Starting phenix.real_space_refine on Fri Oct 10 16:09:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r84_18994/10_2025/8r84_18994.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r84_18994/10_2025/8r84_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_18994/10_2025/8r84_18994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r84_18994/10_2025/8r84_18994.map" model { file = "/net/cci-nas-00/data/ceres_data/8r84_18994/10_2025/8r84_18994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r84_18994/10_2025/8r84_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-2.0-5842/lib/python3.9/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, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.91, per 1000 atoms: 0.26 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: 0.57 Conformation dependent library (CDL) restraints added in 400.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.33 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: 1.18 Time building geometry restraints manager: 0.80 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 2.510 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: 19.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.660 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 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 aren 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 covalent geometry : bond 0.00675 ( 7648) covalent geometry : angle 0.85044 (10439) SS BOND : bond 0.00261 ( 19) SS BOND : angle 1.13269 ( 38) hydrogen bonds : bond 0.29505 ( 212) hydrogen bonds : angle 8.61119 ( 654) link_BETA1-4 : bond 0.02222 ( 1) link_BETA1-4 : angle 4.41619 ( 3) link_NAG-ASN : bond 0.04175 ( 1) link_NAG-ASN : angle 15.50682 ( 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 : 0.328 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: 0.9128 (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: 0.1035 time to fit residues: 21.6502 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 : 0.301 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 419 ASN L 439 GLN A 465 ASN J 80 ASN J 106 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.180700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.143227 restraints weight = 10413.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.143807 restraints weight = 11265.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.144856 restraints weight = 9371.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.145175 restraints weight = 7881.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.146011 restraints weight = 7525.116| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7669 Z= 0.179 Angle : 0.635 8.340 10483 Z= 0.326 Chirality : 0.046 0.184 1184 Planarity : 0.005 0.073 1359 Dihedral : 4.152 26.803 1078 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.91 % Allowed : 20.52 % Favored : 75.56 % 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 aren not related in a simple way. whole: -0.22 (0.27), residues: 937 helix: 0.04 (0.56), residues: 79 sheet: 1.01 (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 0.016 0.002 TYR J 109 PHE 0.018 0.002 PHE A 516 TRP 0.020 0.001 TRP N 235 HIS 0.007 0.001 HIS B 518 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 7648) covalent geometry : angle 0.62665 (10439) SS BOND : bond 0.00398 ( 19) SS BOND : angle 1.64671 ( 38) hydrogen bonds : bond 0.04784 ( 212) hydrogen bonds : angle 5.76368 ( 654) link_BETA1-4 : bond 0.00509 ( 1) link_BETA1-4 : angle 2.16072 ( 3) link_NAG-ASN : bond 0.00070 ( 1) link_NAG-ASN : angle 1.34629 ( 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 143 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 160 TYR cc_start: 0.6196 (m-80) cc_final: 0.5981 (m-80) REVERT: N 312 ASN cc_start: 0.8780 (m110) cc_final: 0.8448 (m-40) REVERT: N 324 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7865 (tt0) REVERT: N 337 HIS cc_start: 0.7529 (m90) cc_final: 0.7306 (m90) REVERT: N 338 GLN cc_start: 0.8447 (mt0) cc_final: 0.8180 (mp10) REVERT: L 360 THR cc_start: 0.8364 (m) cc_final: 0.8140 (p) REVERT: A 483 ASP cc_start: 0.6953 (t0) cc_final: 0.6405 (m-30) REVERT: A 506 MET cc_start: 0.7276 (mtt) cc_final: 0.6848 (mtm) REVERT: A 541 GLU cc_start: 0.6903 (pt0) cc_final: 0.6576 (mm-30) outliers start: 33 outliers final: 17 residues processed: 139 average time/residue: 0.1016 time to fit residues: 18.6238 Evaluate side-chains 106 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 466 LEU 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 A residue 476 VAL Chi-restraints excluded: chain A residue 495 LEU 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: 0.6980 chunk 77 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 20 optimal weight: 0.3980 chunk 62 optimal weight: 0.4980 chunk 88 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 HIS J 29 ASN J 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.178681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.140529 restraints weight = 10574.