Starting phenix.real_space_refine on Wed Mar 4 00:54:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uqy_26702/03_2026/7uqy_26702.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uqy_26702/03_2026/7uqy_26702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uqy_26702/03_2026/7uqy_26702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uqy_26702/03_2026/7uqy_26702.map" model { file = "/net/cci-nas-00/data/ceres_data/7uqy_26702/03_2026/7uqy_26702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uqy_26702/03_2026/7uqy_26702.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.035 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 P 2 5.49 5 S 46 5.16 5 C 6148 2.51 5 N 1612 2.21 5 O 1748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9556 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4750 Classifications: {'peptide': 582} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 554} Chain breaks: 3 Chain: "B" Number of atoms: 4742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4742 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 38, 'TRANS': 546} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.25, per 1000 atoms: 0.24 Number of scatterers: 9556 At special positions: 0 Unit cell: (102.672, 87.768, 111.78, 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) S 46 16.00 P 2 15.00 O 1748 8.00 N 1612 7.00 C 6148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 103 " distance=2.04 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 312 " distance=2.04 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 704 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 626 " - pdb=" SG CYS B 676 " 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 C 2 " - " BMA C 3 " NAG-ASN " NAG C 1 " - " ASN B 637 " Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 483.1 milliseconds 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 11 sheets defined 39.0% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.751A pdb=" N LEU A 108 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 141 Processing helix chain 'A' and resid 173 through 179 removed outlier: 3.806A pdb=" N GLN A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.718A pdb=" N ALA A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 4.051A pdb=" N VAL A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.996A pdb=" N GLN A 305 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 320 removed outlier: 3.677A pdb=" N GLU A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 345 through 353 Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 388 through 396 removed outlier: 3.510A pdb=" N THR A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 415 Processing helix chain 'A' and resid 418 through 432 Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.798A pdb=" N TRP A 445 " --> pdb=" O ASN A 441 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 446' Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 496 through 506 Processing helix chain 'A' and resid 547 through 551 removed outlier: 3.825A pdb=" N PHE A 550 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 551 " --> pdb=" O SER A 548 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 547 through 551' Processing helix chain 'A' and resid 571 through 585 removed outlier: 3.574A pdb=" N SER A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 removed outlier: 3.829A pdb=" N TYR A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 650 removed outlier: 3.832A pdb=" N LYS A 643 " --> pdb=" O PRO A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 Processing helix chain 'A' and resid 697 through 713 removed outlier: 3.671A pdb=" N ARG A 701 " --> pdb=" O HIS A 697 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN A 702 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 139 Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 166 through 177 Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 262 through 277 removed outlier: 3.851A pdb=" N ASP B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.927A pdb=" N LEU B 312 " --> pdb=" O TYR B 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 312' Processing helix chain 'B' and resid 329 through 338 removed outlier: 3.685A pdb=" N ASP B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 372 through 378 Processing helix chain 'B' and resid 381 through 400 Processing helix chain 'B' and resid 402 through 419 Processing helix chain 'B' and resid 420 through 423 Processing helix chain 'B' and resid 425 through 431 Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 466 through 478 removed outlier: 3.894A pdb=" N ARG B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU B 475 " --> pdb=" O ARG B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 502 Processing helix chain 'B' and resid 518 through 524 removed outlier: 4.050A pdb=" N ARG B 522 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 524 " --> pdb=" O ASN B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 559 removed outlier: 3.768A pdb=" N GLU B 558 " --> pdb=" O GLU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 