Starting phenix.real_space_refine on Thu Feb 13 09:22:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jt1_9884/02_2025/6jt1_9884.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jt1_9884/02_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_9884/02_2025/6jt1_9884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jt1_9884/02_2025/6jt1_9884.map" model { file = "/net/cci-nas-00/data/ceres_data/6jt1_9884/02_2025/6jt1_9884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jt1_9884/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 8.83, per 1000 atoms: 1.03 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: 2.31 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: 1.07 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: 3.24 Time building geometry restraints manager: 2.67 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 28.270 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.470 ------------------------------------------------------------------------------- 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 : 0.979 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: 0.1764 time to fit residues: 51.4087 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 : 1.008 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.094632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.074352 restraints weight = 41898.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.076194 restraints weight = 21766.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.078179 restraints weight = 13530.655| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 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 80.633 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 : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8677 (tm) REVERT: A 573 MET cc_start: 0.8149 (mmm) cc_final: 0.7890 (tpt) REVERT: A 583 PHE cc_start: 0.8284 (m-80) cc_final: 0.8040 (m-10) REVERT: B 386 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: B 471 LYS cc_start: 0.9418 (tttm) cc_final: 0.9107 (tttp) REVERT: B 569 TYR cc_start: 0.8036 (t80) cc_final: 0.7540 (t80) REVERT: B 592 MET cc_start: 0.7534 (mtm) cc_final: 0.7102 (mtm) outliers start: 41 outliers final: 24 residues processed: 160 average time/residue: 0.1920 time to fit residues: 43.3300 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 : 1.041 ------------------------------------------------------------------------------- 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: 2.9990 chunk 68 optimal weight: 0.9980 chunk 34 optimal weight: 0.0020 chunk 54 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 491 HIS B 563 ASN ** 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 = 0.3364 r_free = 0.3364 target = 0.095948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.076255 restraints weight = 28443.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.078940 restraints weight = 15447.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.080756 restraints weight = 9649.458| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2428 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= 0.197 Angle : 0.718 15.070 11935 Z= 0.338 Chirality : 0.044 0.194 1390 Planarity : 0.004 0.049 1515 Dihedral : 7.269 78.019 1230 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.55 % Favored : 95.18 % Rotamer: Outliers : 4.40 % Allowed : 14.40 % Favored : 81.21 % 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: -1.04 (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 0.003 0.001 HIS B 524 PHE 0.017 0.002 PHE B 321 TYR 0.016 0.001 TYR B 339 ARG 0.005 0.000 ARG B 494 *********************** 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 146 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.9078 (pt) REVERT: B 62 ASN cc_start: 0.7763 (m110) cc_final: 0.7441 (t0) REVERT: B 347 ASP cc_start: 0.8633 (t0) cc_final: 0.8295 (t0) REVERT: B 386 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7741 (mp0) REVERT: B 471 LYS cc_start: 0.9406 (tttm) cc_final: 0.9069 (tttp) REVERT: B 569 TYR cc_start: 0.7912 (t80) cc_final: 0.7317 (t80) REVERT: B 592 MET cc_start: 0.7562 (mtm) cc_final: 0.7224 (mtm) outliers start: 40 outliers final: 26 residues processed: 142 average time/residue: 0.1680 time to fit residues: 35.3002 Evaluate side-chains 123 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 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 139 ARG Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 0.0170 chunk 45 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 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: 0.9990 chunk 107 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.096500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.076379 restraints weight = 28812.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.079398 restraints weight = 16092.