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.141060 restraints weight = 11859.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.142329 restraints weight = 9840.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.142541 restraints weight = 8192.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.143562 restraints weight = 7841.666| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7669 Z= 0.159 Angle : 0.604 8.814 10483 Z= 0.308 Chirality : 0.045 0.169 1184 Planarity : 0.005 0.062 1359 Dihedral : 4.098 24.062 1078 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.39 % Allowed : 20.40 % Favored : 75.21 % 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 aren not related in a simple way. whole: -0.13 (0.27), residues: 937 helix: 0.36 (0.60), residues: 80 sheet: 1.19 (0.29), residues: 280 loop : -0.84 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 57 TYR 0.030 0.001 TYR J 101 PHE 0.016 0.002 PHE L 479 TRP 0.015 0.001 TRP N 235 HIS 0.008 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 7648) covalent geometry : angle 0.59291 (10439) SS BOND : bond 0.00520 ( 19) SS BOND : angle 1.86942 ( 38) hydrogen bonds : bond 0.04103 ( 212) hydrogen bonds : angle 5.13912 ( 654) link_BETA1-4 : bond 0.00878 ( 1) link_BETA1-4 : angle 2.01675 ( 3) link_NAG-ASN : bond 0.00062 ( 1) link_NAG-ASN : angle 1.32506 ( 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 130 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 160 TYR cc_start: 0.6217 (m-80) cc_final: 0.5943 (m-80) REVERT: N 199 LYS cc_start: 0.7984 (mmtt) cc_final: 0.7480 (mmmm) REVERT: N 312 ASN cc_start: 0.8795 (m110) cc_final: 0.8407 (m-40) REVERT: N 337 HIS cc_start: 0.7609 (m90) cc_final: 0.7365 (m90) REVERT: B 546 ARG cc_start: 0.5798 (OUTLIER) cc_final: 0.5417 (ttt-90) REVERT: L 360 THR cc_start: 0.8262 (m) cc_final: 0.8016 (p) REVERT: L 368 LEU cc_start: 0.7096 (tt) cc_final: 0.6828 (pp) REVERT: L 476 VAL cc_start: 0.8803 (OUTLIER) cc_final: 0.8545 (t) REVERT: A 483 ASP cc_start: 0.6991 (t0) cc_final: 0.6434 (m-30) REVERT: A 506 MET cc_start: 0.7125 (mtt) cc_final: 0.6901 (mtm) REVERT: A 541 GLU cc_start: 0.6869 (pt0) cc_final: 0.6457 (mm-30) outliers start: 37 outliers final: 22 residues processed: 124 average time/residue: 0.1054 time to fit residues: 17.0519 Evaluate side-chains 113 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 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 381 SER Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 530 THR 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 476 VAL Chi-restraints excluded: chain A residue 484 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 71 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 72 optimal weight: 0.0370 chunk 31 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.178121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.142868 restraints weight = 10762.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.141795 restraints weight = 13995.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.143264 restraints weight = 12162.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.143528 restraints weight = 10440.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.144012 restraints weight = 9407.953| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3060 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= 0.138 Angle : 0.564 7.906 10483 Z= 0.287 Chirality : 0.044 0.140 1184 Planarity : 0.005 0.056 1359 Dihedral : 4.031 25.940 1078 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.63 % Allowed : 21.59 % Favored : 73.78 % 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 aren not related in a simple way. whole: -0.11 (0.27), residues: 937 helix: 0.36 (0.60), residues: 80 sheet: 1.36 (0.30), residues: 278 loop : -0.91 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 139 TYR 0.013 0.001 TYR N 160 PHE 0.019 0.002 PHE A 516 TRP 0.014 0.001 TRP N 235 HIS 0.006 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7648) covalent geometry : angle 0.55684 (10439) SS BOND : bond 0.00575 ( 19) SS BOND : angle 1.43879 ( 38) hydrogen bonds : bond 0.03475 ( 212) hydrogen bonds : angle 4.84513 ( 654) link_BETA1-4 : bond 0.00781 ( 1) link_BETA1-4 : angle 1.84315 ( 3) link_NAG-ASN : bond 0.00001 ( 1) link_NAG-ASN : angle 1.35138 ( 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 129 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 90 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 160 TYR cc_start: 0.6314 (m-80) cc_final: 0.6088 (m-80) REVERT: N 199 LYS cc_start: 0.8054 (mmtt) cc_final: 