Starting phenix.real_space_refine on Thu Jul 2 18:23:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uqy_26702/07_2026/7uqy_26702.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uqy_26702/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7uqy_26702/07_2026/7uqy_26702.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uqy_26702/07_2026/7uqy_26702.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uqy_26702/07_2026/7uqy_26702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uqy_26702/07_2026/7uqy_26702.map" model { file = "/net/cci-nas-00/data/ceres_data/7uqy_26702/07_2026/7uqy_26702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uqy_26702/07_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-6108/lib/python3.11/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 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: 2.13, per 1000 atoms: 0.22 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: 1.08 Conformation dependent library (CDL) restraints added in 320.2 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: 0.30 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: 1.67 Time building geometry restraints manager: 1.35 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 - 17.51: 5311 17.51 - 35.03: 432 35.03 - 52.54: 68 52.54 - 70.06: 10 70.06 - 87.57: 10 Dihedral angle restraints: 5831 sinusoidal: 2383 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 5828 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: 1.090 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.890 Find NCS groups from input model: 0.070 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:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 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 : 12.611 79.179 3576 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/Z covalent geometry : bond 0.00319 / 0.17 ( 9815) covalent geometry : angle 0.59078 / 0.32 (13339) SS BOND : bond 0.00380 / 0.20 ( 9) SS BOND : angle 1.21526 / 0.73 ( 18) hydrogen bonds : bond 0.20549 / 12.99 ( 307) hydrogen bonds : angle 6.86654 / 4.84 ( 834) link_BETA1-4 : bond 0.00274 / 0.14 ( 2) link_BETA1-4 : angle 1.31849 / 0.72 ( 6) link_NAG-ASN : bond 0.00195 / 0.10 ( 1) link_NAG-ASN : angle 1.16626 / 0.63 ( 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 : 0.373 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: 0.4890 time to fit residues: 128.0883 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 : 0.381 ------------------------------------------------------------------------------- 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... 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 = 0.149135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.131842 restraints weight = 13797.459| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.31 r_work: 0.3651 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9827 Z= 0.153 Angle : 0.598 8.491 13366 Z= 0.303 Chirality : 0.045 0.163 1451 Planarity : 0.005 0.060 1694 Dihedral : 5.053 108.236 1284 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.63 % Allowed : 11.60 % Favored : 86.77 % 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: 0.92 (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 B 149 TYR 0.021 0.002 TYR B 582 PHE 0.017 0.002 PHE B 652 TRP 0.010 0.001 TRP A 374 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 9815) covalent geometry : angle 0.59670 / 0.30 (13339) SS BOND : bond 0.00301 / 0.17 ( 9) SS BOND : angle 0.79128 / 0.47 ( 18) hydrogen bonds : bond 0.04393 / 2.75 ( 307) hydrogen bonds : angle 5.38747 / 3.79 ( 834) link_BETA1-4 : bond 0.00224 / 0.11 ( 2) link_BETA1-4 : angle 1.61678 / 0.90 ( 6) link_NAG-ASN : bond 0.00495 / 0.26 ( 1) link_NAG-ASN : angle 1.38474 / 0.76 ( 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 260 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 243 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7606 (t0) cc_final: 0.7346 (t0) REVERT: A 115 LYS cc_start: 0.7592 (mmmm) cc_final: 0.7301 (mmmm) REVERT: A 143 PHE cc_start: 0.7872 (m-10) cc_final: 0.7618 (m-10) REVERT: A 265 VAL