Starting phenix.real_space_refine on Sun May 11 05:01:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r84_18994/05_2025/8r84_18994.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r84_18994/05_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_18994/05_2025/8r84_18994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r84_18994/05_2025/8r84_18994.map" model { file = "/net/cci-nas-00/data/ceres_data/8r84_18994/05_2025/8r84_18994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r84_18994/05_2025/8r84_18994.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.11, per 1000 atoms: 1.09 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: 1.66 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.08 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: 2.17 Time building geometry restraints manager: 1.98 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: 11.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.900 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.450 ------------------------------------------------------------------------------- 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 : 4.49 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (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 TRP 0.010 0.001 TRP N 235 HIS 0.005 0.001 HIS N 155 PHE 0.007 0.001 PHE N 332 TYR 0.014 0.001 TYR L 515 ARG 0.007 0.000 ARG A 546 Details of bonding type rmsd link_NAG-ASN : bond 0.04175 ( 1) link_NAG-ASN : angle 15.50682 ( 3) link_BETA1-4 : bond 0.02222 ( 1) link_BETA1-4 : angle 4.41619 ( 3) hydrogen bonds : bond 0.29505 ( 212) hydrogen bonds : angle 8.61119 ( 654) SS BOND : bond 0.00261 ( 19) SS BOND : angle 1.13269 ( 38) covalent geometry : bond 0.00675 ( 7648) covalent geometry : angle 0.85044 (10439) *********************** 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 : 0.855 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: 0.2293 time to fit residues: 47.8075 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 : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 23 optimal weight: 0.6980 chunk 47 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 0.0970 chunk 27 optimal weight: 0.2980 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 HIS L 419 ASN L 439 GLN L 545 ASN A 465 ASN J 80 ASN J 87 GLN J 106 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.200087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.165916 restraints weight = 10441.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.165272 restraints weight = 10992.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.166328 restraints weight = 10199.833| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7669 Z= 0.127 Angle : 0.589 7.352 10483 Z= 0.302 Chirality : 0.044 0.178 1184 Planarity : 0.005 0.070 1359 Dihedral : 3.957 29.841 1078 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.32 % Allowed : 20.17 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.27), residues: 937 helix: 0.05 (0.56), residues: 80 sheet: 1.11 (0.30), residues: 268 loop : -0.69 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 235 HIS 0.005 0.001 HIS B 518 PHE 0.015 0.001 PHE A 516 TYR 0.017 0.001 TYR J 109 ARG 0.005 0.001 ARG L 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 1) link_NAG-ASN : angle 0.93956 ( 3) link_BETA1-4 : bond 0.00796 ( 1) link_BETA1-4 : angle 2.13437 ( 3) hydrogen bonds : bond 0.04551 ( 212) hydrogen bonds : angle 5.71222 ( 654) SS BOND : bond 0.00418 ( 19) SS BOND : angle 1.51558 ( 38) covalent geometry : bond 0.00279 ( 7648) covalent geometry : angle 0.58225 (10439) *********************** 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 140 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 312 ASN cc_start: 0.8745 (m110) cc_final: 0.8470 (m-40) REVERT: N 336 THR cc_start: 0.8636 (m) cc_final: 0.8334 (p) REVERT: N 337 HIS cc_start: 0.7450 (m90) cc_final: 0.7177 (m90) REVERT: N 338 GLN cc_start: 0.8393 (mt0) cc_final: 0.8178 (mp10) REVERT: A 483 ASP cc_start: 0.6818 (t0) cc_final: 0.6403 (m-30) REVERT: J 123 MET cc_start: 0.6167 (mpp) cc_final: 0.5856 (mpp) outliers start: 28 outliers final: 14 residues processed: 136 average time/residue: 0.2221 time to fit residues: 39.3639 Evaluate side-chains 105 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 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 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 129 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 90 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 73 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 0.0770 chunk 88 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 13 optimal weight: 0.2980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.195698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.158875 restraints weight = 10588.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.159124 restraints weight = 11757.