0.7578 (mmmm) REVERT: N 312 ASN cc_start: 0.8790 (m110) cc_final: 0.8453 (m-40) REVERT: N 324 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7764 (tt0) REVERT: N 337 HIS cc_start: 0.7623 (m90) cc_final: 0.7415 (m90) REVERT: N 338 GLN cc_start: 0.8449 (mt0) cc_final: 0.8204 (mp10) REVERT: B 546 ARG cc_start: 0.5839 (OUTLIER) cc_final: 0.5396 (ttt-90) REVERT: L 360 THR cc_start: 0.8278 (m) cc_final: 0.8006 (p) REVERT: L 476 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8533 (t) REVERT: A 483 ASP cc_start: 0.6985 (t0) cc_final: 0.6449 (m-30) REVERT: A 506 MET cc_start: 0.7080 (mtt) cc_final: 0.6857 (mtm) REVERT: A 541 GLU cc_start: 0.6875 (pt0) cc_final: 0.6469 (mm-30) outliers start: 39 outliers final: 26 residues processed: 122 average time/residue: 0.0990 time to fit residues: 16.1703 Evaluate side-chains 111 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 546 ARG Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 381 SER 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 552 VAL 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 70 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 6 optimal weight: 0.1980 chunk 78 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 80 optimal weight: 0.0060 chunk 22 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.192915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.158229 restraints weight = 10535.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.157864 restraints weight = 8267.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.157227 restraints weight = 8424.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.157354 restraints weight = 8594.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.157496 restraints weight = 8148.887| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7669 Z= 0.114 Angle : 0.535 6.293 10483 Z= 0.270 Chirality : 0.043 0.136 1184 Planarity : 0.004 0.051 1359 Dihedral : 3.911 26.381 1078 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.51 % Allowed : 21.83 % Favored : 73.67 % 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 aren not related in a simple way. whole: -0.05 (0.27), residues: 937 helix: 0.38 (0.60), residues: 80 sheet: 1.46 (0.30), residues: 280 loop : -0.92 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 467 TYR 0.011 0.001 TYR N 160 PHE 0.020 0.001 PHE A 516 TRP 0.011 0.001 TRP N 235 HIS 0.005 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7648) covalent geometry : angle 0.52794 (10439) SS BOND : bond 0.00347 ( 19) SS BOND : angle 1.39603 ( 38) hydrogen bonds : bond 0.03094 ( 212) hydrogen bonds : angle 4.57993 ( 654) link_BETA1-4 : bond 0.00747 ( 1) link_BETA1-4 : angle 1.73838 ( 3) link_NAG-ASN : bond 0.00086 ( 1) link_NAG-ASN : angle 1.23627 ( 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 119 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 81 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 312 ASN cc_start: 0.8850 (m110) cc_final: 0.8473 (m-40) REVERT: N 337 HIS cc_start: 0.7695 (m90) cc_final: 0.7425 (m90) REVERT: N 338 GLN cc_start: 0.8533 (mt0) cc_final: 0.8151 (mp10) REVERT: L 360 THR cc_start: 0.8180 (m) cc_final: 0.7950 (p) REVERT: A 483 ASP cc_start: 0.6934 (t0) cc_final: 0.6479 (m-30) REVERT: A 506 MET cc_start: 0.7023 (mtt) cc_final: 0.6773 (mtm) REVERT: A 541 GLU cc_start: 0.6852 (pt0) cc_final: 0.6466 (mm-30) outliers start: 38 outliers final: 27 residues processed: 112 average time/residue: 0.1031 time to fit residues: 15.2471 Evaluate side-chains 107 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 381 SER Chi-restraints excluded: chain L residue 447 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 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 530 THR 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 21 optimal weight: 0.0980 chunk 87 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4325 r_free = 0.4325 target = 0.187827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.153208 restraints weight = 10110.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.153669 restraints weight = 8948.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.153962 restraints weight = 8031.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.154287 restraints weight = 7584.