Starting phenix.real_space_refine on Thu Jul 2 07:19:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r84_18994/07_2026/8r84_18994.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r84_18994/07_2026/8r84_18994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r84_18994/07_2026/8r84_18994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r84_18994/07_2026/8r84_18994.map" model { file = "/net/cci-nas-00/data/ceres_data/8r84_18994/07_2026/8r84_18994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r84_18994/07_2026/8r84_18994.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 Ca 2 9.91 5 S 53 5.16 5 C 4665 2.51 5 N 1299 2.21 5 O 1451 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7470 Number of models: 1 Model: "" Number of chains: 8 Chain: "N" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1686 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 206} Chain: "B" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 972 Classifications: {'peptide': 124} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 111} Chain: "L" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 213} Chain: "K" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 109} Chain: "A" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1002 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 115} Chain: "J" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Time building chain proxies: 1.55, per 1000 atoms: 0.21 Number of scatterers: 7470 At special positions: 0 Unit cell: (71.064, 94.752, 150.588, 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) Ca 2 19.99 S 53 16.00 O 1451 8.00 N 1299 7.00 C 4665 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS N 147 " - pdb=" SG CYS N 181 " distance=2.03 Simple disulfide: pdb=" SG CYS N 163 " - pdb=" SG CYS N 228 " distance=2.03 Simple disulfide: pdb=" SG CYS N 176 " - pdb=" SG CYS N 238 " distance=2.03 Simple disulfide: pdb=" SG CYS N 191 " - pdb=" SG CYS L 414 " distance=2.03 Simple disulfide: pdb=" SG CYS N 208 " - pdb=" SG CYS N 218 " distance=2.04 Simple disulfide: pdb=" SG CYS N 253 " - pdb=" SG CYS N 287 " distance=2.03 Simple disulfide: pdb=" SG CYS N 269 " - pdb=" SG CYS N 335 " distance=2.03 Simple disulfide: pdb=" SG CYS N 282 " - pdb=" SG CYS N 345 " distance=2.03 Simple disulfide: pdb=" SG CYS N 315 " - pdb=" SG CYS N 325 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.03 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 426 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.03 Simple disulfide: pdb=" SG CYS L 575 " - pdb=" SG CYS J 14 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 536 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS J 68 " distance=2.04 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.04 Simple disulfide: pdb=" SG CYS J 71 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN J 48 " Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 494.1 milliseconds 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1796 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 24 sheets defined 11.5% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'N' and resid 168 through 180 removed outlier: 3.638A pdb=" N ALA N 172 " --> pdb=" O SER N 168 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU N 179 " --> pdb=" O VAL N 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 285 removed outlier: 3.699A pdb=" N VAL N 280 " --> pdb=" O LYS N 276 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL N 281 " --> pdb=" O GLU N 277 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN N 284 " --> pdb=" O VAL N 280 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU N 285 " --> pdb=" O VAL N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 297 through 301 removed outlier: 3.685A pdb=" N CYS N 300 " --> pdb=" O ASP N 297 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR N 301 " --> pdb=" O ARG N 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 297 through 301' Processing helix chain 'N' and resid 321 through 325 Processing helix chain 'B' and resid 460 through 466 removed outlier: 3.537A pdb=" N LEU B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 531 removed outlier: 3.630A pdb=" N GLY B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'L' and resid 353 through 361 removed outlier: 3.568A pdb=" N LEU L 359 " --> pdb=" O ALA L 355 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 419 removed outlier: 3.780A pdb=" N TRP L 418 " --> pdb=" O CYS L 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 463 through 467 Processing helix chain 'L' and resid 496 through 498 No H-bonds generated for 'chain 'L' and resid 496 through 498' Processing helix chain 'L' and resid 524 through 531 removed outlier: 3.529A pdb=" N GLY L 531 " --> pdb=" O GLU L 527 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 466 Processing helix chain 'K' and resid 496 through 498 No H-bonds generated for 'chain 'K' and resid 496 through 498' Processing helix chain 'K' and resid 525 through 530 Processing helix chain 'A' and resid 460 through 465 removed outlier: 3.695A pdb=" N LEU A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN A 465 " --> pdb=" O ARG A 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 460 through 465' Processing helix chain 'A' and resid 525 through 531 removed outlier: 3.757A pdb=" N GLY A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 148 through 150 removed outlier: 