Starting phenix.real_space_refine on Thu Mar 13 11:37:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jt1_9884/03_2025/6jt1_9884.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jt1_9884/03_2025/6jt1_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6jt1_9884/03_2025/6jt1_9884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jt1_9884/03_2025/6jt1_9884.map" model { file = "/net/cci-nas-00/data/ceres_data/6jt1_9884/03_2025/6jt1_9884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jt1_9884/03_2025/6jt1_9884.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 18, 'ASP:plan': 8} 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: {'GLN:plan1': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 18, 'ASP:plan': 8} 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: {'PHE:plan': 1, 'GLU:plan': 16, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} 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: {'PHE:plan': 1, 'GLU:plan': 16, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} 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: 9.14, per 1000 atoms: 1.06 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: 2.32 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.00 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: 2.66 Time building geometry restraints manager: 2.65 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 28.360 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.870 ------------------------------------------------------------------------------- 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 : 0.004 0.056 8784 Z= 0.252 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (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 TRP 0.002 0.001 TRP B 22 HIS 0.005 0.001 HIS B 176 PHE 0.025 0.002 PHE A 458 TYR 0.017 0.002 TYR B 454 ARG 0.002 0.000 ARG B 360 *********************** 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 : 0.944 Fit side-chains 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: 0.8715 (tpt170) REVERT: A 252 TYR cc_start: 0.8984 (p90) cc_final: 0.8368 (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: 0.8303 (tpt) REVERT: A 583 PHE cc_start: 0.9178 (m-80) cc_final: 0.8937 (m-10) REVERT: A 606 LYS cc_start: 0.8938 (mmtp) cc_final: 0.8669 (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: 0.7768 (m-80) REVERT: B 62 ASN cc_start: 0.7387 (m110) cc_final: 0.6870 (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: 0.8508 (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: 0.7993 (t80) REVERT: B 571 CYS cc_start: 0.9354 (m) cc_final: 0.9101 (m) REVERT: B 581 GLN cc_start: 0.9383 (mt0) cc_final: 0.8994 (tp-100) REVERT: B 584 LEU cc_start: 0.9638 (mm) cc_final: 0.9418 (mm) outliers start: 42 outliers final: 20 residues processed: 204 average time/residue: 0.1741 time to fit residues: 50.9156 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 : 0.968 ------------------------------------------------------------------------------- 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 93 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 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 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 = 0.3339 r_free = 0.3339 target = 0.094553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.074410 restraints weight = 41859.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.076231 restraints weight = 21967.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.078301 restraints weight = 13673.856| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 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 = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8784 Z= 0.219 Angle : 0.722 17.307 11935 Z= 0.346 Chirality : 0.044 0.198 1390 Planarity : 0.004 0.044 1515 Dihedral : 7.956 80.632 1241 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.09 % Favored : 95.64 % Rotamer: Outliers : 4.51 % Allowed : 13.08 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.23), residues: 1101 helix: -0.08 (0.21), residues: 519 sheet: -1.46 (0.33), residues: 206 loop : -2.20 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.017 0.001 HIS A 100 PHE 0.013 0.002 PHE A 346 TYR 0.019 0.001 TYR B 339 ARG 0.005 0.000 ARG B 416 *********************** 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 165 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8695 (tm) REVERT: A 573 MET cc_start: 0.8133 (mmm) cc_final: 0.7877 (tpt) REVERT: A 583 PHE cc_start: 0.8271 (m-80) cc_final: 0.8030 (m-10) REVERT: B 386 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: B 471 LYS cc_start: 0.9421 (tttm) cc_final: 0.9110 (tttp) REVERT: B 569 TYR cc_start: 0.8021 (t80) cc_final: 0.7530 (t80) REVERT: B 592 MET cc_start: 0.7519 (mtm) cc_final: 0.7089 (mtm) outliers start: 41 outliers final: 24 residues processed: 160 average time/residue: 0.2024 time to fit residues: 45.9609 Evaluate side-chains 118 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 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 40 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 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 = 0.3362 r_free = 0.3362 target = 0.095776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.075820 restraints weight = 28460.