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.154570 restraints weight = 7004.990| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7669 Z= 0.120 Angle : 0.537 6.477 10483 Z= 0.271 Chirality : 0.043 0.147 1184 Planarity : 0.004 0.047 1359 Dihedral : 3.821 22.907 1078 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.86 % Allowed : 21.12 % 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 aren not related in a simple way. whole: -0.02 (0.27), residues: 937 helix: 0.55 (0.61), residues: 78 sheet: 1.45 (0.30), residues: 280 loop : -0.90 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 57 TYR 0.010 0.001 TYR N 160 PHE 0.021 0.002 PHE A 516 TRP 0.014 0.001 TRP N 235 HIS 0.006 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7648) covalent geometry : angle 0.53164 (10439) SS BOND : bond 0.00236 ( 19) SS BOND : angle 1.21744 ( 38) hydrogen bonds : bond 0.03121 ( 212) hydrogen bonds : angle 4.53936 ( 654) link_BETA1-4 : bond 0.00778 ( 1) link_BETA1-4 : angle 1.62908 ( 3) link_NAG-ASN : bond 0.00051 ( 1) link_NAG-ASN : angle 1.25855 ( 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 123 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 82 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 312 ASN cc_start: 0.8858 (m110) cc_final: 0.8527 (m-40) REVERT: N 338 GLN cc_start: 0.8437 (mt0) cc_final: 0.8131 (mp10) REVERT: L 360 THR cc_start: 0.8143 (m) cc_final: 0.7933 (p) REVERT: L 476 VAL cc_start: 0.8787 (OUTLIER) cc_final: 0.8505 (t) REVERT: A 483 ASP cc_start: 0.6840 (t0) cc_final: 0.6449 (m-30) REVERT: A 506 MET cc_start: 0.6976 (mtt) cc_final: 0.6730 (mtm) REVERT: A 541 GLU cc_start: 0.6887 (pt0) cc_final: 0.6506 (mm-30) outliers start: 41 outliers final: 32 residues processed: 116 average time/residue: 0.1000 time to fit residues: 15.5920 Evaluate side-chains 113 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 359 LEU Chi-restraints excluded: chain L residue 381 SER Chi-restraints excluded: chain L residue 417 ASP 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 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 477 THR Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 530 THR 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 0.0370 chunk 3 optimal weight: 0.2980 chunk 81 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4345 r_free = 0.4345 target = 0.192396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.159618 restraints weight = 10539.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.158628 restraints weight = 12911.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.160304 restraints weight = 11333.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.160381 restraints weight = 9681.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.160871 restraints weight = 8886.221| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7669 Z= 0.126 Angle : 0.559 8.274 10483 Z= 0.283 Chirality : 0.043 0.138 1184 Planarity : 0.004 0.045 1359 Dihedral : 3.883 23.936 1078 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.98 % Allowed : 21.35 % Favored : 73.67 % 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 aren not related in a simple way. whole: -0.01 (0.27), residues: 937 helix: 0.54 (0.61), residues: 78 sheet: 1.47 (0.30), residues: 280 loop : -0.89 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 467 TYR 0.009 0.001 TYR N 160 PHE 0.021 0.002 PHE A 516 TRP 0.010 0.001 TRP N 235 HIS 0.006 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7648) covalent geometry : angle 0.54381 (10439) SS BOND : bond 0.00218 ( 19) SS BOND : angle 2.12005 ( 38) hydrogen bonds : bond 0.03108 ( 212) hydrogen bonds : angle 4.51050 ( 654) link_BETA1-4 : bond 0.00643 ( 1) link_BETA1-4 : angle 1.60545 ( 3) link_NAG-ASN : bond 0.00057 ( 1) link_NAG-ASN : angle 1.29157 ( 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 127 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 85 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 312 ASN cc_start: 0.8782 (m110) cc_final: 0.8553 (m-40) REVERT: L 360 THR cc_start: 0.8106 (m) cc_final: 0.7895 (p) REVERT: L 476 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8522 (t) REVERT: A 483 ASP cc_start: 0.6869 (t0) cc_final: 0.6472 (m-30) REVERT: A 506 MET cc_start: 0.7013 (mtt) cc_final: 0.6774 (mtm) REVERT: A 541 GLU cc_start: 0.6801 (pt0) cc_final: 0.6489 (mm-30) outliers start: 42 outliers final: 34 residues processed: 121 average time/residue: 0.0851 time to fit residues: 13.9655 Evaluate side-chains 116 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 81 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 381 SER Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 414 CYS Chi-restraints excluded: chain L residue 417 ASP 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 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 477 THR Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 530 THR 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 501 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 67 optimal weight: 0.0060 chunk 78 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 188 GLN N 337 HIS ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.190750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.157483 restraints weight = 10617.