610 Processing helix chain 'B' and resid 613 through 624 removed outlier: 3.781A pdb=" N LYS B 617 " --> pdb=" O PRO B 613 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN B 618 " --> pdb=" O GLY B 614 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TRP B 619 " --> pdb=" O ASP B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 640 Processing helix chain 'B' and resid 671 through 685 Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 145 removed outlier: 6.168A pdb=" N VAL A 116 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE A 154 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N PHE A 193 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N HIS A 190 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ALA A 217 " --> pdb=" O HIS A 190 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE A 192 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 297 removed outlier: 3.602A pdb=" N THR A 297 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N MET A 263 " --> pdb=" O PHE A 333 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU A 335 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL A 265 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR A 332 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL A 358 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N CYS A 334 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 510 through 517 removed outlier: 7.135A pdb=" N PHE A 480 " --> pdb=" O GLN A 512 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ILE A 514 " --> pdb=" O PHE A 480 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA A 482 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU A 516 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A 484 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS A 485 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 624 " --> pdb=" O SER A 563 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 605 through 609 Processing sheet with id=AA5, first strand: chain 'A' and resid 724 through 726 Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 189 removed outlier: 6.341A pdb=" N LEU B 188 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B 212 " --> pdb=" O VAL B 228 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 280 through 283 removed outlier: 8.280A pdb=" N LEU B 281 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU B 254 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LEU B 283 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER B 256 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE B 253 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL B 319 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU B 255 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 340 " --> pdb=" O THR B 316 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 509 through 513 removed outlier: 6.161A pdb=" N PHE B 456 " --> pdb=" O LYS B 484 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU B 486 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA B 458 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL B 488 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 460 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 461 " --> pdb=" O ILE B 537 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE B 644 " --> pdb=" O LEU B 563 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 570 through 574 removed outlier: 3.623A pdb=" N GLU B 583 " --> pdb=" O LEU B 570 " (cutoff:3.500A) 307 hydrogen bonds defined for protein. 834 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1529 1.32 - 1.45: 2807 1.45 - 1.57: 5405 1.57 - 1.70: 3 1.70 - 1.82: 71 Bond restraints: 9815 Sorted by residual: bond pdb=" O1A UDP A 801 " pdb=" PA UDP A 801 " ideal model delta sigma weight residual 1.482 1.526 -0.044 1.00e-02 1.00e+04 1.89e+01 bond pdb=" N ILE B 449 " pdb=" CA ILE B 449 " ideal model delta sigma weight residual 1.458 1.487 -0.030 7.70e-03 1.69e+04 1.47e+01 bond pdb=" C PRO B 443 " pdb=" O PRO B 443 " ideal model delta sigma weight residual 1.237 1.194 0.044 1.28e-02 6.10e+03 1.16e+01 bond pdb=" N ASN B 442 " pdb=" CA ASN B 442 " ideal model delta sigma weight residual 1.455 1.499 -0.044 1.39e-02 5.18e+03 1.01e+01 bond pdb=" N PHE B 445 " pdb=" CA PHE B 445 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.26e-02 6.30e+03 7.00e+00 ... (remaining 9810 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 12883 1.43 - 2.86: 365 2.86 - 4.30: 66 4.30 - 5.73: 23 5.73 - 7.16: 2 Bond angle restraints: 13339 Sorted by residual: angle pdb=" O5' UDP A 801 " pdb=" PA UDP A 801 " pdb=" O1A UDP A 801 " ideal model delta sigma weight residual 106.70 111.14 -4.44 1.00e+00 1.00e+00 1.97e+01 angle pdb=" O2A UDP A 801 " pdb=" PA UDP A 801 " pdb=" O3A UDP A 801 " ideal model delta sigma weight residual 105.97 110.22 -4.25 1.00e+00 1.00e+00 1.81e+01 angle pdb=" O5' UDP A 801 " pdb=" PA UDP A 801 " pdb=" O2A UDP A 801 " ideal model delta sigma weight residual 110.83 106.97 3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" O1A UDP A 801 " pdb=" PA UDP A 801 " pdb=" O3A UDP A 801 " ideal model delta sigma