3.562A pdb=" N ASP N 233 " --> pdb=" O ARG N 190 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN N 188 " --> pdb=" O TRP N 235 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU N 186 " --> pdb=" O GLU N 237 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 152 through 153 Processing sheet with id=AA3, first strand: chain 'N' and resid 243 through 248 removed outlier: 4.246A pdb=" N ASP N 243 " --> pdb=" O LEU N 260 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU N 257 " --> pdb=" O VAL N 268 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL N 268 " --> pdb=" O LEU N 257 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TRP N 309 " --> pdb=" O TRP N 265 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N SER N 267 " --> pdb=" O TRP N 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.552A pdb=" N THR B 473 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.552A pdb=" N THR B 473 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 493 through 494 removed outlier: 3.524A pdb=" N VAL B 537 " --> pdb=" O GLN B 487 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 564 through 569 removed outlier: 6.650A pdb=" N SER B 565 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N MET A 568 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 567 " --> pdb=" O MET A 568 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER A 565 " --> pdb=" O PHE J 60 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N TYR J 62 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A 567 " --> pdb=" O TYR J 62 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 346 through 350 removed outlier: 4.103A pdb=" N THR L 366 " --> pdb=" O ILE L 350 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY L 409 " --> pdb=" O CYS L 367 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP L 371 " --> pdb=" O PHE L 405 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE L 405 " --> pdb=" O ASP L 371 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 389 through 390 removed outlier: 4.485A pdb=" N TRP L 382 " --> pdb=" O VAL L 390 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR L 383 " --> pdb=" O THR L 425 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR L 425 " --> pdb=" O THR L 383 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 453 through 457 removed outlier: 6.045A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 453 through 457 removed outlier: 6.045A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 493 through 494 Processing sheet with id=AB4, first strand: chain 'K' and resid 565 through 567 removed outlier: 7.299A pdb=" N SER K 565 " --> pdb=" O TYR L 562 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL L 564 " --> pdb=" O SER K 565 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VAL K 567 " --> pdb=" O VAL L 564 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU L 566 " --> pdb=" O VAL K 567 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER L 569 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE J 32 " --> pdb=" O ILE J 22 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE J 22 " --> pdb=" O ILE J 32 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA J 15 " --> pdb=" O ASP J 9 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP J 9 " --> pdb=" O ALA J 15 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE J 17 " --> pdb=" O LEU J 7 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 574 through 575 Processing sheet with id=AB6, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.526A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE K 472 " --> pdb=" O LEU K 521 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY K 478 " --> pdb=" O TYR K 515 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR K 515 " --> pdb=" O GLY K 478 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 485 through 486 removed outlier: 3.506A pdb=" N PHE K 485 " --> pdb=" O ALA K 539 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 489 through 490 Processing sheet with id=AB9, first strand: chain 'K' and resid 534 through 535 removed outlier: 4.261A pdb=" N TYR K 534 " --> pdb=" O VAL K 552 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL K 552 " --> pdb=" O TYR K 534 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 453 through 457 removed outlier: 3.629A pdb=" N THR A 473 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 453 through 457 removed outlier: 3.629A pdb=" N THR A 473 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 516 " --> pdb=" O MET A 506 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.631A pdb=" N PHE A 485 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 74 through 77 Processing sheet with id=AC5, first strand: chain 'J' and resid 110 through 113 removed outlier: 3.592A pdb=" N ALA J 111 " --> pdb=" O THR J 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 116 through 117 removed outlier: 3.618A pdb=" N GLU J 120 " --> pdb=" O TYR J 117 " (cutoff:3.500A) 255 hydrogen bonds defined for protein. 