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.079029 restraints weight = 15456.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.080166 restraints weight = 9176.374| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8784 Z= 0.209 Angle : 0.717 14.950 11935 Z= 0.339 Chirality : 0.044 0.194 1390 Planarity : 0.004 0.048 1515 Dihedral : 7.270 78.057 1230 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.36 % Favored : 95.36 % Rotamer: Outliers : 4.51 % Allowed : 14.40 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.24), residues: 1101 helix: 0.36 (0.22), residues: 521 sheet: -1.14 (0.34), residues: 206 loop : -1.80 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.005 0.001 HIS B 492 PHE 0.017 0.002 PHE B 321 TYR 0.016 0.001 TYR B 339 ARG 0.003 0.000 ARG B 416 *********************** 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 147 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9101 (pt) REVERT: B 62 ASN cc_start: 0.7752 (m110) cc_final: 0.7394 (t0) REVERT: B 347 ASP cc_start: 0.8552 (t0) cc_final: 0.8227 (t0) REVERT: B 386 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: B 471 LYS cc_start: 0.9398 (tttm) cc_final: 0.9058 (tttp) REVERT: B 569 TYR cc_start: 0.7958 (t80) cc_final: 0.7353 (t80) REVERT: B 592 MET cc_start: 0.7568 (mtm) cc_final: 0.7224 (mtm) outliers start: 41 outliers final: 30 residues processed: 142 average time/residue: 0.1599 time to fit residues: 34.1673 Evaluate side-chains 123 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 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 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 160 THR 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 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 73 optimal weight: 0.0060 chunk 45 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 0.0870 chunk 106 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 25 optimal weight: 0.0770 chunk 107 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 overall best weight: 0.2532 ------------------------------------------------------------------------------- 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 B 93 ASN B 437 HIS B 491 HIS B 563 ASN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.098053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.077755 restraints weight = 28782.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.081418 restraints weight = 15244.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.082652 restraints weight = 8794.190| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8784 Z= 0.169 Angle : 0.708 13.473 11935 Z= 0.331 Chirality : 0.044 0.269 1390 Planarity : 0.004 0.065 1515 Dihedral : 7.033 80.388 1227 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 4.73 % Allowed : 15.38 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.25), residues: 1101 helix: 0.74 (0.23), residues: 520 sheet: -0.85 (0.34), residues: 214 loop : -1.62 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.003 0.001 HIS B 524 PHE 0.024 0.002 PHE A 656 TYR 0.014 0.001 TYR B 339 ARG 0.003 0.000 ARG A 614 *********************** 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 160 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 573 MET cc_start: 0.8367 (mmm) cc_final: 0.8080 (mmm) REVERT: B 62 ASN cc_start: 0.7841 (m110) cc_final: 0.7398 (t0) REVERT: B 347 ASP cc_start: 0.8580 (t0) cc_final: 0.8208 (t0) REVERT: B 386 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: B 457 PHE cc_start: 0.8774 (m-10) cc_final: 0.8441 (m-80) REVERT: B 471 LYS cc_start: 0.9339 (tttm) cc_final: 0.8980 (tttp) REVERT: B 502 ASP cc_start: 0.8421 (m-30) cc_final: 0.8175 (m-30) REVERT: B 569 TYR cc_start: 0.7952 (t80) cc_final: 0.7599 (t80) outliers start: 43 outliers final: 27 residues processed: 152 average time/residue: 0.1776 time to fit residues: 39.0519 Evaluate side-chains 122 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 LEU 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 66 ILE Chi-restraints excluded: chain B residue 90 LEU 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 548 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 0.3980 chunk 99 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 86 optimal weight: 0.0770 chunk 30 optimal weight: 0.0050 chunk 87 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 98 optimal weight: 0.0870 overall best weight: 0.2330 ------------------------------------------------------------------------------- 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 548 GLN B 93 ASN B 437 HIS B 577 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 = 0.3415 r_free = 0.3415 target = 0.098838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.079254 restraints weight = 28304.