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.156548 restraints weight = 13199.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.159483 restraints weight = 11556.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.158832 restraints weight = 8432.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.159157 restraints weight = 8294.023| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7669 Z= 0.150 Angle : 0.584 7.432 10483 Z= 0.298 Chirality : 0.044 0.143 1184 Planarity : 0.004 0.044 1359 Dihedral : 3.924 18.644 1078 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.98 % Allowed : 21.71 % Favored : 73.31 % 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 aren not related in a simple way. whole: -0.08 (0.27), residues: 937 helix: 0.55 (0.61), residues: 78 sheet: 1.35 (0.30), residues: 282 loop : -0.91 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 307 TYR 0.011 0.001 TYR N 160 PHE 0.021 0.002 PHE A 516 TRP 0.008 0.001 TRP N 235 HIS 0.006 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 7648) covalent geometry : angle 0.57466 (10439) SS BOND : bond 0.00224 ( 19) SS BOND : angle 1.73516 ( 38) hydrogen bonds : bond 0.03349 ( 212) hydrogen bonds : angle 4.57755 ( 654) link_BETA1-4 : bond 0.00538 ( 1) link_BETA1-4 : angle 1.59353 ( 3) link_NAG-ASN : bond 0.00050 ( 1) link_NAG-ASN : angle 1.44135 ( 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 126 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 84 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 312 ASN cc_start: 0.8781 (m110) cc_final: 0.8532 (m-40) REVERT: L 476 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8548 (t) REVERT: A 483 ASP cc_start: 0.6857 (t0) cc_final: 0.6463 (m-30) REVERT: A 506 MET cc_start: 0.7085 (mtt) cc_final: 0.6838 (mtm) REVERT: A 541 GLU cc_start: 0.6769 (pt0) cc_final: 0.6475 (mm-30) outliers start: 42 outliers final: 35 residues processed: 118 average time/residue: 0.0867 time to fit residues: 14.0892 Evaluate side-chains 116 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 80 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 359 LEU Chi-restraints excluded: chain L residue 381 SER 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 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 477 THR Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 530 THR 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 501 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: 0.9980 chunk 1 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 49 optimal weight: 0.0000 chunk 6 optimal weight: 0.0470 chunk 77 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.4482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 ASN ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.191381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.158726 restraints weight = 10554.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.157719 restraints weight = 12502.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.160975 restraints weight = 11228.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.160409 restraints weight = 8093.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.160736 restraints weight = 7700.932| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7669 Z= 0.122 Angle : 0.558 6.600 10483 Z= 0.283 Chirality : 0.043 0.137 1184 Planarity : 0.004 0.043 1359 Dihedral : 3.821 18.850 1078 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.27 % Allowed : 22.06 % Favored : 73.67 % 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 aren not related in a simple way. whole: -0.01 (0.27), residues: 937 helix: 0.55 (0.61), residues: 78 sheet: 1.41 (0.30), residues: 282 loop : -0.87 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 467 TYR 0.009 0.001 TYR N 160 PHE 0.021 0.002 PHE A 516 TRP 0.006 0.001 TRP N 235 HIS 0.006 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7648) covalent geometry : angle 0.55062 (10439) SS BOND : bond 0.00221 ( 19) SS BOND : angle 1.47985 ( 38) hydrogen bonds : bond 0.03052 ( 212) hydrogen bonds : angle 4.47930 ( 654) link_BETA1-4 : bond 0.00598 ( 1) link_BETA1-4 : angle 1.52430 ( 3) link_NAG-ASN : bond 0.00046 ( 1) link_NAG-ASN : angle 1.33593 ( 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 114 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 78 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 312 ASN cc_start: 0.8813 (m110) cc_final: 0.8541 (m-40) REVERT: L 476 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8523 (t) REVERT: A 483 ASP cc_start: 0.6847 (t0) cc_final: 0.6451 (m-30) REVERT: A 506 MET cc_start: 0.7036 (mtt) cc_final: 0.6789 (mtm) REVERT: A 541 GLU cc_start: 0.6824 (pt0) cc_final: 0.6489 (mm-30) outliers start: 36 outliers final: 32 residues processed: 110 average time/residue: 0.0862 time to fit residues: 13.3111 Evaluate