Starting phenix.real_space_refine on Tue Mar 3 21:43:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jt1_9884/03_2026/6jt1_9884.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jt1_9884/03_2026/6jt1_9884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6jt1_9884/03_2026/6jt1_9884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jt1_9884/03_2026/6jt1_9884.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jt1_9884/03_2026/6jt1_9884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jt1_9884/03_2026/6jt1_9884.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 59 5.16 5 C 5529 2.51 5 N 1462 2.21 5 O 1551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8602 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4087 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 542, 4084 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 515} Chain breaks: 5 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 18, 'PHE:plan': 3, 'GLN:plan1': 6, 'ASP:plan': 8, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 166 Conformer: "B" Number of residues, atoms: 542, 4084 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 515} Chain breaks: 5 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 18, 'PHE:plan': 3, 'GLN:plan1': 6, 'ASP:plan': 8, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 166 bond proxies already assigned to first conformer: 4165 Chain: "B" Number of atoms: 4472 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 576, 4468 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552} Chain breaks: 2 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 114 Planarities with less than four sites: {'GLU:plan': 16, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 Conformer: "B" Number of residues, atoms: 576, 4468 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552} Chain breaks: 2 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 114 Planarities with less than four sites: {'GLU:plan': 16, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 bond proxies already assigned to first conformer: 4553 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLU A 147 " occ=0.91 ... (3 atoms not shown) pdb=" CB GLU A 147 " occ=0.91 Time building chain proxies: 3.70, per 1000 atoms: 0.43 Number of scatterers: 8602 At special positions: 0 Unit cell: (148.39, 93.005, 73.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 59 16.00 O 1551 8.00 N 1462 7.00 C 5529 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 823.5 milliseconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 10 sheets defined 49.1% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 70 through 83 Processing helix chain 'A' and resid 85 through 101 Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 128 through 149 removed outlier: 3.640A pdb=" N ASP A 148 " --> pdb=" O CYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 158 through 174 removed outlier: 4.596A pdb=" N SER A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 228 removed outlier: 4.285A pdb=" N ILE A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 237 through 242 removed outlier: 4.097A pdb=" N HIS A 241 " --> pdb=" O PRO A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 286 Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.817A pdb=" N TYR A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 319 through 323' Processing helix chain 'A' and resid 334 through 341 removed outlier: 4.038A pdb=" N MET A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 394 removed outlier: 3.934A pdb=" N THR A 394 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 419 removed outlier: 4.472A pdb=" N GLY A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU A 417 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 425 removed outlier: 4.509A pdb=" N LEU A 425 " --> pdb=" O GLN A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 458 removed outlier: 3.930A pdb=" N GLY A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 468 removed outlier: 3.616A pdb=" N GLN A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 496 removed outlier: 3.800A pdb=" N ILE A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 521 Processing helix chain 'A' and resid 544 through 561 Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.978A pdb=" N THR A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 627 removed outlier: 4.193A pdb=" N LEU A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 30 removed outlier: 3.673A pdb=" N ASN B 6 " --> pdb=" O TYR B 2 " (cutoff:3.500A) Proline residue: B 19 - end of helix removed outlier: 3.929A pdb=" N TRP B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.938A pdb=" N THR