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.081395 restraints weight = 15313.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.083377 restraints weight = 9799.886| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 8784 Z= 0.156 Angle : 0.688 12.480 11935 Z= 0.324 Chirality : 0.043 0.191 1390 Planarity : 0.004 0.047 1515 Dihedral : 6.816 80.981 1225 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.82 % Rotamer: Outliers : 3.96 % Allowed : 16.48 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.25), residues: 1101 helix: 0.93 (0.23), residues: 522 sheet: -0.66 (0.35), residues: 215 loop : -1.48 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.006 0.001 HIS B 491 PHE 0.014 0.001 PHE A 292 TYR 0.013 0.001 TYR B 339 ARG 0.004 0.000 ARG A 637 *********************** 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 145 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 62 ASN cc_start: 0.7655 (m110) cc_final: 0.7277 (t0) REVERT: B 238 ARG cc_start: 0.8649 (ttp-110) cc_final: 0.8287 (tmm-80) REVERT: B 347 ASP cc_start: 0.8562 (t0) cc_final: 0.8253 (t0) REVERT: B 386 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: B 457 PHE cc_start: 0.8633 (m-10) cc_final: 0.8283 (m-80) REVERT: B 471 LYS cc_start: 0.9328 (tttm) cc_final: 0.8933 (tttp) REVERT: B 569 TYR cc_start: 0.7973 (t80) cc_final: 0.7709 (t80) outliers start: 36 outliers final: 30 residues processed: 136 average time/residue: 0.1843 time to fit residues: 36.1406 Evaluate side-chains 133 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 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 380 LEU 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 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 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 43 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 105 optimal weight: 0.2980 chunk 84 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 ** 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 = 0.3403 r_free = 0.3403 target = 0.098010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.077665 restraints weight = 31680.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.080701 restraints weight = 17020.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.082004 restraints weight = 9864.891| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 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 = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8784 Z= 0.184 Angle : 0.693 13.351 11935 Z= 0.326 Chirality : 0.043 0.189 1390 Planarity : 0.004 0.047 1515 Dihedral : 6.643 80.596 1225 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.36 % Favored : 95.45 % Rotamer: Outliers : 4.29 % Allowed : 16.81 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.25), residues: 1101 helix: 1.10 (0.23), residues: 515 sheet: -0.62 (0.35), residues: 214 loop : -1.47 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 467 HIS 0.005 0.001 HIS B 524 PHE 0.014 0.002 PHE A 83 TYR 0.014 0.001 TYR A 623 ARG 0.004 0.000 ARG A 637 *********************** 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 141 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 102 time to evaluate : 0.973 Fit side-chains REVERT: B 62 ASN cc_start: 0.7758 (m110) cc_final: 0.7342 (t0) REVERT: B 238 ARG cc_start: 0.8651 (ttp-110) cc_final: 0.8270 (tmm-80) REVERT: B 347 ASP cc_start: 0.8475 (t0) cc_final: 0.8168 (t0) REVERT: B 386 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7743 (mp0) REVERT: B 457 PHE cc_start: 0.8791 (m-10) cc_final: 0.8589 (m-80) REVERT: B 458 ASP cc_start: 0.9018 (m-30) cc_final: 0.8792 (m-30) REVERT: B 471 LYS cc_start: 0.9322 (tttm) cc_final: 0.8973 (tttp) outliers start: 39 outliers final: 33 residues processed: 133 average time/residue: 0.1754 time to fit residues: 34.0076 Evaluate side-chains 128 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 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 380 LEU 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 624 ARG 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 229 VAL Chi-restraints excluded: chain B residue 263 ILE 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 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 13 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 105 HIS ** 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 = 0.3389 r_free = 0.3389 target = 0.097216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.077420 restraints weight = 36991.