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.160977 restraints weight = 9978.493| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7669 Z= 0.133 Angle : 0.573 6.110 10483 Z= 0.292 Chirality : 0.044 0.168 1184 Planarity : 0.005 0.060 1359 Dihedral : 3.915 26.912 1078 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.03 % Allowed : 21.47 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.27), residues: 937 helix: 0.38 (0.61), residues: 79 sheet: 1.48 (0.30), residues: 280 loop : -0.74 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 235 HIS 0.009 0.001 HIS L 518 PHE 0.015 0.001 PHE L 479 TYR 0.020 0.001 TYR N 160 ARG 0.003 0.000 ARG L 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00002 ( 1) link_NAG-ASN : angle 1.19226 ( 3) link_BETA1-4 : bond 0.00859 ( 1) link_BETA1-4 : angle 1.91557 ( 3) hydrogen bonds : bond 0.03798 ( 212) hydrogen bonds : angle 5.07006 ( 654) SS BOND : bond 0.00267 ( 19) SS BOND : angle 1.62676 ( 38) covalent geometry : bond 0.00324 ( 7648) covalent geometry : angle 0.56430 (10439) *********************** 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 129 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 312 ASN cc_start: 0.8762 (m110) cc_final: 0.8459 (m-40) REVERT: N 337 HIS cc_start: 0.7490 (m90) cc_final: 0.7254 (m90) REVERT: N 338 GLN cc_start: 0.8399 (mt0) cc_final: 0.8178 (mp10) REVERT: N 345 CYS cc_start: 0.6241 (OUTLIER) cc_final: 0.5987 (m) REVERT: L 545 ASN cc_start: 0.7051 (OUTLIER) cc_final: 0.6788 (t0) REVERT: A 483 ASP cc_start: 0.6827 (t0) cc_final: 0.6386 (m-30) outliers start: 34 outliers final: 22 residues processed: 123 average time/residue: 0.2020 time to fit residues: 33.5431 Evaluate side-chains 107 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 282 CYS Chi-restraints excluded: chain N residue 344 ILE Chi-restraints excluded: chain N residue 345 CYS 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 530 THR Chi-restraints excluded: chain L residue 545 ASN Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain J residue 6 VAL 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 27 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 17 optimal weight: 0.0770 chunk 49 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.193188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.156148 restraints weight = 10551.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.156278 restraints weight = 12121.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.158659 restraints weight = 9639.220| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7669 Z= 0.149 Angle : 0.572 6.061 10483 Z= 0.292 Chirality : 0.044 0.143 1184 Planarity : 0.005 0.055 1359 Dihedral : 3.966 27.173 1078 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.51 % Allowed : 22.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.27), residues: 937 helix: 0.34 (0.62), residues: 79 sheet: 1.56 (0.30), residues: 278 loop : -0.79 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 235 HIS 0.008 0.001 HIS L 518 PHE 0.018 0.002 PHE A 516 TYR 0.012 0.001 TYR N 160 ARG 0.002 0.000 ARG L 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00031 ( 1) link_NAG-ASN : angle 1.34003 ( 3) link_BETA1-4 : bond 0.00994 ( 1) link_BETA1-4 : angle 1.72488 ( 3) hydrogen bonds : bond 0.03667 ( 212) hydrogen bonds : angle 4.91095 ( 654) SS BOND : bond 0.00712 ( 19) SS BOND : angle 1.58691 ( 38) covalent geometry : bond 0.00356 ( 7648) covalent geometry : angle 0.56444 (10439) *********************** 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 124 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 86 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 199 LYS cc_start: 0.7876 (mmtt) cc_final: 0.7380 (mmmm) REVERT: N 312 ASN cc_start: 0.8793 (m110) cc_final: 0.8472 (m-40) REVERT: N 337 HIS cc_start: 0.7564 (m90) cc_final: 0.7344 (m90) REVERT: N 338 GLN cc_start: 0.8419 (mt0) cc_final: 0.8133 (mp10) REVERT: B 546 ARG cc_start: 0.5930 (OUTLIER) cc_final: 0.5467 (ttt-90) REVERT: L 476 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8513 (t) REVERT: A 483 ASP cc_start: 0.6877 (t0) cc_final: 0.6443 (m-30) outliers start: 38 outliers final: 27 residues processed: 119 average time/residue: 0.1950 time to fit residues: 31.4573 Evaluate side-chains 108 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 282 CYS 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 530 THR Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain 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 515 TYR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 44 optimal weight: 0.0970 chunk 16 optimal weight: 6.9990 chunk 21 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 0.0030 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.179385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.141671 restraints weight = 10609.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.141890 restraints weight = 12424.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.144549 restraints weight = 9507.457| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7669 Z= 0.114 Angle : 0.561 10.771 10483 Z= 0.286 Chirality : 0.044 0.221 1184 Planarity : 0.004 0.048 1359 Dihedral : 3.813 25.530 1078 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.34 % Allowed : 21.