cc_start: 0.6529 (m) cc_final: 0.4765 (t) REVERT: A 359 MET cc_start: 0.7988 (mpp) cc_final: 0.7673 (mmt) REVERT: A 447 LYS cc_start: 0.8195 (tppt) cc_final: 0.7935 (mttp) REVERT: A 664 VAL cc_start: 0.8558 (m) cc_final: 0.8310 (t) REVERT: B 174 MET cc_start: 0.4659 (OUTLIER) cc_final: 0.4139 (mtt) REVERT: B 367 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7549 (mt-10) REVERT: B 573 TRP cc_start: 0.7976 (t-100) cc_final: 0.7496 (t-100) outliers start: 17 outliers final: 2 residues processed: 248 average time/residue: 0.4517 time to fit residues: 121.4857 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 : 0.230 ------------------------------------------------------------------------------- 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: 0.8980 chunk 113 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 80 optimal weight: 0.0370 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 34 optimal weight: 0.0970 chunk 41 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 GLN B 623 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.149759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.132288 restraints weight = 13719.340| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.32 r_work: 0.3652 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9827 Z= 0.127 Angle : 0.566 7.681 13366 Z= 0.285 Chirality : 0.044 0.167 1451 Planarity : 0.004 0.054 1694 Dihedral : 3.980 15.167 1282 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.40 % Allowed : 13.81 % Favored : 83.80 % 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: 0.11 (0.25), residues: 1151 helix: 1.19 (0.28), residues: 358 sheet: -0.44 (0.42), residues: 154 loop : -0.39 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 149 TYR 0.020 0.001 TYR B 582 PHE 0.017 0.001 PHE B 400 TRP 0.010 0.001 TRP A 374 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 9815) covalent geometry : angle 0.56462 / 0.28 (13339) SS BOND : bond 0.00753 / 0.36 ( 9) SS BOND : angle 0.66997 / 0.37 ( 18) hydrogen bonds : bond 0.03850 / 2.42 ( 307) hydrogen bonds : angle 5.03765 / 3.54 ( 834) link_BETA1-4 : bond 0.00258 / 0.12 ( 2) link_BETA1-4 : angle 1.46982 / 0.81 ( 6) link_NAG-ASN : bond 0.00394 / 0.21 ( 1) link_NAG-ASN : angle 1.34903 / 0.72 ( 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 259 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 234 time to evaluate : 0.375 Fit side-chains REVERT: A 105 ASP cc_start: 0.7571 (t0) cc_final: 0.7329 (t0) REVERT: A 265 VAL cc_start: 0.6596 (m) cc_final: 0.4843 (t) REVERT: A 295 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7350 (mt) REVERT: A 413 GLU cc_start: 0.7685 (tt0) cc_final: 0.7388 (tt0) REVERT: A 447 LYS cc_start: 0.8133 (tppt) cc_final: 0.7921 (mmtp) REVERT: A 549 ARG cc_start: 0.7723 (ptp90) cc_final: 0.7465 (ptm160) REVERT: A 664 VAL cc_start: 0.8597 (m) cc_final: 0.8374 (t) REVERT: B 109 TYR cc_start: 0.7670 (m-80) cc_final: 0.7403 (m-80) REVERT: B 129 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6556 (mm-30) REVERT: B 270 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6986 (mm-30) REVERT: B 367 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7596 (mt-10) REVERT: B 512 VAL cc_start: 0.8150 (t) cc_final: 0.7940 (m) REVERT: B 573 TRP cc_start: 0.7994 (t-100) cc_final: 0.7656 (t-100) outliers start: 25 outliers final: 7 residues processed: 244 average time/residue: 0.4301 time to fit residues: 114.0111 Evaluate side-chains 229 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 221 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 3 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 13 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 ASN ** A 194 ASN ** 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 = 0.3997 r_free = 0.3997 target = 0.149407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.131838 restraints weight = 13956.207| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.36 r_work: 0.3645 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1765 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= 0.131 Angle : 0.564 8.472 