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.081373 restraints weight = 9052.379| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2695 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= 0.193 Angle : 0.718 14.352 11935 Z= 0.337 Chirality : 0.044 0.256 1390 Planarity : 0.005 0.073 1515 Dihedral : 7.048 79.371 1226 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.73 % Favored : 95.18 % Rotamer: Outliers : 4.84 % Allowed : 14.84 % Favored : 80.33 % 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: -0.64 (0.25), residues: 1101 helix: 0.72 (0.22), residues: 519 sheet: -0.91 (0.34), residues: 214 loop : -1.69 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.005 0.001 HIS B 492 PHE 0.022 0.002 PHE A 656 TYR 0.015 0.001 TYR A 623 ARG 0.003 0.000 ARG B 416 *********************** 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 148 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 104 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 ASP cc_start: 0.8475 (p0) cc_final: 0.8157 (p0) REVERT: B 62 ASN cc_start: 0.7912 (m110) cc_final: 0.7446 (t0) REVERT: B 347 ASP cc_start: 0.8465 (t0) cc_final: 0.8120 (t0) REVERT: B 386 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7891 (mp0) REVERT: B 471 LYS cc_start: 0.9379 (tttm) cc_final: 0.9027 (tttp) REVERT: B 569 TYR cc_start: 0.7939 (t80) cc_final: 0.7669 (t80) REVERT: B 592 MET cc_start: 0.7420 (mtm) cc_final: 0.7214 (mtm) outliers start: 44 outliers final: 33 residues processed: 140 average time/residue: 0.1736 time to fit residues: 36.4687 Evaluate side-chains 124 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 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 548 GLN 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 139 ARG Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 548 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 98 optimal weight: 0.0970 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 93 ASN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.095040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.075282 restraints weight = 28517.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.078900 restraints weight = 14904.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.079835 restraints weight = 8825.478| |-----------------------------------------------------------------------------| 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: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | 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: 10 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8784 Z= 0.231 Angle : 0.711 14.538 11935 Z= 0.336 Chirality : 0.044 0.214 1390 Planarity : 0.004 0.052 1515 Dihedral : 6.945 79.108 1226 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.82 % Favored : 94.91 % Rotamer: Outliers : 4.84 % Allowed : 15.49 % Favored : 79.67 % 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: -0.46 (0.25), residues: 1101 helix: 0.93 (0.23), residues: 519 sheet: -0.92 (0.35), residues: 208 loop : -1.61 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 353 HIS 0.003 0.001 HIS B 260 PHE 0.014 0.002 PHE A 141 TYR 0.016 0.001 TYR B 339 ARG 0.005 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 140 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 96 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 573 MET cc_start: 0.8430 (mmm) cc_final: 0.7973 (tpt) REVERT: B 62 ASN cc_start: 0.7903 (m110) cc_final: 0.7481 (t0) REVERT: B 347 ASP cc_start: 0.8499 (t0) cc_final: 0.8136 (t0) REVERT: B 386 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: B 458 ASP cc_start: 0.9135 (m-30) cc_final: 0.8797 (m-30) REVERT: B 471 LYS cc_start: 0.9389 (tttm) cc_final: 0.9027 (tttp) REVERT: B 592 MET cc_start: 0.7469 (mtm) cc_final: 0.6149 (mtm) outliers start: 44 outliers final: 37 residues processed: 130 average time/residue: 0.1683 time to fit residues: 32.9063 Evaluate side-chains 130 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 92 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 277 ILE 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 548 GLN Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL 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 449 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.0040 chunk 95 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 102 optimal weight: 0.0030 chunk 105 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.4402 ------------------------------------------------------------------------------- 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 93 ASN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 577 ASN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.098076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.078495 restraints weight = 31375.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.081301 restraints weight = 16001.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.082637 restraints weight = 9881.218| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3231 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= 0.164 Angle : 0.702 13.644 11935 Z= 0.328 Chirality : 0.043 0.253 1390 Planarity : 0.004 0.046 1515 Dihedral : 6.706 81.436 1226 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.36 % Favored : 95.55 % Rotamer: Outliers : 4.18 % Allowed : 16.15 % Favored : 79.67 % 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: -0.16 (0.26), residues: 1101 helix: 1.17 (0.23), residues: 518 sheet: -0.74 (0.34), residues: 214 loop : -1.48 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 602 HIS 0.003 0.001 HIS B 524 PHE 0.013 0.001 PHE A 83 TYR 0.021 0.001 TYR B 569 ARG 0.005 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 147 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 573 MET cc_start: 0.8397 (mmm) cc_final: 0.7974 (tpt) REVERT: B 62 ASN cc_start: 0.7747 (m110) cc_final: 0.7336 (t0) REVERT: B 238 ARG cc_start: 0.8679 (ttp-110) cc_final: 0.8262 (tmm-80) REVERT: B 347 ASP cc_start: 0.8568 (t0) cc_final: 0.8263 (t0) REVERT: B 471 LYS cc_start: 0.9333 (tttm) cc_final: 0.9004 (tttp) REVERT: B 569 TYR cc_start: 0.8082 (t80) cc_final: 0.7641 (t80) outliers start: 38 outliers final: 31 residues processed: 140 average time/residue: 0.1888 time to fit residues: 37.7970 Evaluate side-chains 128 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 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 548 GLN Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 164 MET 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 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 548 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 13 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 102 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 105 HIS ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.098028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.077102 restraints weight = 36320.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.081733 restraints weight = 18881.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.082510 restraints weight = 9381.507| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3428 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= 0.189 Angle : 0.708 13.310 11935 Z= 0.333 Chirality : 0.044 0.297 1390 Planarity : 0.004 0.051 1515 Dihedral : 6.344 80.570 1221 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.18 % Favored : 95.64 % Rotamer: Outliers : 3.85 % Allowed : 17.14 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (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: -0.16 (0.25), residues: 1101 helix: 1.14 (0.23), residues: 515 sheet: -0.69 (0.35), residues: 214 loop : -1.46 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 467 HIS 0.005 0.001 HIS B 524 PHE 0.013 0.002 PHE A 513 TYR 0.015 0.001 TYR B 569 ARG 0.004 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 138 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 103 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 573 MET cc_start: 0.8404 (mmm) cc_final: 0.8011 (tpt) REVERT: B 62 ASN cc_start: 0.7715 (m110) cc_final: 0.7265 (t0) REVERT: B 238 ARG cc_start: 0.8697 (ttp-110) cc_final: 0.8263 (tmm-80) REVERT: B 347 ASP cc_start: 0.8503 (t0) cc_final: 0.8190 (t0) REVERT: B 471 LYS cc_start: 0.9340 (tttm) cc_final: 0.8964 (tttp) REVERT: B 569 TYR cc_start: 0.8193 (t80) cc_final: 0.7840 (t80) outliers start: 35 outliers final: 31 residues processed: 133 average time/residue: 0.1919 time to fit residues: 36.5884 Evaluate side-chains 127 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 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 42 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 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 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: 0.9990 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 20 optimal weight: 0.0870 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 GLN B 93 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.098467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.077736 restraints weight = 31165.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.081116 restraints weight = 16447.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.083169 restraints weight = 9452.951| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3617 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= 0.190 Angle : 0.735 14.766 11935 Z= 0.344 Chirality : 0.044 0.292 1390 Planarity : 0.004 0.050 1515 Dihedral : 6.315 81.680 1221 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.36 % Favored : 95.45 % Rotamer: Outliers : 3.63 % Allowed : 17.69 % Favored : 78.68 % 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: -0.13 (0.26), residues: 1101 helix: 1.08 (0.23), residues: 520 sheet: -0.74 (0.36), residues: 209 loop : -1.29 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 467 HIS 0.004 0.001 HIS B 524 PHE 0.029 0.002 PHE A 513 TYR 0.015 0.001 TYR A 623 ARG 0.004 0.000 ARG A 637 *********************** 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 132 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 556 MET cc_start: 0.8922 (tpp) cc_final: 0.8366 (mpp) REVERT: A 573 MET cc_start: 0.8426 (mmm) cc_final: 0.8066 (tpt) REVERT: B 62 ASN cc_start: 0.7691 (m110) cc_final: 0.7260 (t0) REVERT: B 238 ARG cc_start: 0.8679 (ttp-110) cc_final: 0.8279 (tmm-80) REVERT: B 347 ASP cc_start: 0.8468 (t0) cc_final: 0.8161 (t0) REVERT: B 471 LYS cc_start: 0.9335 (tttm) cc_final: 0.9014 (tttp) REVERT: B 569 TYR cc_start: 0.8210 (t80) cc_final: 0.7754 (t80) outliers start: 33 outliers final: 31 residues processed: 126 average time/residue: 0.1779 time to fit residues: 32.5563 Evaluate side-chains 126 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 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 446 GLU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ** 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 = 0.3381 r_free = 0.3381 target = 0.096816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.076574 restraints weight = 37326.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.078896 restraints weight = 20300.