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.28), residues: 937 helix: 0.36 (0.61), residues: 79 sheet: 1.60 (0.30), residues: 289 loop : -0.74 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 235 HIS 0.005 0.001 HIS N 155 PHE 0.011 0.001 PHE L 479 TYR 0.025 0.001 TYR J 101 ARG 0.005 0.000 ARG B 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 1) link_NAG-ASN : angle 1.24825 ( 3) link_BETA1-4 : bond 0.00656 ( 1) link_BETA1-4 : angle 1.70352 ( 3) hydrogen bonds : bond 0.03143 ( 212) hydrogen bonds : angle 4.64365 ( 654) SS BOND : bond 0.00350 ( 19) SS BOND : angle 1.93444 ( 38) covalent geometry : bond 0.00277 ( 7648) covalent geometry : angle 0.54865 (10439) *********************** 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 128 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 83 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 312 ASN cc_start: 0.8836 (m110) cc_final: 0.8477 (m-40) REVERT: N 337 HIS cc_start: 0.7597 (m90) cc_final: 0.7327 (m90) REVERT: N 338 GLN cc_start: 0.8470 (mt0) cc_final: 0.8127 (mp10) REVERT: L 476 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8470 (t) REVERT: L 545 ASN cc_start: 0.6917 (OUTLIER) cc_final: 0.6641 (t0) REVERT: A 483 ASP cc_start: 0.6895 (t0) cc_final: 0.6398 (m-30) outliers start: 45 outliers final: 28 residues processed: 118 average time/residue: 0.1981 time to fit residues: 31.5252 Evaluate side-chains 109 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 282 CYS 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 447 VAL Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 545 ASN 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 530 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 6 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 0 optimal weight: 1.9990 chunk 74 optimal weight: 0.0970 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 0.0970 chunk 55 optimal weight: 2.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- 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 400 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.192281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.158612 restraints weight = 10525.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.158328 restraints weight = 13520.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.160621 restraints weight = 10826.687| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3462 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= 0.131 Angle : 0.564 6.327 10483 Z= 0.288 Chirality : 0.044 0.140 1184 Planarity : 0.004 0.046 1359 Dihedral : 3.834 22.927 1078 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.10 % Allowed : 21.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.27), residues: 937 helix: 0.36 (0.61), residues: 80 sheet: 1.63 (0.30), residues: 280 loop : -0.80 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 235 HIS 0.006 0.001 HIS B 518 PHE 0.022 0.002 PHE A 516 TYR 0.016 0.001 TYR N 160 ARG 0.002 0.000 ARG L 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00015 ( 1) link_NAG-ASN : angle 1.30865 ( 3) link_BETA1-4 : bond 0.00565 ( 1) link_BETA1-4 : angle 1.68807 ( 3) hydrogen bonds : bond 0.03430 ( 212) hydrogen bonds : angle 4.62043 ( 654) SS BOND : bond 0.00244 ( 19) SS BOND : angle 1.86978 ( 38) covalent geometry : bond 0.00321 ( 7648) covalent geometry : angle 0.55218 (10439) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 79 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: N 228 CYS cc_start: 0.4634 (OUTLIER) cc_final: 0.3797 (m) REVERT: N 312 ASN cc_start: 0.8778 (m110) cc_final: 0.8501 (m-40) REVERT: L 476 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8526 (t) REVERT: L 545 ASN cc_start: 0.6905 (OUTLIER) cc_final: 0.6668 (t0) REVERT: A 483 ASP cc_start: 0.6825 (t0) cc_final: 0.6461 (m-30) REVERT: J 70 LYS cc_start: 0.6887 (OUTLIER) cc_final: 0.6422 (tttp) outliers start: 43 outliers final: 32 residues processed: 114 average time/residue: 0.1967 time to fit residues: 30.5240 Evaluate side-chains 112 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 76 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 228 CYS Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 282 CYS 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 447 VAL Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 530 THR Chi-restraints excluded: chain L residue 545 ASN Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain 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 515 TYR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 70 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 3 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 79 optimal weight: 0.1980 chunk 14 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.188145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.155232 restraints weight = 10034.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.154704 restraints weight = 11177.