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.079664 restraints weight = 17066.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.081444 restraints weight = 11460.406| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 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 = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8784 Z= 0.206 Angle : 0.694 13.907 11935 Z= 0.327 Chirality : 0.044 0.269 1390 Planarity : 0.004 0.053 1515 Dihedral : 6.572 80.360 1224 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.82 % Favored : 95.00 % Rotamer: Outliers : 3.96 % Allowed : 17.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.26), residues: 1101 helix: 1.15 (0.23), residues: 516 sheet: -0.61 (0.35), residues: 214 loop : -1.41 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 467 HIS 0.005 0.001 HIS B 524 PHE 0.013 0.002 PHE B 321 TYR 0.023 0.001 TYR B 569 ARG 0.003 0.000 ARG A 637 *********************** 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 132 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.959 Fit side-chains REVERT: A 573 MET cc_start: 0.8406 (mmm) cc_final: 0.8033 (tpt) REVERT: B 62 ASN cc_start: 0.7718 (m110) cc_final: 0.7280 (t0) REVERT: B 238 ARG cc_start: 0.8701 (ttp-110) cc_final: 0.8269 (tmm-80) REVERT: B 347 ASP cc_start: 0.8497 (t0) cc_final: 0.8213 (t0) REVERT: B 386 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: B 471 LYS cc_start: 0.9372 (tttm) cc_final: 0.8984 (tttp) outliers start: 36 outliers final: 32 residues processed: 127 average time/residue: 0.1824 time to fit residues: 33.3648 Evaluate side-chains 125 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 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 380 LEU 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 624 ARG 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 229 VAL Chi-restraints excluded: chain B residue 263 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 448 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 = 0.3377 r_free = 0.3377 target = 0.096678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.076577 restraints weight = 31456.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.079337 restraints weight = 16660.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.080900 restraints weight = 10070.270| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8784 Z= 0.228 Angle : 0.726 17.005 11935 Z= 0.339 Chirality : 0.044 0.322 1390 Planarity : 0.004 0.056 1515 Dihedral : 6.555 80.407 1224 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.09 % Favored : 94.73 % Rotamer: Outliers : 4.07 % Allowed : 17.14 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.26), residues: 1101 helix: 1.16 (0.23), residues: 520 sheet: -0.67 (0.35), residues: 215 loop : -1.29 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 602 HIS 0.004 0.001 HIS B 524 PHE 0.013 0.002 PHE A 141 TYR 0.025 0.001 TYR A 623 ARG 0.003 0.000 ARG A 512 *********************** 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 129 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 92 time to evaluate : 1.058 Fit side-chains REVERT: B 62 ASN cc_start: 0.7682 (m110) cc_final: 0.7251 (t0) REVERT: B 238 ARG cc_start: 0.8747 (ttp-110) cc_final: 0.8294 (tmm-80) REVERT: B 335 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8454 (tpp-160) REVERT: B 347 ASP cc_start: 0.8501 (t0) cc_final: 0.8199 (t0) REVERT: B 386 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: B 471 LYS cc_start: 0.9399 (tttm) cc_final: 0.9036 (tttp) REVERT: B 535 GLN cc_start: 0.8356 (pm20) cc_final: 0.8139 (tt0) outliers start: 37 outliers final: 32 residues processed: 124 average time/residue: 0.1802 time to fit residues: 32.8144 Evaluate side-chains 125 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 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 380 LEU 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 624 ARG 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 229 VAL Chi-restraints excluded: chain B residue 263 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 14 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 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 = 0.3400 r_free = 0.3400 target = 0.097849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.077678 restraints weight = 37271.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.080401 restraints weight = 19761.