Starting phenix.real_space_refine on Fri Jul 25 11:29:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r84_18994/07_2025/8r84_18994.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r84_18994/07_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_18994/07_2025/8r84_18994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r84_18994/07_2025/8r84_18994.map" model { file = "/net/cci-nas-00/data/ceres_data/8r84_18994/07_2025/8r84_18994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r84_18994/07_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-5711/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: 8.37, per 1000 atoms: 1.12 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: 1.84 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: 1.07 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: 2.28 Time building geometry restraints manager: 2.14 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: 15.000 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 24.470 Find NCS groups from input model: 0.210 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: 43.100 ------------------------------------------------------------------------------- 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 : 0.794 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: 0.2270 time to fit residues: 47.2519 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 : 0.872 ------------------------------------------------------------------------------- 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 = 52)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.165908 restraints weight = 10441.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.165262 restraints weight = 10970.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.166362 restraints weight = 10230.826| |-----------------------------------------------------------------------------| 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 29.842 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 0.93954 ( 3) link_BETA1-4 : bond 0.00797 ( 1) link_BETA1-4 : angle 2.13419 ( 3) hydrogen bonds : bond 0.04551 ( 212) hydrogen bonds : angle 5.71223 ( 654) SS BOND : bond 0.00418 ( 19) SS BOND : angle 1.51561 ( 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 : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 312 ASN cc_start: 0.8745 (m110) cc_final: 0.8469 (m-40) REVERT: N 324 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7859 (tt0) REVERT: N 336 THR cc_start: 0.8636 (m) cc_final: 0.8333 (p) REVERT: N 337 HIS cc_start: 0.7444 (m90) cc_final: 0.7176 (m90) REVERT: N 338 GLN cc_start: 0.8394 (mt0) cc_final: 0.8179 (mp10) REVERT: A 483 ASP cc_start: 0.6816 (t0) cc_final: 0.6399 (m-30) REVERT: J 123 MET cc_start: 0.6172 (mpp) cc_final: 0.5856 (mpp) outliers start: 28 outliers final: 14 residues processed: 136 average time/residue: 0.2203 time to fit residues: 39.3523 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 : 0.897 ------------------------------------------------------------------------------- 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: 0.4980 chunk 73 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 13 optimal weight: 0.0070 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.4359 r_free = 0.4359 target = 0.194823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.161675 restraints weight = 10612.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.160140 restraints weight = 12634.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.161187 restraints weight = 12481.696| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7669 Z= 0.152 Angle : 0.588 6.663 10483 Z= 0.300 Chirality : 0.045 0.156 1184 Planarity : 0.005 0.060 1359 Dihedral : 3.990 25.877 1078 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.63 % Allowed : 21.00 % Favored : 74.38 % 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: 0.05 (0.27), residues: 937 helix: 0.37 (0.61), residues: 79 sheet: 1.45 (0.30), residues: 280 loop : -0.78 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 235 HIS 0.010 0.001 HIS L 518 PHE 0.018 0.002 PHE L 479 TYR 0.019 0.001 TYR N 160 ARG 0.004 0.000 ARG L 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00077 ( 1) link_NAG-ASN : angle 1.27819 ( 3) link_BETA1-4 : bond 0.00839 ( 1) link_BETA1-4 : angle 1.94663 ( 3) hydrogen bonds : bond 0.04017 ( 212) hydrogen bonds : angle 5.14100 ( 654) SS BOND : bond 0.00314 ( 19) SS BOND : angle 1.71051 ( 38) covalent geometry : bond 0.00369 ( 7648) covalent geometry : angle 0.57842 (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 135 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 96 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 312 ASN cc_start: 0.8737 (m110) cc_final: 0.8452 (m-40) REVERT: N 345 CYS cc_start: 0.6197 (OUTLIER) cc_final: 0.5964 (m) REVERT: B 546 ARG cc_start: 0.5925 (OUTLIER) cc_final: 0.5539 (ttt-90) REVERT: L 545 ASN cc_start: 0.7101 (OUTLIER) cc_final: 0.6850 (t0) REVERT: A 483 ASP cc_start: 0.6841 (t0) cc_final: 0.6411 (m-30) outliers start: 39 outliers final: 26 residues processed: 129 average time/residue: 0.2113 time to fit residues: 36.2755 Evaluate side-chains 113 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 285 LEU Chi-restraints excluded: chain N residue 344 ILE Chi-restraints excluded: chain N residue 345 CYS Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 546 ARG Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 359 LEU Chi-restraints excluded: chain L residue 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 515 TYR 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: 0.7980 chunk 36 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 49 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4336 r_free = 0.4336 target = 0.192871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.155345 restraints weight = 10579.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.154739 restraints weight = 13030.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.157827 restraints weight = 10188.968| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7669 Z= 0.150 Angle : 0.577 6.063 10483 Z= 0.294 Chirality : 0.044 0.140 1184 Planarity : 0.005 0.055 1359 Dihedral : 4.002 26.215 1078 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.86 % Allowed : 21.83 % 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: 0.03 (0.27), residues: 937 helix: 0.34 (0.62), residues: 79 sheet: 1.50 (0.30), residues: 278 loop : -0.82 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 235 HIS 0.007 0.001 HIS L 518 PHE 0.019 0.002 PHE A 516 TYR 0.012 0.001 TYR N 160 ARG 0.003 0.000 ARG L 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00030 ( 1) link_NAG-ASN : angle 1.36031 ( 3) link_BETA1-4 : bond 0.00894 ( 1) link_BETA1-4 : angle 1.76258 ( 3) hydrogen bonds : bond 0.03700 ( 212) hydrogen bonds : angle 4.93106 ( 654) SS BOND : bond 0.00324 ( 19) SS BOND : angle 1.74073 ( 38) covalent geometry : bond 0.00367 ( 7648) covalent geometry : angle 0.56755 (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 126 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 85 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 312 ASN cc_start: 0.8791 (m110) cc_final: 0.8469 (m-40) REVERT: L 476 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8527 (t) REVERT: A 483 ASP cc_start: 0.6880 (t0) cc_final: 0.6427 (m-30) outliers start: 41 outliers final: 30 residues processed: 119 average time/residue: 0.1849 time to fit residues: 30.0735 Evaluate side-chains 111 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 174 VAL 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 551 THR Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 381 SER Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 530 THR Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain K residue 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 K residue 535 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 523 VAL 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: 0.0040 chunk 16 optimal weight: 0.0270 chunk 21 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.2850 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.179575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.144045 restraints weight = 10602.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.143005 restraints weight = 14882.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.145306 restraints weight = 12485.849| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7669 Z= 0.106 Angle : 0.557 10.501 10483 Z= 0.284 Chirality : 0.043 0.209 1184 Planarity : 0.004 0.047 1359 Dihedral : 3.798 25.799 1078 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % 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: 0.17 (0.27), residues: 937 helix: 0.36 (0.61), residues: 79 sheet: 1.59 (0.30), residues: 289 loop : -0.76 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 235 HIS 0.006 0.001 HIS L 518 PHE 0.009 0.001 PHE L 479 TYR 0.033 0.001 TYR J 101 ARG 0.006 0.000 ARG B 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00106 ( 1) link_NAG-ASN : angle 1.22524 ( 3) link_BETA1-4 : bond 0.00763 ( 1) link_BETA1-4 : angle 1.70962 ( 3) hydrogen bonds : bond 0.03000 ( 212) hydrogen bonds : angle 4.60704 ( 654) SS BOND : bond 0.00272 ( 19) SS BOND : angle 1.97793 ( 38) covalent geometry : bond 0.00254 ( 7648) covalent geometry : angle 0.54407 (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 121 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 83 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 312 ASN cc_start: 0.8820 (m110) cc_final: 0.8463 (m-40) REVERT: L 476 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8477 (t) REVERT: L 545 ASN cc_start: 0.6939 (OUTLIER) cc_final: 0.6668 (t0) REVERT: A 483 ASP