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.080115 restraints weight = 12438.227| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3644 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= 0.227 Angle : 0.738 16.702 11935 Z= 0.346 Chirality : 0.044 0.302 1390 Planarity : 0.004 0.052 1515 Dihedral : 6.216 80.502 1218 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.64 % Favored : 95.18 % Rotamer: Outliers : 3.74 % Allowed : 17.80 % 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: -0.10 (0.26), residues: 1101 helix: 1.10 (0.23), residues: 521 sheet: -0.66 (0.35), residues: 214 loop : -1.31 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 467 HIS 0.004 0.001 HIS B 524 PHE 0.037 0.002 PHE A 141 TYR 0.015 0.001 TYR A 623 ARG 0.004 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 136 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 552 MET cc_start: 0.8690 (tmm) cc_final: 0.8396 (tmm) REVERT: A 556 MET cc_start: 0.8923 (tpp) cc_final: 0.8026 (mpp) REVERT: A 573 MET cc_start: 0.8492 (mmm) cc_final: 0.8091 (tpt) REVERT: B 62 ASN cc_start: 0.7762 (m110) cc_final: 0.7280 (t0) REVERT: B 104 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8833 (tp) REVERT: B 238 ARG cc_start: 0.8731 (ttp-110) cc_final: 0.8271 (tmm-80) REVERT: B 328 MET cc_start: 0.7921 (mtm) cc_final: 0.7661 (mtm) REVERT: B 334 THR cc_start: 0.9122 (m) cc_final: 0.8887 (p) REVERT: B 347 ASP cc_start: 0.8509 (t0) cc_final: 0.8230 (t0) REVERT: B 471 LYS cc_start: 0.9343 (tttm) cc_final: 0.9019 (tttp) REVERT: B 569 TYR cc_start: 0.8219 (t80) cc_final: 0.7813 (t80) outliers start: 34 outliers final: 31 residues processed: 131 average time/residue: 0.1888 time to fit residues: 35.5013 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 : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 446 GLU 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 25 ILE 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 104 LEU Chi-restraints excluded: chain B residue 139 ARG 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 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 0.0050 chunk 58 optimal weight: 0.2980 chunk 103 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 94 optimal weight: 0.0970 chunk 54 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 92 optimal weight: 0.0770 overall best weight: 0.1750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.100189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.080489 restraints weight = 37248.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.082839 restraints weight = 16957.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.084409 restraints weight = 11319.460| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3924 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= 0.174 Angle : 0.752 14.309 11935 Z= 0.351 Chirality : 0.043 0.327 1390 Planarity : 0.004 0.047 1515 Dihedral : 6.235 83.223 1218 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.82 % Favored : 96.09 % Rotamer: Outliers : 3.08 % Allowed : 19.01 % Favored : 77.91 % 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: -0.12 (0.26), residues: 1101 helix: 1.00 (0.23), residues: 524 sheet: -0.54 (0.36), residues: 207 loop : -1.28 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 467 HIS 0.004 0.001 HIS B 524 PHE 0.033 0.002 PHE A 141 TYR 0.034 0.001 TYR A 623 ARG 0.004 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 135 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 573 MET cc_start: 0.8348 (mmm) cc_final: 0.8024 (tpt) REVERT: B 62 ASN cc_start: 0.7700 (m110) cc_final: 0.7186 (t0) REVERT: B 238 ARG cc_start: 0.8565 (ttp-110) cc_final: 0.8221 (tmm-80) REVERT: B 347 ASP cc_start: 0.8553 (t0) cc_final: 0.8252 (t0) REVERT: B 471 LYS cc_start: 0.9279 (tttm) cc_final: 0.8985 (tttp) REVERT: B 503 MET cc_start: 0.9110 (mtm) cc_final: 0.8890 (mtm) REVERT: B 569 TYR cc_start: 0.8213 (t80) cc_final: 0.7665 (t80) outliers start: 28 outliers final: 27 residues processed: 128 average time/residue: 0.1844 time to fit residues: 34.3303 Evaluate side-chains 125 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 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 446 GLU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 16 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 21 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.3371 r_free = 0.3371 target = 0.096146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.075865 restraints weight = 34801.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.079704 restraints weight = 18393.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.080416 restraints weight = 10522.434| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8784 Z= 0.284 Angle : 0.784 17.126 11935 Z= 0.369 Chirality : 0.045 0.307 1390 Planarity : 0.004 0.050 1515 Dihedral : 6.240 79.545 1217 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.91 % Favored : 95.00 % Rotamer: Outliers : 3.52 % Allowed : 19.34 % Favored : 77.14 % 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: -0.09 (0.26), residues: 1101 helix: 1.12 (0.23), residues: 516 sheet: -0.65 (0.36), residues: 214 loop : -1.31 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 467 HIS 0.005 0.001 HIS B 524 PHE 0.030 0.002 PHE A 141 TYR 0.029 0.002 TYR A 623 ARG 0.005 0.000 ARG A 410 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2665.36 seconds wall clock time: 48 minutes 33.29 seconds (2913.29 seconds total)