654 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: 0.97 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2309 1.34 - 1.46: 1457 1.46 - 1.58: 3815 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 7648 Sorted by residual: bond pdb=" CA PRO K 458 " pdb=" C PRO K 458 " ideal model delta sigma weight residual 1.514 1.535 -0.020 5.50e-03 3.31e+04 1.37e+01 bond pdb=" C PRO A 494 " pdb=" N LEU A 495 " ideal model delta sigma weight residual 1.328 1.279 0.049 1.44e-02 4.82e+03 1.18e+01 bond pdb=" N VAL K 484 " pdb=" CA VAL K 484 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.14e-02 7.69e+03 1.11e+01 bond pdb=" N VAL J 124 " pdb=" CA VAL J 124 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.14e-02 7.69e+03 1.08e+01 bond pdb=" N VAL L 378 " pdb=" CA VAL L 378 " ideal model delta sigma weight residual 1.457 1.494 -0.038 1.15e-02 7.56e+03 1.07e+01 ... (remaining 7643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 8988 1.14 - 2.28: 1048 2.28 - 3.41: 342 3.41 - 4.55: 51 4.55 - 5.69: 10 Bond angle restraints: 10439 Sorted by residual: angle pdb=" C ALA J 132 " pdb=" CA ALA J 132 " pdb=" CB ALA J 132 " ideal model delta sigma weight residual 116.54 111.44 5.10 1.15e+00 7.56e-01 1.97e+01 angle pdb=" N LYS L 361 " pdb=" CA LYS L 361 " pdb=" C LYS L 361 " ideal model delta sigma weight residual 113.38 109.03 4.35 1.17e+00 7.31e-01 1.38e+01 angle pdb=" CA CYS N 228 " pdb=" C CYS N 228 " pdb=" O CYS N 228 " ideal model delta sigma weight residual 122.64 118.11 4.53 1.25e+00 6.40e-01 1.31e+01 angle pdb=" CA PRO K 458 " pdb=" C PRO K 458 " pdb=" O PRO K 458 " ideal model delta sigma weight residual 120.90 118.38 2.52 7.20e-01 1.93e+00 1.22e+01 angle pdb=" N THR N 227 " pdb=" CA THR N 227 " pdb=" C THR N 227 " ideal model delta sigma weight residual 113.17 108.82 4.35 1.26e+00 6.30e-01 1.19e+01 ... (remaining 10434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 4133 16.94 - 33.89: 422 33.89 - 50.83: 109 50.83 - 67.78: 35 67.78 - 84.72: 10 Dihedral angle restraints: 4709 sinusoidal: 1937 harmonic: 2772 Sorted by residual: dihedral pdb=" CB CYS N 191 " pdb=" SG CYS N 191 " pdb=" SG CYS L 414 " pdb=" CB CYS L 414 " ideal model delta sinusoidal sigma weight residual 93.00 42.78 50.22 1 1.00e+01 1.00e-02 3.46e+01 dihedral pdb=" CB CYS J 108 " pdb=" SG CYS J 108 " pdb=" SG CYS J 133 " pdb=" CB CYS J 133 " ideal model delta sinusoidal sigma weight residual 93.00 130.46 -37.46 1 1.00e+01 1.00e-02 1.98e+01 dihedral pdb=" CA CYS A 575 " pdb=" CB CYS A 575 " pdb=" SG CYS A 575 " pdb=" SG CYS J 68 " ideal model delta sinusoidal sigma weight residual -73.00 -8.24 -64.76 1 2.00e+01 2.50e-03 1.38e+01 ... (remaining 4706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 918 0.075 - 0.149: 230 0.149 - 0.224: 35 0.224 - 0.298: 0 0.298 - 0.373: 1 Chirality restraints: 1184 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN J 48 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA ILE L 380 " pdb=" N ILE L 380 " pdb=" C ILE L 380 " pdb=" CB ILE L 380 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA ILE L 472 " pdb=" N ILE L 472 " pdb=" C ILE L 472 " pdb=" CB ILE L 472 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1181 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN J 48 " 0.122 2.00e-02 2.50e+03 1.30e-01 2.10e+02 pdb=" CG ASN J 48 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN J 48 " -0.037 2.00e-02 2.50e+03 pdb=" ND2 ASN J 48 " -0.201 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " 0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 506 " 0.062 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO B 507 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO B 507 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 507 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 511 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO B 512 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 512 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 512 " -0.038 5.00e-02 4.00e+02 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1035 2.77 - 3.30: 6611 3.30 - 3.83: 10975 3.83 - 4.37: 12706 4.37 - 4.90: 22315 Nonbonded interactions: 53642 Sorted by model distance: nonbonded pdb=" OD1 ASN N 312 " pdb="CA CA N 402 " model vdw 2.234 3.250 nonbonded pdb=" OG SER N 254 " pdb=" OH TYR N 301 " model vdw 2.325 3.040 nonbonded pdb=" O THR L 556 " pdb=" OG1 THR L 556 " model vdw 2.345 3.040 nonbonded pdb=" ND2 ASN J 48 " pdb=" N2 NAG C 1 " model vdw 2.412 2.560 nonbonded pdb=" OE2 GLU L 525 " pdb=" ND2 ASN L 529 " model vdw 2.436 3.120 ... (remaining 53637 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 449 through 569) selection = (chain 'B' and resid 449 through 569) selection = (chain 'K' and resid 449 through 569) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 20.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 8.080 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 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 : 0.007 0.049 7669 Z= 0.508 Angle : 0.894 20.023 10483 Z= 0.587 Chirality : 0.062 0.373 1184 Planarity : 0.006 0.094 1359 Dihedral : 15.420 84.720 2856 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.12 % Allowed : 21.95 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.26), residues: 937 helix: -0.80 (0.57), residues: 76 sheet: 0.20 (0.30), residues: 270 loop : -1.00 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 546 TYR 0.014 0.001 TYR L 515 PHE 0.007 0.001 PHE N 332 TRP 0.010 0.001 TRP N 235 HIS 0.005 0.001 HIS N 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00675 / 0.51 ( 7648) covalent geometry : angle 0.85044 / 0.58 (10439) SS BOND : bond 0.00261 / 0.22 ( 19) SS BOND : angle 1.13269 / 0.91 ( 38) hydrogen bonds : bond 0.29505 / 19.35 ( 212) hydrogen bonds : angle 8.61119 / 6.09 ( 654) link_BETA1-4 : bond 0.02222 / 1.17 ( 1) link_BETA1-4 : angle 4.41619 / 2.32 ( 3) link_NAG-ASN : bond 0.04175 / 2.20 ( 1) link_NAG-ASN : angle 15.50682 / 8.