B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 81 Processing helix chain 'B' and resid 83 through 90 Processing helix chain 'B' and resid 93 through 100 Processing helix chain 'B' and resid 102 through 112 removed outlier: 3.809A pdb=" N ILE B 111 " --> pdb=" O HIS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 157 Processing helix chain 'B' and resid 210 through 217 Processing helix chain 'B' and resid 233 through 240 Processing helix chain 'B' and resid 241 through 244 Processing helix chain 'B' and resid 264 through 271 Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.734A pdb=" N LEU B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 354 removed outlier: 4.183A pdb=" N ASP B 351 " --> pdb=" O ASP B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 395 removed outlier: 4.375A pdb=" N TYR B 363 " --> pdb=" O PHE B 359 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 378 " --> pdb=" O ASP B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 407 Processing helix chain 'B' and resid 429 through 437 removed outlier: 3.579A pdb=" N HIS B 437 " --> pdb=" O PHE B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 461 removed outlier: 3.802A pdb=" N LYS B 445 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 508 removed outlier: 4.012A pdb=" N GLY B 508 " --> pdb=" O MET B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 557 removed outlier: 3.972A pdb=" N ASN B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 573 Processing sheet with id=AA1, first strand: chain 'A' and resid 189 through 193 removed outlier: 4.034A pdb=" N SER A 189 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 258 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU A 232 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 300 removed outlier: 6.740A pdb=" N MET A 291 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 290 " --> pdb=" O PHE A 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 482 removed outlier: 5.527A pdb=" N LYS A 476 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ALA A 584 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER A 478 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N VAL A 582 " --> pdb=" O SER A 478 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 486 through 487 removed outlier: 7.611A pdb=" N MET A 573 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ASN A 617 " --> pdb=" O MET A 573 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE A 575 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE A 616 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 523 through 525 removed outlier: 3.739A pdb=" N TYR A 523 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N CYS A 533 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 123 through 124 removed outlier: 6.608A pdb=" N GLN B 178 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.668A pdb=" N ILE B 222 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N CYS B 232 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N HIS B 220 " --> pdb=" O CYS B 232 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 223 " --> pdb=" O ILE B 319 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 470 through 472 removed outlier: 4.890A pdb=" N MET B 480 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ARG B 416 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR B 530 " --> pdb=" O ARG B 416 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ASP B 418 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 528 " --> pdb=" O ASP B 418 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 529 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 470 through 472 removed outlier: 4.890A pdb=" N MET B 480 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ARG B 416 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR B 530 " --> pdb=" O ARG B 416 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ASP B 418 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 528 " --> pdb=" O ASP B 418 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 521 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N SER B 565 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE B 523 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE B 562 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL B 601 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY B 588 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N PHE B 603 " --> pdb=" O HIS B 586 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N HIS B 586 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER B 605 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU B 584 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 511 through 512 465 hydrogen bonds defined for protein. 