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.081726 restraints weight = 11581.855| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 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 = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8784 Z= 0.187 Angle : 0.701 15.966 11935 Z= 0.328 Chirality : 0.044 0.339 1390 Planarity : 0.004 0.054 1515 Dihedral : 6.453 81.467 1222 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.55 % Favored : 95.27 % Rotamer: Outliers : 3.85 % Allowed : 17.25 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1101 helix: 1.17 (0.23), residues: 522 sheet: -0.58 (0.35), residues: 214 loop : -1.32 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 467 HIS 0.004 0.001 HIS B 524 PHE 0.012 0.002 PHE A 141 TYR 0.034 0.001 TYR A 623 ARG 0.003 0.000 ARG A 637 *********************** 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 134 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 1.086 Fit side-chains REVERT: B 62 ASN cc_start: 0.7712 (m110) cc_final: 0.7266 (t0) REVERT: B 238 ARG cc_start: 0.8659 (ttp-110) cc_final: 0.8239 (tmm-80) REVERT: B 347 ASP cc_start: 0.8577 (t0) cc_final: 0.8259 (t0) REVERT: B 386 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: B 471 LYS cc_start: 0.9369 (tttm) cc_final: 0.9013 (tttp) REVERT: B 535 GLN cc_start: 0.8393 (pm20) cc_final: 0.8164 (tt0) outliers start: 35 outliers final: 31 residues processed: 129 average time/residue: 0.1769 time to fit residues: 33.3081 Evaluate side-chains 124 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 380 LEU 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 624 ARG 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 263 ILE 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 548 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 59 optimal weight: 0.0570 chunk 6 optimal weight: 0.9980 chunk 55 optimal weight: 0.0980 chunk 101 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.098338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.078030 restraints weight = 37419.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.079704 restraints weight = 21641.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.081986 restraints weight = 12927.581| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 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 = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8784 Z= 0.183 Angle : 0.722 15.100 11935 Z= 0.337 Chirality : 0.044 0.353 1390 Planarity : 0.004 0.053 1515 Dihedral : 6.408 81.796 1220 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.82 % Rotamer: Outliers : 3.52 % Allowed : 18.68 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 1101 helix: 1.13 (0.23), residues: 521 sheet: -0.64 (0.36), residues: 207 loop : -1.24 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 602 HIS 0.004 0.001 HIS B 524 PHE 0.012 0.001 PHE A 141 TYR 0.032 0.001 TYR A 623 ARG 0.003 0.000 ARG A 637 ********************** 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 129 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 1.079 Fit side-chains REVERT: A 607 PHE cc_start: 0.8658 (m-80) cc_final: 0.8402 (m-80) REVERT: B 62 ASN cc_start: 0.7832 (m110) cc_final: 0.7323 (t0) REVERT: B 238 ARG cc_start: 0.8649 (ttp-110) cc_final: 0.8248 (tmm-80) REVERT: B 347 ASP cc_start: 0.8554 (t0) cc_final: 0.8253 (t0) REVERT: B 386 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: B 471 LYS cc_start: 0.9363 (tttm) cc_final: 0.8982 (tttp) REVERT: B 503 MET cc_start: 0.9176 (mtm) cc_final: 0.8891 (mtm) REVERT: B 535 GLN cc_start: 0.8384 (pm20) cc_final: 0.8169 (tt0) outliers start: 32 outliers final: 31 residues processed: 124 average time/residue: 0.1648 time to fit residues: 30.6988 Evaluate side-chains 125 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 380 LEU 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 624 ARG Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 25 ILE 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 263 ILE 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 548 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.098004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.077900 restraints weight = 34659.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.081061 restraints weight = 19029.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.081965 restraints weight = 11261.712| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 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 = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8784 Z= 0.194 Angle : 0.723 15.402 11935 Z= 0.338 Chirality : 0.044 0.367 1390 Planarity : 0.004 0.052 1515 Dihedral : 6.394 81.413 1220 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.55 % Favored : 95.36 % Rotamer: Outliers : 3.63 % Allowed : 18.35 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1101 helix: 1.13 (0.23), residues: 523 sheet: -0.55 (0.36), residues: 207 loop : -1.21 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 467 HIS 0.003 0.001 HIS B 524 PHE 0.013 0.002 PHE A 513 TYR 0.031 0.001 TYR A 623 ARG 0.003 0.000 ARG A 637 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2757.36 seconds wall clock time: 48 minutes 33.81 seconds (2913.81 seconds total)