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 160 TYR cc_start: 0.6295 (m-80) cc_final: 0.5579 (m-10) REVERT: N 312 ASN cc_start: 0.8263 (m110) cc_final: 0.7960 (m-40) REVERT: N 336 THR cc_start: 0.8645 (m) cc_final: 0.8242 (p) REVERT: N 337 HIS cc_start: 0.7475 (m90) cc_final: 0.6995 (m90) REVERT: N 338 GLN cc_start: 0.8588 (mt0) cc_final: 0.8099 (mp10) REVERT: B 450 HIS cc_start: 0.7343 (m90) cc_final: 0.7093 (m-70) REVERT: B 554 LYS cc_start: 0.8191 (ttpp) cc_final: 0.7913 (ttmt) REVERT: L 360 THR cc_start: 0.8690 (m) cc_final: 0.8394 (p) REVERT: K 527 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7124 (tt0) REVERT: K 563 ASN cc_start: 0.8058 (t0) cc_final: 0.7809 (t0) REVERT: A 483 ASP cc_start: 0.7402 (t0) cc_final: 0.6524 (m-30) REVERT: A 506 MET cc_start: 0.7460 (mtt) cc_final: 0.7003 (mtm) REVERT: A 541 GLU cc_start: 0.7378 (pt0) cc_final: 0.6368 (mm-30) REVERT: A 551 THR cc_start: 0.9129 (m) cc_final: 0.8905 (t) REVERT: J 9 ASP cc_start: 0.8690 (t0) cc_final: 0.8443 (t0) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.0910 time to fit residues: 19.1293 Evaluate side-chains 107 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 540 HIS L 419 ASN L 439 GLN A 465 ASN J 80 ASN J 106 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.180708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.142900 restraints weight = 10399.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.142958 restraints weight = 11404.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.144212 restraints weight = 9591.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.144537 restraints weight = 8384.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.145869 restraints weight = 7675.596| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7669 Z= 0.175 Angle : 0.646 8.465 10483 Z= 0.330 Chirality : 0.046 0.163 1184 Planarity : 0.005 0.073 1359 Dihedral : 4.210 26.367 1078 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.03 % Allowed : 20.52 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.27), residues: 937 helix: 0.01 (0.56), residues: 79 sheet: 1.00 (0.29), residues: 280 loop : -0.79 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 546 TYR 0.017 0.002 TYR J 109 PHE 0.017 0.002 PHE A 516 TRP 0.022 0.001 TRP N 235 HIS 0.007 0.001 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 ( 7648) covalent geometry : angle 0.63837 / 0.33 (10439) SS BOND : bond 0.00420 / 0.37 ( 19) SS BOND : angle 1.65162 / 1.01 ( 38) hydrogen bonds : bond 0.04367 / 2.89 ( 212) hydrogen bonds : angle 5.71020 / 4.08 ( 654) link_BETA1-4 : bond 0.01031 / 0.54 ( 1) link_BETA1-4 : angle 1.98461 / 1.05 ( 3) link_NAG-ASN : bond 0.00145 / 0.08 ( 1) link_NAG-ASN : angle 1.18721 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 324 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7867 (tt0) REVERT: N 337 HIS cc_start: 0.7527 (m90) cc_final: 0.7263 (m90) REVERT: N 338 GLN cc_start: 0.8441 (mt0) cc_final: 0.8176 (mp10) REVERT: L 360 THR cc_start: 0.8350 (m) cc_final: 0.8139 (p) REVERT: A 483 ASP cc_start: 0.6940 (t0) cc_final: 0.6411 (m-30) REVERT: A 506 MET cc_start: 0.7272 (mtt) cc_final: 0.6812 (mtm) REVERT: A 541 GLU cc_start: 0.6886 (pt0) cc_final: 0.6570 (mm-30) outliers start: 34 outliers final: 18 residues processed: 140 average time/residue: 0.0916 time to fit residues: 17.1553 Evaluate side-chains 106 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 344 ILE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain L residue 359 LEU Chi-restraints excluded: chain L residue 381 SER Chi-restraints excluded: chain L residue 530 THR Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain K residue 535 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 129 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 78 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 62 optimal weight: 0.0020 chunk 88 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 29 ASN J 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.175041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.140534 restraints weight = 10657.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.138970 restraints weight = 12653.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.140909 restraints weight = 12303.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.140958 restraints weight = 9715.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.141295 restraints weight = 8956.143| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 7669 Z= 0.249 Angle : 0.696 8.427 10483 Z= 0.360 Chirality : 0.049 0.190 1184 Planarity : 0.006 0.067 1359 Dihedral : 4.463 23.949 1078 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 5.81 % Allowed : 20.17 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.27), residues: 937 helix: 0.40 (0.60), residues: 78 sheet: 0.94 (0.29), residues: 278 loop : -1.02 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 256 TYR 0.030 0.002 TYR N 160 PHE 0.027 0.003 PHE L 479 TRP 0.022 0.002 TRP N 235 HIS 0.010 0.002 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.25 ( 7648) covalent geometry : angle 0.68728 / 0.36 (10439) SS BOND : bond 0.00663 / 0.54 ( 19) SS BOND : angle 1.78668 / 1.42 ( 38) hydrogen bonds : bond 0.05074 / 3.25 ( 212) hydrogen bonds : angle 5.37255 / 3.87 ( 654) link_BETA1-4 : bond 0.00874 / 0.46 ( 1) link_BETA1-4 : angle 2.08021 / 1.09 ( 3) link_NAG-ASN : bond 0.00281 / 0.15 ( 1) link_NAG-ASN : angle 1.72929 / 0.98 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 99 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 199 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7545 (mmmm) REVERT: B 546 ARG cc_start: 0.5888 (OUTLIER) cc_final: 0.5402 (ttt-90) REVERT: L 360 THR cc_start: 0.8296 (m) cc_final: 0.8047 (p) REVERT: L 368 LEU cc_start: 0.7211 (tt) cc_final: 0.6951 (pp) REVERT: A 483 ASP cc_start: 0.7014 (t0) cc_final: 0.6480 (m-30) REVERT: A 506 MET cc_start: 0.7188 (mtt) cc_final: 0.6976 (mtm) REVERT: A 541 GLU cc_start: 0.6805 (pt0) cc_final: 0.6435 (mm-30) outliers start: 49 outliers final: 37 residues processed: 141 average time/residue: 0.0743 time to fit residues: 14.1270 Evaluate side-chains 127 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 89 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 344 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 546 ARG Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 359 LEU Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 530 THR Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 131 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN J 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.176657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.141397 restraints weight = 10773.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.140590 restraints weight = 13519.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.142005 restraints weight = 12088.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.142518 restraints weight = 9976.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.142719 restraints weight = 8889.547| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7669 Z= 0.145 Angle : 0.584 8.994 10483 Z= 0.299 Chirality : 0.045 0.141 1184 Planarity : 0.005 0.056 1359 Dihedral : 4.170 21.876 1078 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.51 % Allowed : 22.06 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.27), residues: 937 helix: 0.42 (0.60), residues: 78 sheet: 1.11 (0.30), residues: 280 loop : -1.01 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 467 TYR 0.031 0.001 TYR N 160 PHE 0.020 0.002 PHE A 516 TRP 0.014 0.001 TRP N 235 HIS 0.005 0.001 HIS B 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.14 ( 7648) covalent geometry : angle 0.57718 / 0.30 (10439) SS BOND : bond 0.00475 / 0.34 ( 19) SS BOND : angle 1.44736 / 1.18 ( 38) hydrogen bonds : bond 0.03578 / 2.29 ( 212) hydrogen bonds : angle 4.96583 / 3.60 ( 654) link_BETA1-4 : bond 0.00743 / 0.39 ( 1) link_BETA1-4 : angle 1.88501 / 0.99 ( 3) link_NAG-ASN : bond 0.00006 / 0.00 ( 1) link_NAG-ASN : angle 1.48185 / 0.86 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 90 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: L 360 THR cc_start: 0.8281 (m) cc_final: 0.7987 (p) REVERT: A 483 ASP cc_start: 0.7059 (t0) cc_final: 0.6457 (m-30) REVERT: A 541 GLU cc_start: 0.6800 (pt0) cc_final: 0.6317 (mm-30) outliers start: 38 outliers final: 27 residues processed: 118 average time/residue: 0.0909 time to fit residues: 14.4033 Evaluate side-chains 110 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 344 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 530 THR Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 131 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 70 optimal weight: 0.5980 chunk 60 optimal weight: 0.3980 chunk 8 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 42 optimal weight: 0.0060 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 337 HIS ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 545 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.177345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.140444 restraints weight = 10689.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.140315 restraints weight = 12090.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.143301 restraints weight = 9736.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.142885 restraints weight = 7522.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.143278 restraints weight = 7319.357| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7669 Z= 0.112 Angle : 0.542 6.402 10483 Z= 0.275 Chirality : 0.043 0.136 1184 Planarity : 0.004 0.050 1359 Dihedral : 3.967 24.157 1078 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.39 % Allowed : 22.18 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.27), residues: 937 helix: 0.56 (0.62), residues: 78 sheet: 1.31 (0.30), residues: 280 loop : -0.96 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 57 TYR 0.031 0.001 TYR N 160 PHE 0.021 0.001 PHE A 516 TRP 0.015 0.001 TRP N 235 HIS 0.005 0.001 HIS B 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 ( 7648) covalent geometry : angle 0.53576 / 0.27 (10439) SS BOND : bond 0.00295 / 0.26 ( 19) SS BOND : angle 1.39117 / 1.01 ( 38) hydrogen bonds : bond 0.03164 / 2.00 ( 212) hydrogen bonds : angle 4.66927 / 3.41 ( 654) link_BETA1-4 : bond 0.00694 / 0.37 ( 1) link_BETA1-4 : angle 1.74834 / 0.91 ( 3) link_NAG-ASN : bond 0.00076 / 0.04 ( 1) link_NAG-ASN : angle 1.32172 / 0.77 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 80 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: L 360 THR cc_start: 0.8243 (m) cc_final: 0.7929 (p) REVERT: L 476 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8466 (t) REVERT: A 483 ASP cc_start: 0.7034 (t0) cc_final: 0.6432 (m-30) REVERT: A 493 GLN cc_start: 0.7624 (mp10) cc_final: 0.7423 (mp10) REVERT: A 541 GLU cc_start: 0.6898 (pt0) cc_final: 0.6330 (mm-30) REVERT: J 70 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6210 (tttp) outliers start: 37 outliers final: 30 residues processed: 111 average time/residue: 0.0757 time to fit residues: 11.4197 Evaluate side-chains 108 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 344 ILE Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 530 THR Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 70 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 21 optimal weight: 0.1980 chunk 87 optimal weight: 0.3980 chunk 72 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 15 optimal weight: 0.0060 chunk 86 optimal weight: 1.9990 chunk 46 optimal weight: 0.0670 chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 83 optimal weight: 0.6980 overall best weight: 0.2334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 465 ASN ** B 490 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 = 0.4206 r_free = 0.4206 target = 0.180263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.142741 restraints weight = 10520.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.141967 restraints weight = 11230.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.144665 restraints weight = 9793.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.144877 restraints weight = 7597.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.144974 restraints weight = 7717.223| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7669 Z= 0.091 Angle : 0.515 6.364 10483 Z= 0.260 Chirality : 0.043 0.140 1184 Planarity : 0.004 0.044 1359 Dihedral : 3.724 23.614 1078 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.39 % Allowed : 22.78 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.27), residues: 937 helix: 0.57 (0.61), residues: 78 sheet: 1.43 (0.30), residues: 282 loop : -0.85 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 467 TYR 0.026 0.001 TYR N 160 PHE 0.021 0.001 PHE A 516 TRP 0.004 0.001 TRP N 235 HIS 0.004 0.001 HIS B 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.09 ( 7648) covalent geometry : angle 0.51056 / 0.26 (10439) SS BOND : bond 0.00214 / 0.17 ( 19) SS BOND : angle 1.11953 / 0.83 ( 38) hydrogen bonds : bond 0.02751 / 1.76 ( 212) hydrogen bonds : angle 4.45055 / 3.25 ( 654) link_BETA1-4 : bond 0.00714 / 0.38 ( 1) link_BETA1-4 : angle 1.66388 / 0.87 ( 3) link_NAG-ASN : bond 0.00188 / 0.10 ( 1) link_NAG-ASN : angle 1.12198 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: N 206 MET cc_start: 0.8083 (mtp) cc_final: 0.7840 (mtt) REVERT: L 360 THR cc_start: 0.8159 (m) cc_final: 0.7884 (p) REVERT: A 483 ASP cc_start: 0.6978 (t0) cc_final: 0.6424 (m-30) REVERT: A 541 GLU cc_start: 0.6928 (pt0) cc_final: 0.6425 (mm-30) REVERT: J 70 LYS cc_start: 0.6819 (OUTLIER) cc_final: 0.6160 (tttp) outliers start: 37 outliers final: 22 residues processed: 115 average time/residue: 0.0814 time to fit residues: 12.6958 Evaluate side-chains 103 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 169 LEU Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 344 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 70 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 0.0020 chunk 18 optimal weight: 0.9980 chunk 80 optimal weight: 0.0670 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 overall best weight: 0.4726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 490 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 = 0.4176 r_free = 0.4176 target = 0.177308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.139940 restraints weight = 10458.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.140141 restraints weight = 11487.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.142113 restraints weight = 9804.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.142403 restraints weight = 7569.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.142593 restraints weight = 7110.585| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7669 Z= 0.125 Angle : 0.565 7.271 10483 Z= 0.288 Chirality : 0.043 0.140 1184 Planarity : 0.004 0.043 1359 Dihedral : 3.841 21.820 1078 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.63 % Allowed : 22.54 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.27), residues: 937 helix: 0.62 (0.61), residues: 78 sheet: 1.38 (0.30), residues: 284 loop : -0.85 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 4 TYR 0.027 0.001 TYR N 160 PHE 0.020 0.002 PHE A 516 TRP 0.004 0.001 TRP N 235 HIS 0.013 0.001 HIS N 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 7648) covalent geometry : angle 0.55361 / 0.28 (10439) SS BOND : bond 0.00195 / 0.18 ( 19) SS BOND : angle 1.92213 / 1.16 ( 38) hydrogen bonds : bond 0.03050 / 1.95 ( 212) hydrogen bonds : angle 4.46928 / 3.26 ( 654) link_BETA1-4 : bond 0.00742 / 0.39 ( 1) link_BETA1-4 : angle 1.61008 / 0.83 ( 3) link_NAG-ASN : bond 0.00040 / 0.02 ( 1) link_NAG-ASN : angle 1.24939 / 0.