cc_start: 0.6906 (t0) cc_final: 0.6447 (m-30) REVERT: J 70 LYS cc_start: 0.6742 (OUTLIER) cc_final: 0.6144 (tttm) outliers start: 38 outliers final: 22 residues processed: 112 average time/residue: 0.2150 time to fit residues: 32.2413 Evaluate side-chains 102 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 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 545 ASN Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 70 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 0 optimal weight: 1.9990 chunk 74 optimal weight: 0.0770 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 17 optimal weight: 0.0470 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 55 optimal weight: 0.1980 overall best weight: 0.2236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 400 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.194647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.161030 restraints weight = 10541.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.160095 restraints weight = 13835.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.163060 restraints weight = 11401.713| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7669 Z= 0.091 Angle : 0.527 6.368 10483 Z= 0.268 Chirality : 0.042 0.130 1184 Planarity : 0.004 0.045 1359 Dihedral : 3.648 26.415 1078 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.03 % Allowed : 22.54 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.25 (0.28), residues: 937 helix: 0.44 (0.61), residues: 79 sheet: 1.76 (0.31), residues: 281 loop : -0.74 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 235 HIS 0.007 0.001 HIS N 155 PHE 0.021 0.001 PHE A 516 TYR 0.014 0.001 TYR N 160 ARG 0.005 0.000 ARG N 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 1) link_NAG-ASN : angle 1.05915 ( 3) link_BETA1-4 : bond 0.00673 ( 1) link_BETA1-4 : angle 1.62172 ( 3) hydrogen bonds : bond 0.02883 ( 212) hydrogen bonds : angle 4.36240 ( 654) SS BOND : bond 0.00256 ( 19) SS BOND : angle 1.85485 ( 38) covalent geometry : bond 0.00215 ( 7648) covalent geometry : angle 0.51500 (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 117 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 83 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: N 228 CYS cc_start: 0.4521 (OUTLIER) cc_final: 0.4020 (m) REVERT: N 312 ASN cc_start: 0.8785 (m110) cc_final: 0.8504 (m-40) REVERT: L 476 VAL cc_start: 0.8769 (OUTLIER) cc_final: 0.8459 (t) REVERT: L 545 ASN cc_start: 0.6897 (OUTLIER) cc_final: 0.6617 (t0) REVERT: A 483 ASP cc_start: 0.6745 (t0) cc_final: 0.6411 (m-30) REVERT: J 70 LYS cc_start: 0.6750 (OUTLIER) cc_final: 0.6299 (tttm) outliers start: 34 outliers final: 23 residues processed: 109 average time/residue: 0.2004 time to fit residues: 29.4803 Evaluate side-chains 108 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP 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 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 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 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: 0.5980 chunk 72 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 15 optimal weight: 0.0170 chunk 79 optimal weight: 0.0000 chunk 14 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 0.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 337 HIS N 338 GLN ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.192306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.158077 restraints weight = 10171.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.157514 restraints weight = 10679.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.158468 restraints weight = 8864.792| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3512 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= 0.109 Angle : 0.536 6.463 10483 Z= 0.272 Chirality : 0.043 0.134 1184 Planarity : 0.004 0.044 1359 Dihedral : 3.667 25.337 1078 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.39 % Allowed : 22.18 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.29 (0.28), residues: 937 helix: 0.42 (0.61), residues: 80 sheet: 1.65 (0.30), residues: 293 loop : -0.68 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 235 HIS 0.008 0.001 HIS N 155 PHE 0.011 0.001 PHE L 479 TYR 0.012 0.001 TYR N 160 ARG 0.006 0.000 ARG B 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00119 ( 1) link_NAG-ASN : angle 1.13036 ( 3) link_BETA1-4 : bond 0.00632 ( 1) link_BETA1-4 : angle 1.58845 ( 3) hydrogen bonds : bond 0.02934 ( 212) hydrogen bonds : angle 4.33046 ( 654) SS BOND : bond 0.00229 ( 19) SS BOND : angle 1.73809 ( 38) covalent geometry : bond 0.00264 ( 7648) covalent geometry : angle 0.52558 (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 120 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 83 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: N 276 LYS cc_start: 0.8646 (mtmm) cc_final: 0.8346 (mtpp) REVERT: N 312 