weight residual 109.95 106.32 3.63 1.00e+00 1.00e+00 1.32e+01 angle pdb=" CA TRP B 396 " pdb=" C TRP B 396 " pdb=" O TRP B 396 " ideal model delta sigma weight residual 120.55 116.95 3.60 1.07e+00 8.73e-01 1.13e+01 ... (remaining 13334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.61: 5540 21.61 - 43.21: 329 43.21 - 64.82: 33 64.82 - 86.42: 17 86.42 - 108.03: 5 Dihedral angle restraints: 5924 sinusoidal: 2476 harmonic: 3448 Sorted by residual: dihedral pdb=" CB CYS B 85 " pdb=" SG CYS B 85 " pdb=" SG CYS B 90 " pdb=" CB CYS B 90 " ideal model delta sinusoidal sigma weight residual -86.00 -173.57 87.57 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CB CYS B 96 " pdb=" SG CYS B 96 " pdb=" SG CYS B 151 " pdb=" CB CYS B 151 " ideal model delta sinusoidal sigma weight residual 93.00 9.45 83.55 1 1.00e+01 1.00e-02 8.52e+01 dihedral pdb=" CB CYS A 298 " pdb=" SG CYS A 298 " pdb=" SG CYS A 312 " pdb=" CB CYS A 312 " ideal model delta sinusoidal sigma weight residual 93.00 150.67 -57.67 1 1.00e+01 1.00e-02 4.47e+01 ... (remaining 5921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1151 0.053 - 0.105: 252 0.105 - 0.158: 45 0.158 - 0.210: 1 0.210 - 0.263: 2 Chirality restraints: 1451 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CG LEU B 160 " pdb=" CB LEU B 160 " pdb=" CD1 LEU B 160 " pdb=" CD2 LEU B 160 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE B 449 " pdb=" N ILE B 449 " pdb=" C ILE B 449 " pdb=" CB ILE B 449 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1448 not shown) Planarity restraints: 1695 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 697 " 0.049 5.00e-02 4.00e+02 7.48e-02 8.94e+00 pdb=" N PRO B 698 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 698 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 698 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 395 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" C PHE B 395 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE B 395 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP B 396 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 638 " -0.041 5.00e-02 4.00e+02 6.07e-02 5.90e+00 pdb=" N PRO A 639 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 639 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 639 " -0.034 5.00e-02 4.00e+02 ... (remaining 1692 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 652 2.74 - 3.28: 9656 3.28 - 3.82: 16181 3.82 - 4.36: 19400 4.36 - 4.90: 33136 Nonbonded interactions: 79025 Sorted by model distance: nonbonded pdb=" OD2 ASP A 147 " pdb=" OG SER A 149 " model vdw 2.197 3.040 nonbonded pdb=" OH TYR B 130 " pdb=" O PRO B 155 " model vdw 2.248 3.040 nonbonded pdb=" OG SER A 439 " pdb=" NZ LYS B 359 " model vdw 2.257 3.120 nonbonded pdb=" O GLU A 587 " pdb=" OH TYR A 630 " model vdw 2.263 3.040 nonbonded pdb=" N ASN A 254 " pdb=" OE2 GLU B 532 " model vdw 2.279 3.120 ... (remaining 79020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.390 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 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 : 0.003 0.068 9827 Z= 0.171 Angle : 0.593 7.160 13366 Z= 0.322 Chirality : 0.045 0.263 1451 Planarity : 0.005 0.075 1694 Dihedral : 13.643 108.028 3669 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.25), residues: 1151 helix: 0.74 (0.28), residues: 359 sheet: -0.35 (0.42), residues: 152 loop : -0.50 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 383 TYR 0.018 0.001 TYR B 582 PHE 0.010 0.001 PHE A 250 TRP 0.013 0.001 TRP B 619 HIS 0.005 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9815) covalent geometry : angle 0.59078 (13339) SS BOND : bond 0.00380 ( 9) SS BOND : angle 1.21526 ( 18) hydrogen bonds : bond 0.20549 ( 307) hydrogen bonds : angle 6.86654 ( 834) link_BETA1-4 : bond 0.00274 ( 2) link_BETA1-4 : angle 1.31849 ( 6) link_NAG-ASN : bond 0.00195 ( 1) link_NAG-ASN : angle 1.16626 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.328 Fit side-chains REVERT: A 250 PHE cc_start: 0.6036 (t80) cc_final: 0.5787 (t80) REVERT: A 265 VAL cc_start: 0.6249 (m) cc_final: 0.4518 (t) REVERT: B 92 ASP cc_start: 0.7698 (t0) cc_final: 0.7492 (t70) outliers start: 0 outliers final: 1 residues processed: 242 average time/residue: 0.4841 time to fit residues: 126.2943 Evaluate side-chains 213 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.0980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 185 ASN A 189 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 384 GLN B 625 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.149085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.131722 restraints weight = 13801.668| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.32 r_work: 0.3648 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9827 Z= 0.152 Angle : 0.602 8.421 13366 Z= 0.304 Chirality : 0.045 0.161 1451 Planarity : 0.005 0.060 1694 Dihedral : 8.364 107.686 1377 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.73 % Allowed : 11.41 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.25), residues: 1151 helix: 0.91 (0.28), residues: 362 sheet: -0.31 (0.43), residues: 