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 79 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: L 360 THR cc_start: 0.8170 (m) cc_final: 0.7915 (p) REVERT: A 483 ASP cc_start: 0.6982 (t0) cc_final: 0.6460 (m-30) REVERT: A 541 GLU cc_start: 0.6910 (pt0) cc_final: 0.6360 (mm-30) REVERT: J 70 LYS cc_start: 0.6802 (OUTLIER) cc_final: 0.6247 (tttm) outliers start: 39 outliers final: 31 residues processed: 111 average time/residue: 0.0787 time to fit residues: 12.0248 Evaluate side-chains 109 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 77 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 169 LEU Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 344 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 414 CYS Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 70 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 0.0050 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 490 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 = 0.4180 r_free = 0.4180 target = 0.177538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.141324 restraints weight = 10709.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.140881 restraints weight = 12193.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.142368 restraints weight = 10672.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.142524 restraints weight = 9042.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.143148 restraints weight = 8445.064| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7669 Z= 0.140 Angle : 0.594 9.013 10483 Z= 0.301 Chirality : 0.044 0.141 1184 Planarity : 0.004 0.045 1359 Dihedral : 3.919 21.674 1078 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.39 % Allowed : 23.25 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.27), residues: 937 helix: 0.57 (0.61), residues: 78 sheet: 1.32 (0.30), residues: 284 loop : -0.89 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 467 TYR 0.032 0.001 TYR N 160 PHE 0.021 0.002 PHE A 516 TRP 0.005 0.001 TRP N 202 HIS 0.012 0.001 HIS N 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 ( 7648) covalent geometry : angle 0.57981 / 0.29 (10439) SS BOND : bond 0.00232 / 0.19 ( 19) SS BOND : angle 2.17575 / 1.37 ( 38) hydrogen bonds : bond 0.03236 / 2.07 ( 212) hydrogen bonds : angle 4.50160 / 3.28 ( 654) link_BETA1-4 : bond 0.00555 / 0.29 ( 1) link_BETA1-4 : angle 1.59885 / 0.83 ( 3) link_NAG-ASN : bond 0.00003 / 0.00 ( 1) link_NAG-ASN : angle 1.36412 / 0.80 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 80 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: N 276 LYS cc_start: 0.8707 (mtpp) cc_final: 0.8303 (mmmt) REVERT: L 360 THR cc_start: 0.8154 (m) cc_final: 0.7924 (p) REVERT: L 476 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8515 (t) REVERT: A 483 ASP cc_start: 0.6993 (t0) cc_final: 0.6490 (m-30) REVERT: A 541 GLU cc_start: 0.6874 (pt0) cc_final: 0.6378 (mm-30) REVERT: J 4 ARG cc_start: 0.7055 (mmt180) cc_final: 0.6598 (mtp180) REVERT: J 11 LYS cc_start: 0.8396 (tptt) cc_final: 0.8167 (mmtt) outliers start: 37 outliers final: 33 residues processed: 111 average time/residue: 0.0707 time to fit residues: 10.9841 Evaluate side-chains 113 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 169 LEU Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 344 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 414 CYS Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 530 THR Chi-restraints excluded: chain L residue 545 ASN Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 131 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 0.0370 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 465 ASN ** B 490 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 = 0.4175 r_free = 0.4175 target = 0.177018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.142442 restraints weight = 10568.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.141109 restraints weight = 13093.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.143359 restraints weight = 12121.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.143323 restraints weight = 8698.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.143681 restraints weight = 8502.662| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7669 Z= 0.142 Angle : 0.577 6.746 10483 Z= 0.294 Chirality : 0.044 0.141 1184 Planarity : 0.004 0.042 1359 Dihedral : 3.881 18.373 1078 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.51 % Allowed : 22.66 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.27), residues: 937 helix: 0.63 (0.61), residues: 78 sheet: 1.34 (0.30), residues: 282 loop : -0.92 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 105 TYR 0.033 0.001 TYR N 160 PHE 0.021 0.002 PHE A 516 TRP 0.010 0.001 TRP N 202 HIS 0.011 0.001 HIS N 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 ( 7648) covalent geometry : angle 0.57090 / 0.29 (10439) SS BOND : bond 0.00259 / 0.20 ( 19) SS BOND : angle 1.39608 / 0.98 ( 38) hydrogen bonds : bond 0.03247 / 2.07 ( 212) hydrogen bonds : angle 4.50269 / 3.28 ( 654) link_BETA1-4 : bond 0.00554 / 0.29 ( 1) link_BETA1-4 : angle 1.56102 / 0.81 ( 3) link_NAG-ASN : bond 0.00018 / 0.01 ( 1) link_NAG-ASN : angle 1.40170 / 0.82 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 82 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: N 276 LYS cc_start: 0.8747 (mtpp) cc_final: 0.8312 (mmmt) REVERT: L 360 THR cc_start: 0.8162 (m) cc_final: 0.7910 (p) REVERT: L 476 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8507 (t) REVERT: A 483 ASP cc_start: 0.7031 (t0) cc_final: 0.6487 (m-30) REVERT: A 541 GLU