034 0.133 1991 Planarity : 0.003 0.049 2089 Dihedral : 7.098 77.720 1827 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.64 % Allowed : 13.57 % Favored : 85.79 % 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: 3.47 (0.22), residues: 1593 helix: 2.81 (0.15), residues: 1313 sheet: None (None), residues: 0 loop : -0.38 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 184 HIS 0.003 0.000 HIS A 288 PHE 0.012 0.001 PHE C 413 TYR 0.010 0.001 TYR A 357 ARG 0.001 0.000 ARG B 539 ********************** 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 TYR 109 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 LEU 610 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 204 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 196 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7976 (mttt) cc_final: 0.7699 (mtpt) REVERT: A 421 LYS cc_start: 0.8072 (mttm) cc_final: 0.7851 (mtpt) REVERT: A 613 CYS cc_start: 0.7056 (m) cc_final: 0.6719 (m) REVERT: B 158 GLU cc_start: 0.7902 (pm20) cc_final: 0.7221 (pm20) REVERT: B 370 MET cc_start: 0.7897 (mtm) cc_final: 0.7586 (mtp) REVERT: B 598 MET cc_start: 0.7521 (tpt) cc_final: 0.7049 (tpt) REVERT: C 257 MET cc_start: 0.7066 (ptt) cc_final: 0.6718 (ptp) REVERT: C 485 GLN cc_start: 0.8374 (mp10) cc_final: 0.8118 (mp10) outliers start: 8 outliers final: 8 residues processed: 203 average time/residue: 0.4559 time to fit residues: 142.5416 Evaluate side-chains 201 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 193 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 110 optimal weight: 0.1980 chunk 7 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.143424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108716 restraints weight = 41655.849| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.99 r_work: 0.3123 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12660 Z= 0.142 Angle : 0.429 5.626 17229 Z= 0.223 Chirality : 0.034 0.129 1991 Planarity : 0.003 0.048 2089 Dihedral : 6.990 77.005 1827 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.96 % Allowed : 13.49 % Favored : 85.55 % 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: 3.62 (0.22), residues: 1593 helix: 2.91 (0.15), residues: 1315 sheet: None (None), residues: 0 loop : -0.32 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 184 HIS 0.002 0.000 HIS A 288 PHE 0.016 0.001 PHE B 279 TYR 0.009 0.001 TYR A 357 ARG 0.001 0.000 ARG A 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5119.96 seconds wall clock time: 89 minutes 49.82 seconds (5389.82 seconds total)