148 loop : -0.41 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 142 TYR 0.020 0.002 TYR B 582 PHE 0.019 0.002 PHE B 652 TRP 0.011 0.001 TRP B 556 HIS 0.003 0.001 HIS B 601 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9815) covalent geometry : angle 0.59972 (13339) SS BOND : bond 0.00248 ( 9) SS BOND : angle 0.77640 ( 18) hydrogen bonds : bond 0.04360 ( 307) hydrogen bonds : angle 5.36900 ( 834) link_BETA1-4 : bond 0.00092 ( 2) link_BETA1-4 : angle 2.30271 ( 6) link_NAG-ASN : bond 0.00427 ( 1) link_NAG-ASN : angle 1.29801 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 244 time to evaluate : 0.336 Fit side-chains REVERT: A 105 ASP cc_start: 0.7592 (t0) cc_final: 0.7325 (t0) REVERT: A 115 LYS cc_start: 0.7593 (mmmm) cc_final: 0.7293 (mmmm) REVERT: A 265 VAL cc_start: 0.6524 (m) cc_final: 0.4758 (t) REVERT: A 413 GLU cc_start: 0.7727 (tt0) cc_final: 0.7288 (tt0) REVERT: A 447 LYS cc_start: 0.8192 (tppt) cc_final: 0.7931 (mttp) REVERT: A 664 VAL cc_start: 0.8559 (m) cc_final: 0.8309 (t) REVERT: B 174 MET cc_start: 0.4656 (OUTLIER) cc_final: 0.4133 (mtt) REVERT: B 367 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7574 (mt-10) REVERT: B 573 TRP cc_start: 0.7979 (t-100) cc_final: 0.7503 (t-100) outliers start: 18 outliers final: 2 residues processed: 249 average time/residue: 0.4925 time to fit residues: 132.5363 Evaluate side-chains 225 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 222 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 45 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 189 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 412 GLN B 623 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.149309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.131630 restraints weight = 13729.106| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.35 r_work: 0.3635 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9827 Z= 0.139 Angle : 0.578 7.716 13366 Z= 0.290 Chirality : 0.045 0.166 1451 Planarity : 0.004 0.058 1694 Dihedral : 6.992 58.829 1375 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.59 % Allowed : 14.09 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.25), residues: 1151 helix: 1.05 (0.28), residues: 364 sheet: -0.45 (0.42), residues: 154 loop : -0.39 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 149 TYR 0.020 0.001 TYR B 582 PHE 0.018 0.001 PHE B 400 TRP 0.011 0.001 TRP A 374 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9815) covalent geometry : angle 0.57610 (13339) SS BOND : bond 0.00235 ( 9) SS BOND : angle 0.63709 ( 18) hydrogen bonds : bond 0.03953 ( 307) hydrogen bonds : angle 5.06553 ( 834) link_BETA1-4 : bond 0.00243 ( 2) link_BETA1-4 : angle 2.34279 ( 6) link_NAG-ASN : bond 0.00430 ( 1) link_NAG-ASN : angle 1.36936 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 231 time to evaluate : 0.299 Fit side-chains REVERT: A 105 ASP cc_start: 0.7622 (t0) cc_final: 0.7311 (t0) REVERT: A 147 ASP cc_start: 0.7900 (t0) cc_final: 0.7644 (t0) REVERT: A 265 VAL cc_start: 0.6564 (m) cc_final: 0.4857 (t) REVERT: A 295 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7329 (mt) REVERT: A 413 GLU cc_start: 0.7715 (tt0) cc_final: 0.7439 (tt0) REVERT: A 447 LYS cc_start: 0.8155 (tppt) cc_final: 0.7927 (mmtp) REVERT: A 645 MET cc_start: 0.7247 (tmm) cc_final: 0.7007 (tmm) REVERT: A 664 VAL cc_start: 0.8602 (m) cc_final: 0.8380 (t) REVERT: B 174 MET cc_start: 0.4558 (OUTLIER) cc_final: 0.3919 (mtt) REVERT: B 266 ARG cc_start: 0.8183 (tpp-160) cc_final: 0.7799 (tpp-160) REVERT: B 270 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7039 (mm-30) REVERT: B 367 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7569 (mt-10) REVERT: B 386 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7679 (mt-10) REVERT: B 512 VAL cc_start: 0.8123 (t) cc_final: 0.7895 (m) REVERT: B 573 TRP cc_start: 0.7964 (t-100) cc_final: 0.7606 (t-100) outliers start: 27 outliers final: 7 residues processed: 241 average time/residue: 0.4708 time to fit residues: 123.0026 Evaluate side-chains 228 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 219 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 7 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 56 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 189 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.148896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.131465 restraints weight = 13938.061| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.33 r_work: 0.3639 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9827 Z= 0.130 Angle : 0.558 8.195 13366 Z= 0.279 Chirality : 0.044 0.142 1451 Planarity : 0.004 0.052 1694 Dihedral : 6.403 59.640 1375 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.78 % Allowed : 15.44 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.25), residues: 1151 helix: 1.26 (0.28), residues: 359 sheet: -0.38 (0.43), residues: 153 loop : -0.43 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 149 TYR 0.021 0.001 TYR B 582 PHE 0.030 0.002 PHE B 551 TRP 0.010 0.001 TRP A 374 HIS 0.004 0.001 HIS B 575 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9815) covalent