1322 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 3536 1.40 - 1.58: 5154 1.58 - 1.77: 0 1.77 - 1.95: 90 1.95 - 2.13: 4 Bond restraints: 8784 Sorted by residual: bond pdb=" C ASP B 106 " pdb=" O ASP B 106 " ideal model delta sigma weight residual 1.237 1.269 -0.033 1.17e-02 7.31e+03 7.83e+00 bond pdb=" CA THR B 110 " pdb=" C THR B 110 " ideal model delta sigma weight residual 1.523 1.555 -0.032 1.30e-02 5.92e+03 5.91e+00 bond pdb=" C ALA B 103 " pdb=" O ALA B 103 " ideal model delta sigma weight residual 1.237 1.263 -0.026 1.17e-02 7.31e+03 5.13e+00 bond pdb=" N THR B 110 " pdb=" CA THR B 110 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 4.06e+00 bond pdb=" CA ALA B 103 " pdb=" C ALA B 103 " ideal model delta sigma weight residual 1.523 1.549 -0.025 1.30e-02 5.92e+03 3.82e+00 ... (remaining 8779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.74: 11909 4.74 - 9.48: 23 9.48 - 14.22: 1 14.22 - 18.96: 0 18.96 - 23.69: 2 Bond angle restraints: 11935 Sorted by residual: angle pdb=" C THR B 110 " pdb=" N ILE B 111 " pdb=" CA ILE B 111 " ideal model delta sigma weight residual 120.56 130.64 -10.08 1.28e+00 6.10e-01 6.20e+01 angle pdb=" C LEU B 338 " pdb=" N TYR B 339 " pdb=" CA TYR B 339 " ideal model delta sigma weight residual 121.54 128.92 -7.38 1.91e+00 2.74e-01 1.49e+01 angle pdb=" C LEU B 108 " pdb=" N ALA B 109 " pdb=" CA ALA B 109 " ideal model delta sigma weight residual 120.28 125.27 -4.99 1.34e+00 5.57e-01 1.39e+01 angle pdb=" C LEU A 398 " pdb=" N TYR A 399 " pdb=" CA TYR A 399 " ideal model delta sigma weight residual 121.54 127.87 -6.33 1.91e+00 2.74e-01 1.10e+01 angle pdb=" CA ALA B 103 " pdb=" C ALA B 103 " pdb=" N LEU B 104 " ideal model delta sigma weight residual 117.30 113.72 3.58 1.16e+00 7.43e-01 9.50e+00 ... (remaining 11930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4901 17.82 - 35.64: 284 35.64 - 53.46: 47 53.46 - 71.28: 17 71.28 - 89.10: 3 Dihedral angle restraints: 5252 sinusoidal: 1996 harmonic: 3256 Sorted by residual: dihedral pdb=" CA LEU A 398 " pdb=" C LEU A 398 " pdb=" N TYR A 399 " pdb=" CA TYR A 399 " ideal model delta harmonic sigma weight residual 180.00 153.49 26.51 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA SER B 209 " pdb=" C SER B 209 " pdb=" N PRO B 210 " pdb=" CA PRO B 210 " ideal model delta harmonic sigma weight residual 180.00 -154.95 -25.05 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA ASP B 262 " pdb=" C ASP B 262 " pdb=" N ILE B 263 " pdb=" CA ILE B 263 " ideal model delta harmonic sigma weight residual -180.00 -155.25 -24.75 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 5249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 837 0.034 - 0.067: 389 0.067 - 0.101: 116 0.101 - 0.134: 41 0.134 - 0.168: 7 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CA HIS B 105 " pdb=" N HIS B 105 " pdb=" C HIS B 105 " pdb=" CB HIS B 105 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" CA PRO B 210 " pdb=" N PRO B 210 " pdb=" C PRO B 210 " pdb=" CB PRO B 210 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CA ILE B 343 " pdb=" N ILE B 343 " pdb=" C ILE B 343 " pdb=" CB ILE B 343 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.34e-01 ... (remaining 1387 not shown) Planarity restraints: 1515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 112 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO B 113 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 452 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C ASP B 452 " -0.029 2.00e-02 2.50e+03 pdb=" O ASP B 452 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU B 453 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 453 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" C LEU B 453 " 0.028 2.00e-02 2.50e+03 pdb=" O LEU B 453 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR B 454 " -0.010 2.00e-02 2.50e+03 ... (remaining 1512 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 916 2.75 - 3.29: 8595 3.29 - 3.82: 13875 3.82 - 4.36: 15973 4.36 - 4.90: 27325 Nonbonded interactions: 66684 Sorted by model distance: nonbonded pdb=" NH2 ARG A 410 " pdb=" OD1 ASN B 100 " model vdw 2.212 3.120 nonbonded pdb=" O THR B 392 " pdb=" OG SER B 396 " model vdw 2.254 3.040 nonbonded pdb=" O LEU A 74 " pdb=" OG SER A 77 " model vdw 2.274 3.040 nonbonded pdb=" O SER A 581 " pdb=" ND2 ASN A 600 " model vdw 2.290 3.120 nonbonded pdb=" O VAL A 154 " pdb=" N LEU B 340 " model vdw 2.294 3.120 ... (remaining 66679 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.290 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 : 0.008 0.671 8785 Z= 0.200 Angle : 0.770 23.695 11935 Z= 0.392 Chirality : 0.044 0.168 1390 Planarity : 0.004 0.043 1515 Dihedral : 12.201 89.097 3144 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.82 % Favored : 93.82 % Rotamer: Outliers : 4.62 % Allowed : 6.15 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.22), residues: 1101 helix: -1.13 (0.20), residues: 506 sheet: -2.21 (0.31), residues: 212 loop : -2.67 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 360 TYR 0.017 0.002 TYR B 454 PHE 0.025 0.002 PHE A 458 TRP 0.002 0.001 TRP B 22 HIS 0.005 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8784) covalent geometry : angle 0.76982 (11935) hydrogen bonds : bond 0.14479 ( 450) hydrogen bonds : angle 6.53248 ( 1322) Misc. bond : bond 0.67092 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.9258 (mttm) cc_final: 0.9005 (mtmm) REVERT: A 159 LEU cc_start: 0.8786 (pp) cc_final: 0.8431 (tt) REVERT: A 161 ASP cc_start: 0.8632 (m-30) cc_final: 0.8404 (m-30) REVERT: A 209 ARG cc_start: 0.9090 (mtt180) cc_final: 0.8716 (tpt170) REVERT: A 252 TYR cc_start: 0.8984 (p90) cc_final: 0.8369 (p90) REVERT: A 351 ARG cc_start: 0.8084 (ptm160) cc_final: 0.7693 (ptt-90) REVERT: A 364 MET cc_start: 0.8900 (ttp) cc_final: 0.8442 (ttp) REVERT: A 573 MET cc_start: 0.8673 (mmm) cc_final: 0.8304 (tpt) REVERT: A 606 LYS cc_start: 0.8938 (mmtp) cc_final: 0.8672 (tppt) REVERT: A 645 ASN cc_start: 0.9225 (m-40) cc_final: 0.8859 (p0) REVERT: A 656 PHE cc_start: 0.8463 (m-80) cc_final: 0.7767 (m-80) REVERT: B 62 ASN cc_start: 0.7387 (m110) cc_final: 0.6869 (t0) REVERT: B 65 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8065 (tp30) REVERT: B 328 MET cc_start: 0.8442 (mtm) cc_final: 0.8208 (mtm) REVERT: B 335 ARG cc_start: 0.8808 (mtt180) cc_final: 0.8434 (mtm-85) REVERT: B 379 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8507 (t) REVERT: B 386 GLU cc_start: 0.9495 (OUTLIER) cc_final: 0.9069 (mp0) REVERT: B 471 LYS cc_start: 0.9182 (tttm) cc_final: 0.8892 (tttp) REVERT: B 569 TYR cc_start: 0.8503 (t80) cc_final: 0.7995 (t80) REVERT: B 571 CYS cc_start: 0.9354 (m) cc_final: 0.9101 (m) REVERT: B 584 LEU cc_start: 0.9638 (mm) cc_final: 0.9417 (mm) outliers start: 42 outliers final: 20 residues processed: 204 average time/residue: 0.0740 time to fit residues: 22.0142 Evaluate side-chains 127 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 449 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.0030 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.7912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 201 HIS B 93 ASN B 134 HIS ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 GLN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.094894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.075406 restraints weight = 34190.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.076833 restraints weight = 15710.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.077695 restraints weight = 12021.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.078146 restraints weight = 10062.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.078539 restraints weight = 9236.057| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.316 8785 Z= 0.141 Angle : 0.716 17.120 11935 Z= 0.342 Chirality : 0.044 0.196 1390 Planarity : 0.004 0.043 1515 Dihedral : 7.919 81.130 1241 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.91 % Favored : 95.82 % Rotamer: Outliers : 4.40 % Allowed : 13.30 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.24), residues: 1101 helix: -0.05 (0.21), residues: 519 sheet: -1.45 (0.33), residues: 206 loop : -2.13 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 416 TYR 0.018 0.001 TYR B 339 PHE 0.012 0.002 PHE A 458 TRP 0.009 0.001 TRP A 353 HIS 0.016 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8784) covalent geometry : angle 0.71619 (11935) hydrogen bonds : bond 0.04179 ( 450) hydrogen bonds : angle 4.96023 ( 1322) Misc. bond : bond 0.31644 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 ASN cc_start: 0.7649 (m110) cc_final: 0.7285 (t0) REVERT: B 386 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: B 471 LYS cc_start: 0.9410 (tttm) cc_final: 0.9080 (tttp) REVERT: B 569 TYR cc_start: 0.8022 (t80) cc_final: 0.7518 (t80) REVERT: B 592 MET cc_start: 0.7500 (mtm) cc_final: 0.7068 (mtm) outliers start: 40 outliers final: 26 residues processed: 157 average time/residue: 0.0804 time to fit residues: 18.0610 Evaluate side-chains 122 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 548 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.0030 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.096515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.075428 restraints weight = 36456.