cc_start: 0.6912 (pt0) cc_final: 0.6334 (mm-30) REVERT: J 11 LYS cc_start: 0.8336 (tptt) cc_final: 0.8054 (mmtt) REVERT: J 70 LYS cc_start: 0.6829 (OUTLIER) cc_final: 0.6246 (tttp) outliers start: 38 outliers final: 32 residues processed: 113 average time/residue: 0.0723 time to fit residues: 11.3563 Evaluate side-chains 113 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 169 LEU Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 344 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 414 CYS Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 530 THR Chi-restraints excluded: chain L residue 545 ASN Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 70 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 86 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 57 optimal weight: 0.0020 chunk 78 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 chunk 77 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 430 HIS J 29 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.178044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.143303 restraints weight = 10643.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.141837 restraints weight = 12940.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.144517 restraints weight = 11703.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.144338 restraints weight = 8323.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.144698 restraints weight = 8074.638| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7669 Z= 0.119 Angle : 0.557 6.873 10483 Z= 0.283 Chirality : 0.043 0.137 1184 Planarity : 0.004 0.043 1359 Dihedral : 3.820 19.118 1078 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.15 % Allowed : 22.78 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.27), residues: 937 helix: 0.62 (0.61), residues: 78 sheet: 1.38 (0.30), residues: 284 loop : -0.87 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 467 TYR 0.030 0.001 TYR N 160 PHE 0.022 0.001 PHE A 516 TRP 0.004 0.001 TRP N 265 HIS 0.011 0.001 HIS N 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 7648) covalent geometry : angle 0.55045 / 0.28 (10439) SS BOND : bond 0.00327 / 0.21 ( 19) SS BOND : angle 1.44343 / 0.98 ( 38) hydrogen bonds : bond 0.02988 / 1.92 ( 212) hydrogen bonds : angle 4.38501 / 3.19 ( 654) link_BETA1-4 : bond 0.00561 / 0.30 ( 1) link_BETA1-4 : angle 1.49815 / 0.77 ( 3) link_NAG-ASN : bond 0.00069 / 0.04 ( 1) link_NAG-ASN : angle 1.29619 / 0.76 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 79 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: N 276 LYS cc_start: 0.8759 (mtpp) cc_final: 0.8324 (mmmt) REVERT: L 360 THR cc_start: 0.8148 (m) cc_final: 0.7896 (p) REVERT: L 476 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8479 (t) REVERT: A 483 ASP cc_start: 0.7023 (t0) cc_final: 0.6479 (m-30) REVERT: A 541 GLU cc_start: 0.6914 (pt0) cc_final: 0.6349 (mm-30) REVERT: J 4 ARG cc_start: 0.7074 (mmt180) cc_final: 0.6730 (mtp180) REVERT: J 11 LYS cc_start: 0.8296 (tptt) cc_final: 0.8039 (mmtt) REVERT: J 70 LYS cc_start: 0.6761 (OUTLIER) cc_final: 0.6187 (tttp) outliers start: 35 outliers final: 32 residues processed: 107 average time/residue: 0.0769 time to fit residues: 11.5430 Evaluate side-chains 113 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 169 LEU Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 344 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 414 CYS Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 530 THR Chi-restraints excluded: chain L residue 545 ASN Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 70 LYS Chi-restraints excluded: chain J residue 131 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 43 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 49 optimal weight: 0.0040 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.177314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.142817 restraints weight = 10592.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.141732 restraints weight = 13429.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.143564 restraints weight = 11680.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.143574 restraints weight = 9230.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.143865 restraints weight = 8951.942| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7669 Z= 0.129 Angle : 0.565 7.047 10483 Z= 0.288 Chirality : 0.043 0.139 1184 Planarity : 0.004 0.042 1359 Dihedral : 3.842 18.435 1078 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.27 % Allowed : 23.13 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.27), residues: 937 helix: 0.62 (0.61), residues: 78 sheet: 1.38 (0.30), residues: 282 loop : -0.90 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 105 TYR 0.031 0.001 TYR N 160 PHE 0.020 0.002 PHE A 516 TRP 0.005 0.001 TRP N 235 HIS 0.010 0.001 HIS N 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 7648) covalent geometry : angle 0.55926 / 0.29 (10439) SS BOND : bond 0.00277 / 0.20 ( 19) SS BOND : angle 1.34452 / 0.94 ( 38) hydrogen bonds : bond 0.03139 / 2.00 ( 212) hydrogen bonds : angle 4.36381 / 3.17 ( 654) link_BETA1-4 : bond 0.00508 / 0.27 ( 1) link_BETA1-4 : angle 1.45449 / 0.75 ( 3) link_NAG-ASN : bond 0.00014 / 0.01 ( 1) link_NAG-ASN : angle 1.34665 / 0.79 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1498.10 seconds wall clock time: 26 minutes 37.82 seconds (1597.82 seconds total)