13366 Z= 0.281 Chirality : 0.043 0.140 1451 Planarity : 0.004 0.053 1694 Dihedral : 3.946 15.367 1282 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.68 % Allowed : 15.05 % Favored : 82.26 % 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: 0.15 (0.25), residues: 1151 helix: 1.28 (0.28), residues: 359 sheet: -0.40 (0.42), residues: 154 loop : -0.40 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 149 TYR 0.021 0.001 TYR B 582 PHE 0.027 0.002 PHE B 551 TRP 0.010 0.001 TRP A 374 HIS 0.003 0.001 HIS B 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 9815) covalent geometry : angle 0.56259 / 0.28 (13339) SS BOND : bond 0.00267 / 0.14 ( 9) SS BOND : angle 0.58992 / 0.34 ( 18) hydrogen bonds : bond 0.03552 / 2.24 ( 307) hydrogen bonds : angle 4.90710 / 3.46 ( 834) link_BETA1-4 : bond 0.00364 / 0.18 ( 2) link_BETA1-4 : angle 1.47816 / 0.81 ( 6) link_NAG-ASN : bond 0.00350 / 0.18 ( 1) link_NAG-ASN : angle 1.30462 / 0.70 ( 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 254 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 0.368 Fit side-chains REVERT: A 105 ASP cc_start: 0.7611 (t0) cc_final: 0.7285 (t0) REVERT: A 132 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6743 (mp-120) REVERT: A 169 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: A 265 VAL cc_start: 0.6588 (m) cc_final: 0.4849 (t) REVERT: A 295 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7322 (mt) REVERT: A 413 GLU cc_start: 0.7718 (tt0) cc_final: 0.7451 (tt0) REVERT: B 109 TYR cc_start: 0.7726 (m-80) cc_final: 0.7462 (m-80) REVERT: B 174 MET cc_start: 0.4581 (OUTLIER) cc_final: 0.3924 (mtt) REVERT: B 270 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7060 (mm-30) REVERT: B 367 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7569 (mt-10) REVERT: B 427 GLU cc_start: 0.7408 (mp0) cc_final: 0.7034 (mp0) REVERT: B 512 VAL cc_start: 0.8136 (t) cc_final: 0.7905 (m) outliers start: 28 outliers final: 11 residues processed: 239 average time/residue: 0.4594 time to fit residues: 119.3762 Evaluate side-chains 236 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 221 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 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 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 174 MET 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: 3.9990 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 0.0670 chunk 113 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.148898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.131472 restraints weight = 13957.943| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.34 r_work: 0.3645 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9827 Z= 0.135 Angle : 0.571 9.100 13366 Z= 0.284 Chirality : 0.043 0.174 1451 Planarity : 0.004 0.060 1694 Dihedral : 3.985 15.801 1282 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.16 % Allowed : 15.63 % Favored : 81.21 % 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: 0.15 (0.25), residues: 1151 helix: 1.31 (0.28), residues: 359 sheet: -0.39 (0.43), residues: 153 loop : -0.44 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 149 TYR 0.020 0.001 TYR B 582 PHE 0.025 0.002 PHE B 400 TRP 0.010 0.001 TRP A 374 HIS 0.019 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 9815) covalent geometry : angle 0.57003 / 0.28 (13339) SS BOND : bond 0.00231 / 0.13 ( 9) SS BOND : angle 0.57801 / 0.33 ( 18) hydrogen bonds : bond 0.03482 / 2.20 ( 307) hydrogen bonds : angle 4.84236 / 3.43 ( 834) link_BETA1-4 : bond 0.00286 / 0.14 ( 2) link_BETA1-4 : angle 1.46456 / 0.80 ( 6) link_NAG-ASN : bond 0.00345 / 0.18 ( 1) link_NAG-ASN : angle 1.29264 / 0.69 ( 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 263 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 230 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7564 (t0) cc_final: 0.7264 (t0) REVERT: A 115 LYS cc_start: 0.7713 (mmtt) cc_final: 0.7395 (mmmm) REVERT: A 132 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6782 (mp-120) REVERT: A 169 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: A 265 VAL