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.080221 restraints weight = 18894.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.081024 restraints weight = 9405.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.081237 restraints weight = 7510.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.081419 restraints weight = 7367.085| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.246 8785 Z= 0.127 Angle : 0.701 14.473 11935 Z= 0.329 Chirality : 0.044 0.205 1390 Planarity : 0.004 0.046 1515 Dihedral : 7.171 78.557 1230 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.55 % Favored : 95.18 % Rotamer: Outliers : 4.40 % Allowed : 13.85 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.24), residues: 1101 helix: 0.44 (0.22), residues: 521 sheet: -1.12 (0.35), residues: 208 loop : -1.73 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 416 TYR 0.016 0.001 TYR B 339 PHE 0.016 0.002 PHE B 321 TRP 0.009 0.001 TRP A 353 HIS 0.003 0.001 HIS B 524 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8784) covalent geometry : angle 0.70104 (11935) hydrogen bonds : bond 0.03657 ( 450) hydrogen bonds : angle 4.66080 ( 1322) Misc. bond : bond 0.24554 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.9064 (pt) REVERT: B 62 ASN cc_start: 0.7618 (m110) cc_final: 0.7271 (t0) REVERT: B 347 ASP cc_start: 0.8607 (t0) cc_final: 0.8264 (t0) REVERT: B 386 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7826 (mp0) REVERT: B 471 LYS cc_start: 0.9382 (tttm) cc_final: 0.9051 (tttp) REVERT: B 569 TYR cc_start: 0.7991 (t80) cc_final: 0.7320 (t80) REVERT: B 592 MET cc_start: 0.7501 (mtm) cc_final: 0.7157 (mtm) REVERT: B 603 PHE cc_start: 0.7445 (m-10) cc_final: 0.7244 (m-80) outliers start: 40 outliers final: 28 residues processed: 145 average time/residue: 0.0699 time to fit residues: 15.4249 Evaluate side-chains 130 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 86 optimal weight: 0.0970 chunk 4 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 HIS ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.096279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.075698 restraints weight = 53254.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.079581 restraints weight = 24499.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.079932 restraints weight = 15684.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.080926 restraints weight = 11224.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.082019 restraints weight = 9371.174| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.226 8785 Z= 0.135 Angle : 0.713 14.422 11935 Z= 0.333 Chirality : 0.044 0.192 1390 Planarity : 0.004 0.078 1515 Dihedral : 6.994 79.406 1226 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.55 % Favored : 95.36 % Rotamer: Outliers : 4.29 % Allowed : 15.27 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.25), residues: 1101 helix: 0.70 (0.22), residues: 520 sheet: -0.85 (0.35), residues: 214 loop : -1.62 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 494 TYR 0.015 0.001 TYR B 339 PHE 0.021 0.002 PHE A 656 TRP 0.006 0.001 TRP A 353 HIS 0.005 0.001 HIS B 492 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8784) covalent geometry : angle 0.71313 (11935) hydrogen bonds : bond 0.03579 ( 450) hydrogen bonds : angle 4.62769 ( 1322) Misc. bond : bond 0.22558 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 102 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.9043 (pt) REVERT: A 573 MET cc_start: 0.8405 (mmm) cc_final: 0.8026 (tpt) REVERT: B 62 ASN cc_start: 0.7857 (m110) cc_final: 0.7443 (t0) REVERT: B 347 ASP cc_start: 0.8515 (t0) cc_final: 0.8169 (t0) REVERT: B 386 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: B 471 LYS cc_start: 0.9382 (tttm) cc_final: 0.9055 (tttp) REVERT: B 502 ASP cc_start: 0.8476 (m-30) cc_final: 0.8223 (m-30) REVERT: B 569 TYR cc_start: 0.7990 (t80) cc_final: 0.7638 (t80) REVERT: B 592 MET cc_start: 0.7501 (mtm) cc_final: 0.7170 (mtm) REVERT: B 599 MET cc_start: 0.7333 (ttt) cc_final: 0.7123 (ttt) outliers start: 39 outliers final: 29 residues processed: 133 average time/residue: 0.0746 time to fit residues: 14.7124 Evaluate side-chains 122 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 548 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.092625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.072421 restraints weight = 39540.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.076827 restraints weight = 20284.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.077118 restraints weight = 10798.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.077615 restraints weight = 8609.