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.157406 restraints weight = 9942.654| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7669 Z= 0.117 Angle : 0.576 8.969 10483 Z= 0.292 Chirality : 0.043 0.136 1184 Planarity : 0.004 0.045 1359 Dihedral : 3.869 22.655 1078 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.98 % Allowed : 21.95 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.28), residues: 937 helix: 0.37 (0.61), residues: 80 sheet: 1.63 (0.30), residues: 282 loop : -0.76 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 235 HIS 0.006 0.001 HIS N 155 PHE 0.021 0.001 PHE A 516 TYR 0.014 0.001 TYR N 160 ARG 0.007 0.000 ARG B 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00065 ( 1) link_NAG-ASN : angle 1.25450 ( 3) link_BETA1-4 : bond 0.00591 ( 1) link_BETA1-4 : angle 1.61790 ( 3) hydrogen bonds : bond 0.03142 ( 212) hydrogen bonds : angle 4.50011 ( 654) SS BOND : bond 0.00265 ( 19) SS BOND : angle 2.26192 ( 38) covalent geometry : bond 0.00285 ( 7648) covalent geometry : angle 0.55986 (10439) *********************** 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 121 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 79 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: N 312 ASN cc_start: 0.8798 (m110) cc_final: 0.8536 (m-40) REVERT: L 476 VAL cc_start: 0.8835 (OUTLIER) cc_final: 0.8516 (t) REVERT: L 545 ASN cc_start: 0.6894 (OUTLIER) cc_final: 0.6640 (t0) REVERT: A 483 ASP cc_start: 0.6789 (t0) cc_final: 0.6457 (m-30) REVERT: J 70 LYS cc_start: 0.6886 (OUTLIER) cc_final: 0.6406 (tttp) outliers start: 42 outliers final: 34 residues processed: 112 average time/residue: 0.2045 time to fit residues: 31.5156 Evaluate side-chains 114 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 77 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 282 CYS 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 414 CYS Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 530 THR Chi-restraints excluded: chain L residue 545 ASN Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain 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 515 TYR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 70 LYS Chi-restraints excluded: chain J residue 131 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 545 ASN J 29 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.189176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.157451 restraints weight = 10606.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.156200 restraints weight = 12388.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.157417 restraints weight = 11511.843| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7669 Z= 0.200 Angle : 0.664 11.225 10483 Z= 0.341 Chirality : 0.046 0.150 1184 Planarity : 0.005 0.047 1359 Dihedral : 4.414 31.882 1078 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.86 % Allowed : 22.18 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.27), residues: 937 helix: 0.48 (0.62), residues: 78 sheet: 1.32 (0.30), residues: 282 loop : -0.93 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 235 HIS 0.007 0.001 HIS K 518 PHE 0.023 0.002 PHE L 479 TYR 0.017 0.002 TYR N 160 ARG 0.004 0.000 ARG N 256 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 1) link_NAG-ASN : angle 1.73862 ( 3) link_BETA1-4 : bond 0.00496 ( 1) link_BETA1-4 : angle 1.63022 ( 3) hydrogen bonds : bond 0.04112 ( 212) hydrogen bonds : angle 4.90848 ( 654) SS BOND : bond 0.00410 ( 19) SS BOND : angle 2.97783 ( 38) covalent geometry : bond 0.00497 ( 7648) covalent geometry : angle 0.63910 (10439) *********************** 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 118 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 77 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: N 276 LYS cc_start: 0.8559 (mtmm) cc_final: 0.8345 (mtpp) REVERT: N 312 ASN cc_start: 0.8783 (m110) cc_final: 0.8542 (m-40) REVERT: A 483 ASP cc_start: 0.6885 (t0) cc_final: 0.6459 (m-30) REVERT: J 70 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6605 (tttp) outliers start: 41 outliers final: 34 residues processed: 110 average time/residue: 0.1843 time to fit residues: 28.1193 Evaluate side-chains 108 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 73 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 282 CYS 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 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 561 LEU Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain 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 515 TYR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 70 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 337 HIS ** 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 = 0.4303 r_free = 0.4303 target = 0.188512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.154401 restraints weight = 10701.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.153789 restraints weight = 13112.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.156299 restraints weight = 11820.954| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7669 Z= 0.190 Angle : 0.656 9.267 10483 Z= 0.338 Chirality : 0.046 0.145 1184 Planarity : 0.005 0.047 1359 Dihedral : 4.303 18.647 1078 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.66 % Favored : 94.24 % Rotamer: Outliers : 4.39 % Allowed : 23.01 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.27), residues: 937 helix: 0.49 (0.62), residues: 78 sheet: 1.22 (0.30), residues: 285 loop : -1.01 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 528 HIS 0.007 0.001 HIS L 518 PHE 0.021 0.002 PHE L 479 TYR 0.021 0.001 TYR N 160 ARG 0.003 0.000 ARG J 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 1) link_NAG-ASN : angle 1.76116 ( 3) link_BETA1-4 : bond 0.00498 ( 1) link_BETA1-4 : angle 1.59067 ( 3) hydrogen bonds : bond 0.03902 ( 212) hydrogen bonds : angle 4.82497 ( 654) SS BOND : bond 0.00258 ( 19) SS BOND : angle 2.66834 ( 38) covalent geometry : bond 0.00468 ( 7648) covalent geometry : angle 0.63600 (10439) *********************** 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: 37 poor density : 77 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: N 276 LYS cc_start: 0.8633 (mtmm) cc_final: 0.8386 (mtpp) REVERT: N 312 ASN cc_start: 0.8774 (m110) cc_final: 0.8532 (m-40) REVERT: A 483 ASP cc_start: 0.6897 (t0) cc_final: 0.6477 (m-30) REVERT: J 70 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6475 (tttp) outliers start: 37 outliers final: 33 residues processed: 110 average time/residue: 0.1772 time to fit residues: 27.1028 Evaluate side-chains 108 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 74 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 282 CYS 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 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 501 VAL Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain K residue 535 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 520 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 70 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 60 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 0.0980 chunk 87 optimal weight: 0.0980 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 69 optimal weight: 0.3980 chunk 91 optimal weight: 3.9990 overall best weight: 0.1556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 337 HIS L 430 HIS L 545 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.194464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.164695 restraints weight = 10215.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.163575 restraints weight = 8518.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.164056 restraints weight = 7906.323| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7669 Z= 0.097 Angle : 0.564 7.150 10483 Z= 0.289 Chirality : 0.043 0.129 1184 Planarity : 0.004 0.043 1359 Dihedral : 3.920 19.428 1078 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.91 % Favored : 94.98 % Rotamer: Outliers : 3.44 % Allowed : 24.32 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.27), residues: 937 helix: 0.75 (0.63), residues: 77 sheet: 1.48 (0.30), residues: 287 loop : -0.83 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 159 HIS 0.007 0.001 HIS N 155 PHE 0.007 0.001 PHE B 485 TYR 0.018 0.001 TYR N 160 ARG 0.003 0.000 ARG N 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 1) link_NAG-ASN : angle 1.27303 ( 3) link_BETA1-4 : bond 0.00649 ( 1) link_BETA1-4 : angle 1.47944 ( 3) hydrogen bonds : bond 0.02790 ( 212) hydrogen bonds : angle 4.43941 ( 654) SS BOND : bond 0.00172 ( 19) SS BOND : angle 1.97815 ( 38) covalent geometry : bond 0.00228 ( 7648) covalent geometry : angle 0.55106 (10439) ********************** 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 105 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 0.825 Fit side-chains REVERT: N 276 LYS cc_start: 0.8782 (mtmm) cc_final: 0.8496 (mtpp) REVERT: N 312 ASN cc_start: 0.8875 (m110) cc_final: 0.8549 (m-40) REVERT: A 483 ASP cc_start: 0.6799 (t0) cc_final: 0.6461 (m-30) REVERT: J 70 LYS cc_start: 0.6855 (OUTLIER) cc_final: 0.6363 (tttp) outliers start: 29 outliers final: 24 residues processed: 101 average time/residue: 0.1898 time to fit residues: 26.6067 Evaluate side-chains 95 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 282 CYS 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 537 VAL 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 476 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 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 J residue 6 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 70 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 18 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 75 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 518 HIS ** 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 = 0.4384 r_free = 0.4384 target = 0.195444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.164207 restraints weight = 10273.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.163340 restraints weight = 11857.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.165190 restraints weight = 11175.130| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7669 Z= 0.167 Angle : 0.639 12.160 10483 Z= 0.327 Chirality : 0.045 0.157 1184 Planarity : 0.005 0.045 1359 Dihedral : 4.178 18.318 1078 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.08 % Favored : 93.81 % Rotamer: Outliers : 3.32 % Allowed : 24.20 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.27), residues: 937 helix: 0.71 (0.63), residues: 77 sheet: 1.30 (0.30), residues: 282 loop : -0.89 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 528 HIS 0.007 0.001 HIS K 518 PHE 0.019 0.002 PHE L 479 TYR 0.019 0.001 TYR N 160 ARG 0.004 0.000 ARG J 4 Details of bonding type rmsd link_NAG-ASN : bond 0.00089 ( 1) link_NAG-ASN : angle 1.54560 ( 3) link_BETA1-4 : bond 0.00501 ( 1) link_BETA1-4 : angle 1.54289 ( 3) hydrogen bonds : bond 0.03731 ( 212) hydrogen bonds : angle 4.68570 ( 654) SS BOND : bond 0.00369 ( 19) SS BOND : angle 2.91953 ( 38) covalent geometry : bond 0.00412 ( 7648) covalent geometry : angle 0.61469 (10439) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2885.11 seconds wall clock time: 51 minutes 18.21 seconds (3078.21 seconds total)