cc_start: 0.6733 (m) cc_final: 0.4970 (t) REVERT: A 359 MET cc_start: 0.8147 (mpp) cc_final: 0.7608 (mmt) REVERT: A 413 GLU cc_start: 0.7699 (tt0) cc_final: 0.7417 (tt0) REVERT: A 664 VAL cc_start: 0.8594 (m) cc_final: 0.8353 (t) REVERT: A 722 MET cc_start: 0.6402 (OUTLIER) cc_final: 0.6153 (ptp) REVERT: B 129 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6600 (mm-30) REVERT: B 270 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7012 (mm-30) REVERT: B 367 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7566 (mt-10) REVERT: B 428 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7307 (tm-30) REVERT: B 473 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.7269 (tp) REVERT: B 512 VAL cc_start: 0.8156 (t) cc_final: 0.7938 (m) REVERT: B 619 TRP cc_start: 0.8440 (t60) cc_final: 0.8168 (t60) outliers start: 33 outliers final: 13 residues processed: 245 average time/residue: 0.4695 time to fit residues: 124.9848 Evaluate side-chains 235 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 703 SER Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 722 MET 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 473 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 15 optimal weight: 0.0070 chunk 18 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 273 GLN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.149076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.131675 restraints weight = 13819.905| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.34 r_work: 0.3647 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9827 Z= 0.133 Angle : 0.580 8.640 13366 Z= 0.287 Chirality : 0.044 0.144 1451 Planarity : 0.004 0.061 1694 Dihedral : 4.003 15.705 1282 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.97 % Allowed : 16.87 % Favored : 80.15 % 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: 0.08 (0.25), residues: 1151 helix: 1.22 (0.28), residues: 365 sheet: -0.41 (0.42), residues: 153 loop : -0.48 (0.25), residues: 633 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 0.028 0.002 PHE B 400 TRP 0.010 0.001 TRP B 396 HIS 0.018 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 9815) covalent geometry : angle 0.57894 / 0.29 (13339) SS BOND : bond 0.00198 / 0.11 ( 9) SS BOND : angle 0.56159 / 0.32 ( 18) hydrogen bonds : bond 0.03461 / 2.20 ( 307) hydrogen bonds : angle 4.78819 / 3.41 ( 834) link_BETA1-4 : bond 0.00301 / 0.14 ( 2) link_BETA1-4 : angle 1.44949 / 0.79 ( 6) link_NAG-ASN : bond 0.00309 / 0.16 ( 1) link_NAG-ASN : angle 1.27100 / 0.68 ( 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 254 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7628 (t0) cc_final: 0.7306 (t0) REVERT: A 115 LYS cc_start: 0.7720 (mmtt) cc_final: 0.7369 (mmmm) REVERT: A 132 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6790 (mp-120) REVERT: A 169 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7889 (mp10) REVERT: A 250 PHE cc_start: 0.6914 (t80) cc_final: 0.6313 (t80) REVERT: A 265 VAL cc_start: 0.6769 (m) cc_final: 0.5057 (t) REVERT: A 359 MET cc_start: 0.8162 (mpp) cc_final: 0.7696 (mmt) REVERT: A 413 GLU cc_start: 0.7710 (tt0) cc_final: 0.7443 (tt0) REVERT: A 664 VAL cc_start: 0.8573 (m) cc_final: 0.8351 (t) REVERT: B 109 TYR cc_start: 0.7745 (m-80) cc_final: 0.7536 (m-80) REVERT: B 129 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6513 (mm-30) REVERT: B 270 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7067 (mm-30) REVERT: B 367 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7623 (mt-10) REVERT: B 428 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7286 (tm-30) REVERT: B 473 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7236 (tp) REVERT: B 512 VAL cc_start: 0.8175 (t) cc_final: 0.7944 (m) outliers start: 31 outliers final: 14 residues processed: 237 average time/residue: 0.5123 time to fit residues: 131.4149 Evaluate side-chains 232 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 215 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 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 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 