side-chains 112 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 79 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 359 LEU 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 561 LEU 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 530 THR 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 501 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 86 optimal weight: 0.1980 chunk 26 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 78 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 0.0970 chunk 73 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4417 r_free = 0.4417 target = 0.199835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 119)---------------| | r_work = 0.4017 r_free = 0.4017 target = 0.162674 restraints weight = 10553.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.163938 restraints weight = 9602.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.164615 restraints weight = 8125.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.165065 restraints weight = 7674.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.165261 restraints weight = 7622.952| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7669 Z= 0.124 Angle : 0.562 7.533 10483 Z= 0.285 Chirality : 0.043 0.138 1184 Planarity : 0.004 0.042 1359 Dihedral : 3.794 18.760 1078 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.15 % Allowed : 22.06 % Favored : 73.78 % 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 aren not related in a simple way. whole: 0.00 (0.27), residues: 937 helix: 0.57 (0.62), residues: 78 sheet: 1.42 (0.30), residues: 287 loop : -0.88 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 105 TYR 0.009 0.001 TYR N 160 PHE 0.021 0.002 PHE A 516 TRP 0.005 0.001 TRP N 235 HIS 0.006 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7648) covalent geometry : angle 0.55595 (10439) SS BOND : bond 0.00321 ( 19) SS BOND : angle 1.37667 ( 38) hydrogen bonds : bond 0.03017 ( 212) hydrogen bonds : angle 4.44266 ( 654) link_BETA1-4 : bond 0.00576 ( 1) link_BETA1-4 : angle 1.48749 ( 3) link_NAG-ASN : bond 0.00056 ( 1) link_NAG-ASN : angle 1.29095 ( 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 116 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 81 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 312 ASN cc_start: 0.8891 (m110) cc_final: 0.8541 (m-40) REVERT: L 476 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8503 (t) REVERT: A 483 ASP cc_start: 0.6863 (t0) cc_final: 0.6450 (m-30) REVERT: A 506 MET cc_start: 0.6977 (mtt) cc_final: 0.6722 (mtm) REVERT: A 541 GLU cc_start: 0.6850 (pt0) cc_final: 0.6438 (mm-30) outliers start: 35 outliers final: 32 residues processed: 112 average time/residue: 0.0859 time to fit residues: 13.3315 Evaluate side-chains 112 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 79 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 359 LEU 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 561 LEU 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 530 THR 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 501 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 43 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4321 r_free = 0.4321 target = 0.189866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.155819 restraints weight = 10606.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.155059 restraints weight = 12655.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.157775 restraints weight = 11428.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.157236 restraints weight = 8399.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.157595 restraints weight = 8355.108| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7669 Z= 0.155 Angle : 0.605 7.227 10483 Z= 0.308 Chirality : 0.045 0.143 1184 Planarity : 0.004 0.043 1359 Dihedral : 4.012 24.133 1078 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.27 % Allowed : 21.83 % Favored : 73.90 % 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 aren not related in a simple way. whole: -0.09 (0.27), residues: 937 helix: 0.56 (0.62), residues: 78 sheet: 1.33 (0.30), residues: 287 loop : -0.94 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 4 TYR 0.010 0.001 TYR N 160 PHE 0.021 0.002 PHE A 516 TRP 0.005 0.001 TRP N 235 HIS 0.006 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 7648) covalent geometry : angle 0.59434 (10439) SS BOND : bond 0.00381 ( 19) SS BOND : angle 1.92210 ( 38) hydrogen bonds : bond 0.03394 ( 212) hydrogen bonds : angle 4.53980 ( 654) link_BETA1-4 : bond 0.00453 ( 1) link_BETA1-4 : angle 1.48438 ( 3) link_NAG-ASN : bond 0.00051 ( 1) link_NAG-ASN : angle 1.45175 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1700.07 seconds wall clock time: 30 minutes 7.34 seconds (1807.34 seconds total)