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.078509 restraints weight = 8044.068| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.467 8785 Z= 0.219 Angle : 0.742 15.841 11935 Z= 0.356 Chirality : 0.045 0.193 1390 Planarity : 0.004 0.056 1515 Dihedral : 7.068 77.259 1226 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.09 % Favored : 94.64 % Rotamer: Outliers : 4.40 % Allowed : 15.38 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.25), residues: 1101 helix: 0.89 (0.22), residues: 518 sheet: -0.99 (0.36), residues: 207 loop : -1.68 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 494 TYR 0.017 0.002 TYR B 339 PHE 0.016 0.002 PHE A 141 TRP 0.005 0.001 TRP B 602 HIS 0.005 0.001 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 8784) covalent geometry : angle 0.74229 (11935) hydrogen bonds : bond 0.03966 ( 450) hydrogen bonds : angle 4.77557 ( 1322) Misc. bond : bond 0.46670 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 91 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 214 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.9079 (pt) REVERT: A 341 MET cc_start: 0.8548 (mtp) cc_final: 0.8269 (ttm) REVERT: B 62 ASN cc_start: 0.7968 (m110) cc_final: 0.7425 (t0) REVERT: B 347 ASP cc_start: 0.8552 (t0) cc_final: 0.8176 (t0) REVERT: B 386 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: B 569 TYR cc_start: 0.8133 (t80) cc_final: 0.7925 (t80) REVERT: B 592 MET cc_start: 0.7597 (mtm) cc_final: 0.7076 (mtm) REVERT: B 599 MET cc_start: 0.7043 (ttt) cc_final: 0.6830 (ttt) outliers start: 40 outliers final: 32 residues processed: 123 average time/residue: 0.0677 time to fit residues: 12.8415 Evaluate side-chains 118 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 84 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 94 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 73 optimal weight: 0.0040 chunk 26 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 35 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 102 optimal weight: 0.0670 chunk 96 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 overall best weight: 0.3330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN A 548 GLN B 93 ASN B 563 ASN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.097378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.077771 restraints weight = 27513.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.081400 restraints weight = 14236.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.082326 restraints weight = 8543.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.082381 restraints weight = 6930.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.082843 restraints weight = 6924.782| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.290 8785 Z= 0.116 Angle : 0.697 15.778 11935 Z= 0.325 Chirality : 0.042 0.194 1390 Planarity : 0.004 0.045 1515 Dihedral : 6.706 81.689 1226 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.82 % Rotamer: Outliers : 3.74 % Allowed : 17.03 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.25), residues: 1101 helix: 1.15 (0.23), residues: 520 sheet: -0.78 (0.35), residues: 214 loop : -1.51 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 637 TYR 0.013 0.001 TYR B 339 PHE 0.013 0.001 PHE B 321 TRP 0.007 0.001 TRP B 602 HIS 0.003 0.001 HIS B 524 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8784) covalent geometry : angle 0.69650 (11935) hydrogen bonds : bond 0.03314 ( 450) hydrogen bonds : angle 4.50720 ( 1322) Misc. bond : bond 0.29011 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 341 MET cc_start: 0.8571 (mtp) cc_final: 0.8300 (ttm) REVERT: B 62 ASN cc_start: 0.7733 (m110) cc_final: 0.7345 (t0) REVERT: B 347 ASP cc_start: 0.8532 (t0) cc_final: 0.8173 (t0) REVERT: B 386 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7767 (mp0) REVERT: B 471 LYS cc_start: 0.9342 (tttm) cc_final: 0.9017 (tttp) REVERT: B 480 MET cc_start: 0.8689 (ttt) cc_final: 0.8261 (ttp) REVERT: B 569 TYR cc_start: 0.8045 (t80) cc_final: 0.7701 (t80) REVERT: B 592 MET cc_start: 0.7458 (mtm) cc_final: 0.7149 (mtm) outliers start: 34 outliers final: 26 residues processed: 129 average time/residue: 0.0749 time to fit residues: 14.4587 Evaluate side-chains 117 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 29 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 109 optimal weight: 8.9990 chunk 108 optimal weight: 0.3980 chunk 104 optimal weight: 0.0980 chunk 33 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 ASN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.097171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.077435 restraints weight = 36875.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.079774 restraints weight = 17441.