473 ILE 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: 5.9990 chunk 11 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3969 r_free = 0.3969 target = 0.146918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.129342 restraints weight = 13873.806| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.36 r_work: 0.3619 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9827 Z= 0.176 Angle : 0.610 9.959 13366 Z= 0.305 Chirality : 0.045 0.193 1451 Planarity : 0.004 0.064 1694 Dihedral : 4.152 17.109 1282 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.78 % Allowed : 18.22 % Favored : 79.00 % 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: 1.06 (0.28), residues: 371 sheet: -0.43 (0.42), residues: 141 loop : -0.50 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 390 TYR 0.021 0.002 TYR B 582 PHE 0.039 0.002 PHE B 551 TRP 0.014 0.001 TRP A 374 HIS 0.016 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 ( 9815) covalent geometry : angle 0.60931 / 0.30 (13339) SS BOND : bond 0.00351 / 0.18 ( 9) SS BOND : angle 0.61049 / 0.36 ( 18) hydrogen bonds : bond 0.03713 / 2.36 ( 307) hydrogen bonds : angle 4.82735 / 3.45 ( 834) link_BETA1-4 : bond 0.00230 / 0.11 ( 2) link_BETA1-4 : angle 1.63475 / 0.86 ( 6) link_NAG-ASN : bond 0.00502 / 0.26 ( 1) link_NAG-ASN : angle 1.47814 / 0.79 ( 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 257 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 228 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7626 (t0) cc_final: 0.7307 (t0) REVERT: A 115 LYS cc_start: 0.7788 (mmtt) cc_final: 0.7418 (mmmm) REVERT: A 132 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6800 (mp-120) REVERT: A 143 PHE cc_start: 0.7981 (m-10) cc_final: 0.7646 (m-10) REVERT: A 169 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7965 (mp10) REVERT: A 248 ARG cc_start: 0.7494 (mmm160) cc_final: 0.7109 (mmm160) REVERT: A 250 PHE cc_start: 0.6906 (t80) cc_final: 0.6232 (t80) REVERT: A 265 VAL cc_start: 0.6837 (m) cc_final: 0.5157 (t) REVERT: A 359 MET cc_start: 0.8137 (mpp) cc_final: 0.7715 (mmt) REVERT: A 609 THR cc_start: 0.8280 (m) cc_final: 0.7858 (p) REVERT: A 653 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6776 (pt0) REVERT: B 270 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7084 (mm-30) REVERT: B 321 LEU cc_start: 0.8928 (mm) cc_final: 0.8726 (mm) REVERT: B 367 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7591 (mt-10) REVERT: B 397 GLU cc_start: 0.7309 (pt0) cc_final: 0.7082 (mt-10) REVERT: B 428 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7294 (tm-30) REVERT: B 473 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7278 (tp) REVERT: B 512 VAL cc_start: 0.8258 (t) cc_final: 0.8018 (m) REVERT: B 589 GLU cc_start: 0.7299 (pt0) cc_final: 0.7055 (tt0) outliers start: 29 outliers final: 15 residues processed: 242 average time/residue: 0.4812 time to fit residues: 126.9348 Evaluate side-chains 240 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 221 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 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 473 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: 0.9990 chunk 64 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 92 optimal weight: 0.0010 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.147548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.129981 restraints weight = 13894.175| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.34 r_work: 0.3617 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9827 Z= 0.164 Angle : 0.617 11.457 13366 Z= 0.307 Chirality : 0.045 0.202 1451 Planarity : 0.004 0.064 1694 Dihedral : 4.200 17.249 1282 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.78 % Allowed : 19.27 % Favored : 77.95 % 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: 1.06 (0.28), residues: 371 sheet: -0.56 (0.42), residues: 143 loop : -0.46 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 390 TYR 0.021 0.002 TYR B 582 PHE 0.034 0.002 PHE B 400 TRP 0.012 0.001 TRP A 374 HIS 0.015 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 