ASN cc_start: 0.8830 (m110) cc_final: 0.8518 (m-40) REVERT: L 476 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8473 (t) REVERT: L 545 ASN cc_start: 0.6821 (OUTLIER) cc_final: 0.6571 (t0) REVERT: A 483 ASP cc_start: 0.6751 (t0) cc_final: 0.6372 (m-30) outliers start: 37 outliers final: 30 residues processed: 111 average time/residue: 0.1919 time to fit residues: 29.2368 Evaluate side-chains 113 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 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 545 ASN Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 12 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 33 optimal weight: 7.9990 chunk 51 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 188 GLN N 337 HIS ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.187205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.155080 restraints weight = 10182.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.156235 restraints weight = 10492.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.158113 restraints weight = 9033.279| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7669 Z= 0.159 Angle : 0.622 8.658 10483 Z= 0.316 Chirality : 0.045 0.142 1184 Planarity : 0.004 0.044 1359 Dihedral : 3.981 23.495 1078 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.51 % Allowed : 22.42 % 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 (0.27), residues: 937 helix: 0.43 (0.61), residues: 80 sheet: 1.61 (0.30), residues: 282 loop : -0.75 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 235 HIS 0.007 0.001 HIS N 155 PHE 0.018 0.002 PHE L 479 TYR 0.013 0.001 TYR N 160 ARG 0.003 0.000 ARG N 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00085 ( 1) link_NAG-ASN : angle 1.42973 ( 3) link_BETA1-4 : bond 0.00594 ( 1) link_BETA1-4 : angle 1.58554 ( 3) hydrogen bonds : bond 0.03544 ( 212) hydrogen bonds : angle 4.57894 ( 654) SS BOND : bond 0.00275 ( 19) SS BOND : angle 2.62410 ( 38) covalent geometry : bond 0.00389 ( 7648) covalent geometry : angle 0.60174 (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 117 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 79 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: N 312 ASN cc_start: 0.8767 (m110) cc_final: 0.8528 (m-40) REVERT: L 476 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8516 (t) REVERT: L 545 ASN cc_start: 0.6773 (OUTLIER) cc_final: 0.6530 (t0) REVERT: A 483 ASP cc_start: 0.6761 (t0) cc_final: 0.6413 (m-30) REVERT: J 70 LYS cc_start: 0.6847 (OUTLIER) cc_final: 0.6463 (tttm) outliers start: 38 outliers final: 31 residues processed: 111 average time/residue: 0.1855 time to fit residues: 28.4656 Evaluate side-chains 110 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 76 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 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 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 471 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 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: 0.9980 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 0.0470 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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** L 545 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.191197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.157140 restraints weight = 10620.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.157015 restraints weight = 12340.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.157816 restraints weight = 10806.152| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7669 Z= 0.163 Angle : 0.615 8.205 10483 Z= 0.313 Chirality : 0.044 0.143 1184 Planarity : 0.004 0.042 1359 Dihedral : 3.959 18.308 1078 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.27 % Allowed : 22.78 % Favored : 72.95 % 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: 0.57 (0.62), residues: 78 sheet: 1.48 (0.30), residues: 282 loop : -0.82 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 235 HIS 0.007 0.001 HIS N 155 PHE 0.018 0.002 PHE L 479 TYR 0.017 0.001 TYR N 160 ARG 0.003 0.000 ARG J 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00070 ( 1) link_NAG-ASN : angle 1.53124 ( 3) link_BETA1-4 : bond 0.00593 ( 1) link_BETA1-4 : angle 1.55375 ( 3) hydrogen bonds : bond 0.03538 ( 212) hydrogen bonds : angle 4.64881 ( 654) SS BOND : bond 0.00401 ( 19) SS BOND : angle 2.17232 ( 38) covalent geometry : bond 0.00398 ( 7648) covalent geometry : angle 0.60067 (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 112 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 76 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: N 312 ASN cc_start: 0.8798 (m110) cc_final: 0.8546 (m-40) REVERT: L 545 ASN cc_start: 0.6974 (t0) cc_final: 0.6673 (t0) REVERT: A 483 ASP cc_start: 0.6850 (t0) cc_final: 0.6465 (m-30) REVERT: J 70 LYS cc_start: 0.6915 (OUTLIER) cc_final: 0.6446 (tttp) outliers