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.081076 restraints weight = 11335.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.081770 restraints weight = 9069.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.082321 restraints weight = 8257.340| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.294 8785 Z= 0.123 Angle : 0.697 15.594 11935 Z= 0.328 Chirality : 0.042 0.190 1390 Planarity : 0.004 0.044 1515 Dihedral : 6.540 80.806 1224 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.55 % Favored : 95.36 % Rotamer: Outliers : 3.96 % Allowed : 17.03 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.26), residues: 1101 helix: 1.24 (0.23), residues: 517 sheet: -0.76 (0.35), residues: 215 loop : -1.43 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 494 TYR 0.015 0.001 TYR B 339 PHE 0.013 0.001 PHE A 83 TRP 0.016 0.002 TRP A 467 HIS 0.005 0.001 HIS B 524 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8784) covalent geometry : angle 0.69721 (11935) hydrogen bonds : bond 0.03312 ( 450) hydrogen bonds : angle 4.48758 ( 1322) Misc. bond : bond 0.29423 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 344 MET cc_start: 0.8548 (ptp) cc_final: 0.8227 (ptp) REVERT: B 62 ASN cc_start: 0.7762 (m110) cc_final: 0.7329 (t0) REVERT: B 238 ARG cc_start: 0.8707 (ttp-110) cc_final: 0.8276 (tmm-80) REVERT: B 347 ASP cc_start: 0.8580 (t0) cc_final: 0.8267 (t0) REVERT: B 386 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: B 458 ASP cc_start: 0.9058 (m-30) cc_final: 0.8725 (m-30) REVERT: B 471 LYS cc_start: 0.9360 (tttm) cc_final: 0.9021 (tttp) REVERT: B 480 MET cc_start: 0.8692 (ttt) cc_final: 0.8266 (ttp) REVERT: B 569 TYR cc_start: 0.8054 (t80) cc_final: 0.7833 (t80) outliers start: 36 outliers final: 29 residues processed: 125 average time/residue: 0.0742 time to fit residues: 13.7250 Evaluate side-chains 119 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 548 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 60 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.096964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.076365 restraints weight = 48253.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.078420 restraints weight = 23253.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.081534 restraints weight = 14179.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.081771 restraints weight = 9138.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.083727 restraints weight = 8367.042| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.291 8785 Z= 0.133 Angle : 0.712 16.153 11935 Z= 0.332 Chirality : 0.043 0.190 1390 Planarity : 0.004 0.048 1515 Dihedral : 6.505 80.830 1224 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 3.41 % Allowed : 17.14 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.26), residues: 1101 helix: 1.21 (0.23), residues: 517 sheet: -0.75 (0.35), residues: 215 loop : -1.40 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 494 TYR 0.019 0.001 TYR A 623 PHE 0.013 0.002 PHE B 321 TRP 0.012 0.002 TRP A 467 HIS 0.004 0.001 HIS B 524 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8784) covalent geometry : angle 0.71165 (11935) hydrogen bonds : bond 0.03366 ( 450) hydrogen bonds : angle 4.51777 ( 1322) Misc. bond : bond 0.29139 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: B 62 ASN cc_start: 0.7665 (m110) cc_final: 0.7222 (t0) REVERT: B 347 ASP cc_start: 0.8498 (t0) cc_final: 0.8186 (t0) REVERT: B 386 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: B 471 LYS cc_start: 0.9347 (tttm) cc_final: 0.9005 (tttp) outliers start: 31 outliers final: 29 residues processed: 122 average time/residue: 0.0741 time to fit residues: 13.2293 Evaluate side-chains 120 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 69 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.094970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.075400 restraints weight = 46380.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.078198 restraints weight = 21019.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.078789 restraints weight = 14915.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.079653 restraints weight = 10719.