geometry : angle 0.55560 (13339) SS BOND : bond 0.00283 ( 9) SS BOND : angle 0.55079 ( 18) hydrogen bonds : bond 0.03577 ( 307) hydrogen bonds : angle 4.89134 ( 834) link_BETA1-4 : bond 0.00326 ( 2) link_BETA1-4 : angle 2.33254 ( 6) link_NAG-ASN : bond 0.00304 ( 1) link_NAG-ASN : angle 1.27049 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 0.293 Fit side-chains REVERT: A 105 ASP cc_start: 0.7572 (t0) cc_final: 0.7309 (t0) REVERT: A 132 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6764 (mp-120) REVERT: A 147 ASP cc_start: 0.7873 (t0) cc_final: 0.7602 (t0) REVERT: A 265 VAL cc_start: 0.6632 (m) cc_final: 0.4863 (t) REVERT: A 295 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7348 (mt) REVERT: A 413 GLU cc_start: 0.7701 (tt0) cc_final: 0.7417 (tt0) REVERT: A 653 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6628 (pt0) REVERT: B 109 TYR cc_start: 0.7647 (m-80) cc_final: 0.7429 (m-80) REVERT: B 270 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7045 (mm-30) REVERT: B 367 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7606 (mt-10) REVERT: B 386 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7593 (mt-10) REVERT: B 427 GLU cc_start: 0.7381 (mp0) cc_final: 0.7022 (mp0) REVERT: B 512 VAL cc_start: 0.8158 (t) cc_final: 0.7939 (m) REVERT: B 675 GLU cc_start: 0.7699 (tp30) cc_final: 0.7498 (tp30) outliers start: 29 outliers final: 11 residues processed: 238 average time/residue: 0.4678 time to fit residues: 120.4845 Evaluate side-chains 233 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 219 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 61 optimal weight: 4.9990 chunk 35 optimal weight: 0.0980 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 0.0370 chunk 113 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.150040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.132442 restraints weight = 13971.007| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.35 r_work: 0.3656 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9827 Z= 0.112 Angle : 0.571 11.616 13366 Z= 0.280 Chirality : 0.043 0.168 1451 Planarity : 0.004 0.055 1694 Dihedral : 6.060 57.685 1375 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.59 % Allowed : 17.16 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.25), residues: 1151 helix: 1.34 (0.28), residues: 360 sheet: -0.29 (0.43), residues: 152 loop : -0.48 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 248 TYR 0.022 0.001 TYR B 582 PHE 0.024 0.001 PHE B 400 TRP 0.010 0.001 TRP B 396 HIS 0.019 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9815) covalent geometry : angle 0.56866 (13339) SS BOND : bond 0.00297 ( 9) SS BOND : angle 0.53870 ( 18) hydrogen bonds : bond 0.03288 ( 307) hydrogen bonds : angle 4.76513 ( 834) link_BETA1-4 : bond 0.00484 ( 2) link_BETA1-4 : angle 2.42242 ( 6) link_NAG-ASN : bond 0.00116 ( 1) link_NAG-ASN : angle 1.12787 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 229 time to evaluate : 0.356 Fit side-chains REVERT: A 105 ASP cc_start: 0.7579 (t0) cc_final: 0.7261 (t0) REVERT: A 132 GLN cc_start: 0.7161 (OUTLIER) cc_final: 0.6740 (mp-120) REVERT: A 147 ASP cc_start: 0.7885 (t0) cc_final: 0.7613 (t0) REVERT: A 250 PHE cc_start: 0.6802 (t80) cc_final: 0.5972 (t80) REVERT: A 265 VAL cc_start: 0.6649 (m) cc_final: 0.4898 (t) REVERT: A 413 GLU cc_start: 0.7690 (tt0) cc_final: 0.7374 (tt0) REVERT: A 653 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6631 (pt0) REVERT: A 664 VAL cc_start: 0.8574 (m) cc_final: 0.8340 (t) REVERT: B 109 TYR cc_start: 0.7648 (m-80) cc_final: 0.7341 (m-80) REVERT: B 129 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6571 (mm-30) REVERT: B 266 ARG cc_start: 0.8035 (tpp-160) cc_final: 0.7628 (tpp-160) REVERT: B 270 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7013 (mm-30) REVERT: B 367 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7606 (mt-10) REVERT: B 386 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7599 (mt-10) REVERT: B 428 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7310 (tm-30) REVERT: B 473 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7276 (tp) REVERT: B 512 VAL cc_start: 0.8143 (t) cc_final: 0.7922 (m) REVERT: B 516 GLU cc_start: 0.6662 (mp0) cc_final: 0.6323 (mp0) REVERT: B 619 TRP cc_start: 0.8404 (t60) cc_final: 0.8135 (t60) outliers start: 27 outliers final: 12 residues processed: 241 average time/residue: 0.4931 time to fit residues: 128.1462 Evaluate side-chains 233 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 218 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 473 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 56 optimal weight: 0.9990 chunk 69 optimal weight: 0.0170 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 106 optimal weight: 0.0070 chunk 10 optimal weight: 0.7980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.150164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.132401 restraints weight = 13935.018| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.38 r_work: 0.3661 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9827 Z= 