start: 36 outliers final: 31 residues processed: 108 average time/residue: 0.1960 time to fit residues: 29.6935 Evaluate side-chains 103 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 71 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 414 CYS Chi-restraints excluded: chain L residue 417 ASP Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 530 THR Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 60 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 0.0970 chunk 87 optimal weight: 0.3980 chunk 27 optimal weight: 0.0040 chunk 21 optimal weight: 0.4980 chunk 69 optimal weight: 0.0670 chunk 91 optimal weight: 0.9990 overall best weight: 0.2128 ------------------------------------------------------------------------------- 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 = 0.4359 r_free = 0.4359 target = 0.194261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.161442 restraints weight = 10578.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.159798 restraints weight = 13008.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.162769 restraints weight = 11846.392| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 7669 Z= 0.100 Angle : 0.564 8.058 10483 Z= 0.285 Chirality : 0.042 0.152 1184 Planarity : 0.004 0.042 1359 Dihedral : 3.711 21.311 1078 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.20 % Allowed : 23.84 % Favored : 72.95 % 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: 0.26 (0.28), residues: 937 helix: 0.61 (0.62), residues: 78 sheet: 1.72 (0.30), residues: 286 loop : -0.76 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 488 HIS 0.007 0.001 HIS N 155 PHE 0.008 0.001 PHE L 479 TYR 0.014 0.001 TYR N 160 ARG 0.003 0.000 ARG N 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 1) link_NAG-ASN : angle 1.18594 ( 3) link_BETA1-4 : bond 0.00726 ( 1) link_BETA1-4 : angle 1.44832 ( 3) hydrogen bonds : bond 0.02802 ( 212) hydrogen bonds : angle 4.31365 ( 654) SS BOND : bond 0.00194 ( 19) SS BOND : angle 1.62974 ( 38) covalent geometry : bond 0.00236 ( 7648) covalent geometry : angle 0.55554 (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: 27 poor density : 78 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: N 312 ASN cc_start: 0.8781 (m110) cc_final: 0.8540 (m-40) REVERT: L 545 ASN cc_start: 0.6943 (t0) cc_final: 0.6608 (t0) REVERT: A 483 ASP cc_start: 0.6765 (t0) cc_final: 0.6415 (m-30) REVERT: J 70 LYS cc_start: 0.6781 (OUTLIER) cc_final: 0.6310 (tttp) outliers start: 27 outliers final: 25 residues processed: 99 average time/residue: 0.1949 time to fit residues: 27.0392 Evaluate side-chains 98 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 532 GLU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain L residue 381 SER Chi-restraints excluded: chain L residue 414 CYS 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 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 18 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 71 optimal weight: 0.1980 chunk 57 optimal weight: 0.0030 chunk 75 optimal weight: 0.8980 chunk 8 optimal weight: 0.0000 chunk 12 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 90 optimal weight: 0.9990 overall best weight: 0.2994 ------------------------------------------------------------------------------- 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** ** 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 = 0.4353 r_free = 0.4353 target = 0.193764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.160708 restraints weight = 10505.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.159907 restraints weight = 12563.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.162965 restraints weight = 11074.259| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3925 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= 0.103 Angle : 0.549 6.745 10483 Z= 0.279 Chirality : 0.042 0.134 1184 Planarity : 0.004 0.039 1359 Dihedral : 3.645 21.684 1078 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.32 % Allowed : 23.96 % Favored : 72.72 % 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: 0.34 (0.28), residues: 937 helix: 0.80 (0.63), residues: 77 sheet: 1.60 (0.30), residues: 293 loop : -0.64 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 159 HIS 0.007 0.001 HIS N 155 PHE 0.010 0.001 PHE L 479 TYR 0.016 0.001 TYR K 500 ARG 0.003 0.000 ARG J 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00123 ( 1) link_NAG-ASN : angle 1.11997 ( 3) link_BETA1-4 : bond 0.00577 ( 1) link_BETA1-4 : angle 1.46190 ( 3) hydrogen bonds : bond 0.02878 ( 212) hydrogen bonds : angle 4.26799 ( 654) SS BOND : bond 0.00201 ( 19) SS BOND : angle 1.52941 ( 38) covalent geometry : bond 0.00248 ( 7648) covalent geometry : angle 0.54183 (10439) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2970.43 seconds wall clock time: 52 minutes 10.10 seconds (3130.10 seconds total)