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.081536 restraints weight = 9267.480| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.299 8785 Z= 0.183 Angle : 0.754 17.921 11935 Z= 0.354 Chirality : 0.044 0.191 1390 Planarity : 0.004 0.053 1515 Dihedral : 6.555 79.551 1222 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.36 % Favored : 94.45 % Rotamer: Outliers : 3.41 % Allowed : 17.58 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.26), residues: 1101 helix: 1.14 (0.23), residues: 518 sheet: -0.90 (0.36), residues: 207 loop : -1.44 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 494 TYR 0.027 0.002 TYR A 623 PHE 0.028 0.002 PHE A 513 TRP 0.017 0.003 TRP A 467 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 8784) covalent geometry : angle 0.75408 (11935) hydrogen bonds : bond 0.03683 ( 450) hydrogen bonds : angle 4.64628 ( 1322) Misc. bond : bond 0.29916 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 556 MET cc_start: 0.8664 (tpp) cc_final: 0.7951 (mmm) REVERT: B 62 ASN cc_start: 0.7748 (m110) cc_final: 0.7344 (t0) REVERT: B 347 ASP cc_start: 0.8547 (t0) cc_final: 0.8248 (t0) REVERT: B 386 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8114 (mp0) REVERT: B 471 LYS cc_start: 0.9384 (tttm) cc_final: 0.9057 (tttp) REVERT: B 480 MET cc_start: 0.8760 (ttp) cc_final: 0.8392 (ttt) REVERT: B 569 TYR cc_start: 0.8150 (t80) cc_final: 0.7886 (t80) outliers start: 31 outliers final: 27 residues processed: 120 average time/residue: 0.0839 time to fit residues: 14.7070 Evaluate side-chains 115 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 10 optimal weight: 0.0570 chunk 62 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.095913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.076160 restraints weight = 27755.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.079606 restraints weight = 15000.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.080713 restraints weight = 8873.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.080883 restraints weight = 7450.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.081121 restraints weight = 7266.681| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.281 8785 Z= 0.145 Angle : 0.732 16.625 11935 Z= 0.342 Chirality : 0.043 0.192 1390 Planarity : 0.004 0.054 1515 Dihedral : 6.538 80.677 1221 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.09 % Favored : 94.73 % Rotamer: Outliers : 3.08 % Allowed : 18.46 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.26), residues: 1101 helix: 1.21 (0.23), residues: 515 sheet: -0.89 (0.36), residues: 207 loop : -1.28 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 494 TYR 0.017 0.001 TYR B 569 PHE 0.036 0.002 PHE A 141 TRP 0.026 0.004 TRP B 602 HIS 0.004 0.001 HIS B 524 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8784) covalent geometry : angle 0.73191 (11935) hydrogen bonds : bond 0.03519 ( 450) hydrogen bonds : angle 4.57250 ( 1322) Misc. bond : bond 0.28105 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: B 62 ASN cc_start: 0.7687 (m110) cc_final: 0.7254 (t0) REVERT: B 335 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8464 (tpp-160) REVERT: B 347 ASP cc_start: 0.8454 (t0) cc_final: 0.8141 (t0) REVERT: B 386 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: B 458 ASP cc_start: 0.9109 (m-30) cc_final: 0.8834 (m-30) REVERT: B 471 LYS cc_start: 0.9361 (tttm) cc_final: 0.9039 (tttp) REVERT: B 480 MET cc_start: 0.8785 (ttp) cc_final: 0.8401 (ttt) outliers start: 28 outliers final: 26 residues processed: 115 average time/residue: 0.0768 time to fit residues: 13.3638 Evaluate side-chains 116 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 548 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 71 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.095138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.074679 restraints weight = 39780.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.078335 restraints weight = 21662.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.078951 restraints weight = 11903.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.081371 restraints weight = 9515.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.081516 restraints weight = 6889.910| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.285 8785 Z= 0.162 Angle : 0.739 16.876 11935 Z= 0.346 Chirality : 0.043 0.191 1390 Planarity : 0.004 0.056 1515 Dihedral : 6.537 79.923 1221 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.09 % Favored : 94.73 % Rotamer: Outliers : 3.30 % Allowed : 18.35 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.26), residues: 1101 helix: 1.22 (0.23), residues: 515 sheet: -0.84 (0.35), residues: 215 loop : -1.26 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 494 TYR 0.036 0.002 TYR A 623 PHE 0.032 0.002 PHE A 513 TRP 0.025 0.003 TRP A 467 HIS 0.004 0.001 HIS B 524 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8784) covalent geometry : angle 0.73920 (11935) hydrogen bonds : bond 0.03617 ( 450) hydrogen bonds : angle 4.60348 ( 1322) Misc. bond : bond 0.28534 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1408.57 seconds wall clock time: 25 minutes 3.91 seconds (1503.91 seconds total)