0.113 Angle : 0.570 9.311 13366 Z= 0.279 Chirality : 0.043 0.140 1451 Planarity : 0.004 0.064 1694 Dihedral : 5.846 56.008 1375 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.88 % Allowed : 17.16 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.25), residues: 1151 helix: 1.37 (0.29), residues: 360 sheet: -0.24 (0.44), residues: 148 loop : -0.46 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 248 TYR 0.022 0.001 TYR B 582 PHE 0.026 0.001 PHE B 400 TRP 0.011 0.001 TRP B 396 HIS 0.014 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9815) covalent geometry : angle 0.56797 (13339) SS BOND : bond 0.00176 ( 9) SS BOND : angle 0.50366 ( 18) hydrogen bonds : bond 0.03243 ( 307) hydrogen bonds : angle 4.70586 ( 834) link_BETA1-4 : bond 0.00266 ( 2) link_BETA1-4 : angle 2.37572 ( 6) link_NAG-ASN : bond 0.00081 ( 1) link_NAG-ASN : angle 1.08672 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7621 (t0) cc_final: 0.7292 (t0) REVERT: A 115 LYS cc_start: 0.7679 (mmtm) cc_final: 0.7342 (mmmm) REVERT: A 132 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6600 (mp10) REVERT: A 147 ASP cc_start: 0.7910 (t0) cc_final: 0.7607 (t0) REVERT: A 250 PHE cc_start: 0.6923 (t80) cc_final: 0.6261 (t80) REVERT: A 265 VAL cc_start: 0.6661 (m) cc_final: 0.4934 (t) REVERT: A 413 GLU cc_start: 0.7682 (tt0) cc_final: 0.7421 (tt0) REVERT: A 653 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6635 (pt0) REVERT: A 664 VAL cc_start: 0.8554 (m) cc_final: 0.8326 (t) REVERT: B 104 ILE cc_start: 0.7861 (mm) cc_final: 0.7531 (tp) REVERT: B 109 TYR cc_start: 0.7706 (m-80) cc_final: 0.7459 (m-80) REVERT: B 129 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6547 (mm-30) REVERT: B 270 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7067 (mm-30) REVERT: B 386 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7649 (mt-10) REVERT: B 428 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7279 (tm-30) REVERT: B 512 VAL cc_start: 0.8168 (t) cc_final: 0.7939 (m) outliers start: 30 outliers final: 12 residues processed: 231 average time/residue: 0.4901 time to fit residues: 122.1192 Evaluate side-chains 223 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 209 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 488 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 91 optimal weight: 0.3980 chunk 51 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 38 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** 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 = 0.4004 r_free = 0.4004 target = 0.149935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.132316 restraints weight = 13897.286| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.36 r_work: 0.3652 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9827 Z= 0.123 Angle : 0.581 9.216 13366 Z= 0.285 Chirality : 0.043 0.141 1451 Planarity : 0.004 0.055 1694 Dihedral : 5.735 55.203 1375 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.59 % Allowed : 18.79 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.25), residues: 1151 helix: 1.28 (0.28), residues: 365 sheet: -0.24 (0.43), residues: 148 loop : -0.44 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 142 TYR 0.022 0.001 TYR B 582 PHE 0.036 0.002 PHE B 551 TRP 0.024 0.001 TRP A 304 HIS 0.012 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9815) covalent geometry : angle 0.57873 (13339) SS BOND : bond 0.00212 ( 9) SS BOND : angle 0.49912 ( 18) hydrogen bonds : bond 0.03299 ( 307) hydrogen bonds : angle 4.65954 ( 834) link_BETA1-4 : bond 0.00429 ( 2) link_BETA1-4 : angle 2.41228 ( 6) link_NAG-ASN : bond 0.00104 ( 1) link_NAG-ASN : angle 1.10175 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7631 (t0) cc_final: 0.7239 (t0) REVERT: A 115 LYS cc_start: 0.7706 (mmtm) cc_final: 0.7363 (mmmm) REVERT: A 132 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6776 (mp-120) REVERT: A 147 ASP cc_start: 0.7915 (t0) cc_final: 0.7603 (t0) REVERT: A 265 VAL cc_start: 0.6760 (m) cc_final: 0.5047 (t) REVERT: A 413 GLU cc_start: 0.7694 (tt0) cc_final: 0.7441 (tt0) REVERT: A 653 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6689 (pt0) REVERT: B 104 ILE cc_start: 0.7915 (mm) cc_final: 0.7587 (tp) REVERT: B 109 TYR cc_start: 0.7779 (m-80) cc_final: 0.7483 (m-80) REVERT: B 129 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6554 (mm-30) REVERT: B 266 ARG cc_start: 0.8121 (tpp-160) cc_final: 0.7758 (tpp-160) REVERT: B 270 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7052 (mm-30) REVERT: B 386 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7654 (mt-10) REVERT: B 428 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7244 (tm-30) REVERT: B 512 VAL cc_start: 0.8155 (t) cc_final: 0.7932 (m) REVERT: B 675 GLU cc_start: 0.7734 (tp30) cc_final: 0.7508 (tp30) outliers start: 27 outliers final: 17 residues processed: 232 average time/residue: 0.5000 time to fit residues: 125.1832 Evaluate side-chains 234 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 215 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 572 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 92 optimal weight: 0.1980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.147178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.129589 restraints weight = 13947.458| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.36 r_work: 0.3621 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9827 Z= 0.173 Angle : 0.619 10.029 13366 Z= 0.306 Chirality : 0.045 0.200 1451 Planarity : 0.004 0.062 1694 Dihedral : 5.960 52.731 1375 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.78 % Allowed : 18.98 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.25), residues: 1151 helix: 1.10 (0.28), residues: 371 sheet: -0.49 (0.42), residues: 155 loop : -0.46 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 142 TYR 0.020 0.002 TYR B 582 PHE 0.027 0.002 PHE B 400 TRP 0.018 0.002 TRP A 304 HIS 0.010 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 9815) covalent geometry : angle 0.61624 (13339) SS BOND : bond 0.00251 ( 9) SS BOND : angle 0.56232 ( 18) hydrogen bonds : bond 0.03652 ( 307) hydrogen bonds : angle 4.72041 ( 834) link_BETA1-4 : bond 0.00268 ( 2) link_BETA1-4 : angle 2.51723 ( 6) link_NAG-ASN : bond 0.00374 ( 1) link_NAG-ASN : angle 1.30956 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7571 (t0) cc_final: 0.7306 (t0) REVERT: A 115 LYS cc_start: 0.7786 (mmtm) cc_final: 0.7422 (mmmm) REVERT: A 132 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6855 (mp-120) REVERT: A 143 PHE cc_start: 0.8020 (m-10) cc_final: 0.7661 (m-10) REVERT: A 147 ASP cc_start: 0.7894 (t0) cc_final: 0.7545 (t0) REVERT: A 250 PHE cc_start: 0.6874 (t80) cc_final: 0.6348 (t80) REVERT: A 265 VAL cc_start: 0.6831 (m) cc_final: 0.5134 (t) REVERT: A 413 GLU cc_start: 0.7637 (tt0) cc_final: 0.7396 (tt0) REVERT: A 609 THR cc_start: 0.8314 (m) cc_final: 0.7904 (p) REVERT: A 653 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6789 (pt0) REVERT: A 664 VAL cc_start: 0.8595 (m) cc_final: 0.8344 (t) REVERT: B 129 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6604 (mm-30) REVERT: B 270 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7076 (mm-30) REVERT: B 321 LEU cc_start: 0.8915 (mm) cc_final: 0.8709 (mm) REVERT: B 386 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7660 (mt-10) REVERT: B 428 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7298 (tm-30) REVERT: B 512 VAL cc_start: 0.8235 (t) cc_final: 0.8000 (m) REVERT: B 516 GLU cc_start: 0.6703 (mp0) cc_final: 0.6150 (mp0) REVERT: B 558 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6383 (mt-10) REVERT: B 675 GLU cc_start: 0.7811 (tp30) cc_final: 0.7557 (tp30) outliers start: 29 outliers final: 16 residues processed: 237 average time/residue: 0.4687 time to fit residues: 120.3272 Evaluate side-chains 237 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 219 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 488 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 82 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 75 optimal weight: 0.1980 chunk 0 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 104 optimal weight: 0.3980 chunk 92 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.148836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.131598 restraints weight = 13883.281| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.34 r_work: 0.3648 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9827 Z= 0.130 Angle : 0.612 11.971 13366 Z= 0.302 Chirality : 0.044 0.186 1451 Planarity : 0.004 0.060 1694 Dihedral : 5.845 51.918 1375 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.11 % Allowed : 20.04 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.25), residues: 1151 helix: 1.16 (0.28), residues: 365 sheet: -0.49 (0.41), residues: 160 loop : -0.57 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 297 TYR 0.022 0.001 TYR B 582 PHE 0.030 0.002 PHE B 400 TRP 0.017 0.001 TRP A 304 HIS 0.011 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9815) covalent geometry : angle 0.61001 (13339) SS BOND : bond 0.00313 ( 9) SS BOND : angle 0.52492 ( 18) hydrogen bonds : bond 0.03341 ( 307) hydrogen bonds : angle 4.67519 ( 834) link_BETA1-4 : bond 0.00364 ( 2) link_BETA1-4 : angle 2.36968 ( 6) link_NAG-ASN : bond 0.00101 ( 1) link_NAG-ASN : angle 1.09877 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 220 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7660 (t0) cc_final: 0.7342 (t0) REVERT: A 115 LYS cc_start: 0.7733 (mmtm) cc_final: 0.7392 (mmmm) REVERT: A 132 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6757 (mp-120) REVERT: A 143 PHE cc_start: 0.7964 (m-10) cc_final: 0.7623 (m-10) REVERT: A 147 ASP cc_start: 0.7909 (t0) cc_final: 0.7588 (t0) REVERT: A 169 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7927 (mp10) REVERT: A 250 PHE cc_start: 0.6822 (t80) cc_final: 0.6321 (t80) REVERT: A 265 VAL cc_start: 0.6751 (m) cc_final: 0.5023 (t) REVERT: A 359 MET cc_start: 0.8340 (mmt) cc_final: 0.7980 (mmt) REVERT: A 413 GLU cc_start: 0.7615 (tt0) cc_final: 0.7386 (tt0) REVERT: A 609 THR cc_start: 0.8277 (m) cc_final: 0.7810 (p) REVERT: A 653 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6778 (pt0) REVERT: A 664 VAL cc_start: 0.8568 (m) cc_final: 0.8333 (t) REVERT: B 104 ILE cc_start: 0.8134 (mm) cc_final: 0.7823 (tp) REVERT: B 270 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7073 (mm-30) REVERT: B 386 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7616 (mt-10) REVERT: B 428 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7283 (tm-30) REVERT: B 512 VAL cc_start: 0.8215 (t) cc_final: 0.7979 (m) REVERT: B 516 GLU cc_start: 0.6686 (mp0) cc_final: 0.6140 (mp0) REVERT: B 675 GLU cc_start: 0.7814 (tp30) cc_final: 0.7548 (tp30) outliers start: 22 outliers final: 16 residues processed: 231 average time/residue: 0.4952 time to fit residues: 123.6096 Evaluate side-chains 236 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 217 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 572 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.145417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.128382 restraints weight = 13757.641| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.28 r_work: 0.3609 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 9827 Z= 0.218 Angle : 0.669 12.307 13366 Z= 0.334 Chirality : 0.047 0.213 1451 Planarity : 0.005 0.078 1694 Dihedral : 6.219 49.691 1375 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.40 % Allowed : 20.52 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.25), residues: 1151 helix: 0.92 (0.27), residues: 371 sheet: -0.77 (0.40), residues: 155 loop : -0.54 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 340 TYR 0.020 0.002 TYR B 582 PHE 0.040 0.003 PHE B 551 TRP 0.018 0.002 TRP A 374 HIS 0.011 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 9815) covalent geometry : angle 0.66650 (13339) SS BOND : bond 0.00338 ( 9) SS BOND : angle 0.70850 ( 18) hydrogen bonds : bond 0.03948 ( 307) hydrogen bonds : angle 4.82226 ( 834) link_BETA1-4 : bond 0.00247 ( 2) link_BETA1-4 : angle 2.61779 ( 6) link_NAG-ASN : bond 0.00542 ( 1) link_NAG-ASN : angle 1.48430 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 223 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7629 (t0) cc_final: 0.7400 (t0) REVERT: A 115 LYS cc_start: 0.7787 (mmtm) cc_final: 0.7470 (mmmm) REVERT: A 132 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.6843 (mp-120) REVERT: A 143 PHE cc_start: 0.8018 (m-10) cc_final: 0.7706 (m-10) REVERT: A 147 ASP cc_start: 0.7902 (t0) cc_final: 0.7637 (t0) REVERT: A 250 PHE cc_start: 0.6861 (t80) cc_final: 0.6389 (t80) REVERT: A 265 VAL cc_start: 0.6938 (m) cc_final: 0.5299 (t) REVERT: A 413 GLU cc_start: 0.7609 (tt0) cc_final: 0.7403 (tt0) REVERT: A 609 THR cc_start: 0.8323 (m) cc_final: 0.7948 (p) REVERT: A 653 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6833 (pt0) REVERT: A 664 VAL cc_start: 0.8619 (m) cc_final: 0.8375 (t) REVERT: B 270 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7080 (mm-30) REVERT: B 386 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7668 (mt-10) REVERT: B 428 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7298 (tm-30) REVERT: B 512 VAL cc_start: 0.8280 (t) cc_final: 0.8048 (m) REVERT: B 516 GLU cc_start: 0.6760 (mp0) cc_final: 0.6213 (mp0) REVERT: B 675 GLU cc_start: 0.7850 (tp30) cc_final: 0.7586 (tp30) outliers start: 25 outliers final: 19 residues processed: 235 average time/residue: 0.4729 time to fit residues: 120.4547 Evaluate side-chains 241 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 220 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 488 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 80 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 98 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 107 optimal weight: 0.1980 chunk 91 optimal weight: 0.0020 chunk 12 optimal weight: 2.9990 chunk 3 optimal weight: 0.1980 chunk 97 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN B 623 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.149326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.132174 restraints weight = 13943.989| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.33 r_work: 0.3662 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9827 Z= 0.116 Angle : 0.623 11.599 13366 Z= 0.307 Chirality : 0.044 0.228 1451 Planarity : 0.004 0.061 1694 Dihedral : 5.819 48.713 1375 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.73 % Allowed : 21.00 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.25), residues: 1151 helix: 1.03 (0.28), residues: 372 sheet: -0.50 (0.41), residues: 160 loop : -0.61 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 248 TYR 0.024 0.001 TYR B 582 PHE 0.042 0.002 PHE B 551 TRP 0.016 0.001 TRP A 304 HIS 0.011 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9815) covalent geometry : angle 0.62102 (13339) SS BOND : bond 0.00158 ( 9) SS BOND : angle 0.46690 ( 18) hydrogen bonds : bond 0.03192 ( 307) hydrogen bonds : angle 4.67375 ( 834) link_BETA1-4 : bond 0.00439 ( 2) link_BETA1-4 : angle 2.28269 ( 6) link_NAG-ASN : bond 0.00120 ( 1) link_NAG-ASN : angle 0.89782 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2998.45 seconds wall clock time: 51 minutes 53.46 seconds (3113.46 seconds total)