9815) covalent geometry : angle 0.61613 / 0.31 (13339) SS BOND : bond 0.00212 / 0.12 ( 9) SS BOND : angle 0.54442 / 0.32 ( 18) hydrogen bonds : bond 0.03623 / 2.30 ( 307) hydrogen bonds : angle 4.81011 / 3.43 ( 834) link_BETA1-4 : bond 0.00273 / 0.13 ( 2) link_BETA1-4 : angle 1.56707 / 0.83 ( 6) link_NAG-ASN : bond 0.00404 / 0.21 ( 1) link_NAG-ASN : angle 1.37273 / 0.73 ( 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 : 0.459 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7625 (t0) cc_final: 0.7318 (t0) REVERT: A 115 LYS cc_start: 0.7813 (mmtt) cc_final: 0.7440 (mmmm) REVERT: A 132 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6767 (mp-120) REVERT: A 143 PHE cc_start: 0.7968 (m-10) cc_final: 0.7702 (m-10) REVERT: A 147 ASP cc_start: 0.7948 (t0) cc_final: 0.7710 (t0) REVERT: A 169 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7916 (mp10) REVERT: A 250 PHE cc_start: 0.6882 (t80) cc_final: 0.6212 (t80) REVERT: A 265 VAL cc_start: 0.6864 (m) cc_final: 0.5194 (t) REVERT: A 609 THR cc_start: 0.8277 (m) cc_final: 0.7836 (p) REVERT: A 653 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6807 (pt0) REVERT: A 664 VAL cc_start: 0.8597 (m) cc_final: 0.8350 (t) REVERT: B 109 TYR cc_start: 0.7851 (m-80) cc_final: 0.7591 (m-80) REVERT: B 129 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6536 (mm-30) REVERT: B 270 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7078 (mm-30) REVERT: B 367 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7580 (mt-10) REVERT: B 428 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7281 (tm-30) REVERT: B 473 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7335 (tp) REVERT: B 512 VAL cc_start: 0.8222 (t) cc_final: 0.7987 (m) REVERT: B 589 GLU cc_start: 0.7339 (pt0) cc_final: 0.7061 (tt0) outliers start: 29 outliers final: 18 residues processed: 237 average time/residue: 0.4979 time to fit residues: 128.4744 Evaluate side-chains 238 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 142 ARG 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 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 473 ILE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 572 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 82 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 115 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 92 optimal weight: 0.0070 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.148540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.131416 restraints weight = 13935.095| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.33 r_work: 0.3640 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9827 Z= 0.125 Angle : 0.603 12.449 13366 Z= 0.299 Chirality : 0.044 0.233 1451 Planarity : 0.004 0.059 1694 Dihedral : 4.137 15.989 1282 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.21 % Allowed : 20.52 % 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: 0.00 (0.25), residues: 1151 helix: 1.09 (0.28), residues: 371 sheet: -0.31 (0.44), residues: 136 loop : -0.54 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 297 TYR 0.023 0.001 TYR B 582 PHE 0.045 0.002 PHE B 551 TRP 0.012 0.001 TRP B 396 HIS 0.015 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 9815) covalent geometry : angle 0.60197 / 0.30 (13339) SS BOND : bond 0.00204 / 0.12 ( 9) SS BOND : angle 0.50803 / 0.30 ( 18) hydrogen bonds : bond 0.03284 / 2.08 ( 307) hydrogen bonds : angle 4.72578 / 3.37 ( 834) link_BETA1-4 : bond 0.00294 / 0.14 ( 2) link_BETA1-4 : angle 1.39452 / 0.76 ( 6) link_NAG-ASN : bond 0.00159 / 0.08 ( 1) link_NAG-ASN : angle 1.13845 / 0.61 ( 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 247 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7660 (t0) cc_final: 0.7418 (t0) REVERT: A 115 LYS cc_start: 0.7730 (mmtt) cc_final: 0.7391 (mmmm) REVERT: A 132 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6780 (mp-120) REVERT: A 143 PHE cc_start: 0.7915 (m-10) cc_final: 0.7651 (m-10) REVERT: A 250 PHE cc_start: 0.6873 (t80) cc_final: 0.5946 (t80) REVERT: A 265 VAL cc_start: 0.6790 (m) cc_final: 0.5101 (t) REVERT: A 609 THR cc_start: 0.8255 (m) cc_final: 0.7782 (p) REVERT: A 664 VAL cc_start: 0.8555 (m) cc_final: 0.8310 (t) REVERT: B 104 ILE cc_start: 0.8143 (mm) cc_final: 0.7877 (tp) REVERT: B 109 TYR cc_start: 0.7812 (m-80) cc_final: 0.7611 (m-80) REVERT: B 270 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7040 (mm-30) REVERT: B 367 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7603 (mt-10) REVERT: B 393 ARG cc_start: 0.7656 (tpt170) cc_final: 0.7420 (tpt170) REVERT: B 397 GLU cc_start: 0.7261 (pt0) cc_final: 0.7060 (mt-10) REVERT: B 428 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7284 (tm-30) REVERT: B 512 VAL cc_start: 0.8222 (t) cc_final: 0.7990 (m) REVERT: B 589 GLU cc_start: 0.7315 (pt0) cc_final: 0.7047 (tt0) outliers start: 23 outliers final: 14 residues processed: 234 average time/residue: 0.4953 time to fit residues: 125.7541 Evaluate side-chains 236 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 221 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 286 VAL 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 703 SER Chi-restraints excluded: chain A residue 721 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 20 optimal weight: 0.0270 chunk 73 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 overall best weight: 1.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 131 ASN B 623 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.145837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.128412 restraints weight = 13795.395| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.32 r_work: 0.3602 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9827 Z= 0.215 Angle : 0.664 12.713 13366 Z= 0.331 Chirality : 0.047 0.212 1451 Planarity : 0.005 0.074 1694 Dihedral : 4.352 18.175 1282 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.82 % Allowed : 21.28 % Favored : 76.89 % 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: -0.11 (0.25), residues: 1151 helix: 0.97 (0.27), residues: 371 sheet: -0.59 (0.42), residues: 143 loop : -0.52 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 297 TYR 0.020 0.002 TYR B 582 PHE 0.036 0.002 PHE B 551 TRP 0.017 0.002 TRP A 374 HIS 0.014 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 ( 9815) covalent geometry : angle 0.66265 / 0.33 (13339) SS BOND : bond 0.00383 / 0.20 ( 9) SS BOND : angle 0.66762 / 0.40 ( 18) hydrogen bonds : bond 0.03859 / 2.44 ( 307) hydrogen bonds : angle 4.85537 / 3.48 ( 834) link_BETA1-4 : bond 0.00247 / 0.12 ( 2) link_BETA1-4 : angle 1.71194 / 0.90 ( 6) link_NAG-ASN : bond 0.00644 / 0.34 ( 1) link_NAG-ASN : angle 1.57379 / 0.84 ( 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 239 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 220 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7659 (t0) cc_final: 0.7398 (t0) REVERT: A 115 LYS cc_start: 0.7799 (mmtt) cc_final: 0.7447 (mmmm) REVERT: A 132 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6801 (mp-120) REVERT: A 143 PHE cc_start: 0.7989 (m-10) cc_final: 0.7704 (m-10) REVERT: A 250 PHE cc_start: 0.7089 (t80) cc_final: 0.6674 (t80) REVERT: A 265 VAL cc_start: 0.6910 (m) cc_final: 0.5301 (t) REVERT: A 609 THR cc_start: 0.8314 (m) cc_final: 0.7897 (p) REVERT: A 664 VAL cc_start: 0.8600 (m) cc_final: 0.8360 (t) REVERT: B 109 TYR cc_start: 0.7906 (m-80) cc_final: 0.7604 (m-80) REVERT: B 129 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6541 (mm-30) REVERT: B 270 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7065 (mm-30) REVERT: B 367 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7606 (mt-10) REVERT: B 428 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7274 (tm-30) REVERT: B 512 VAL cc_start: 0.8279 (t) cc_final: 0.8042 (m) REVERT: B 589 GLU cc_start: 0.7368 (pt0) cc_final: 0.7159 (pp20) outliers start: 19 outliers final: 16 residues processed: 231 average time/residue: 0.4827 time to fit residues: 120.8769 Evaluate side-chains 236 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 219 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 391 SER Chi-restraints excluded: chain A residue 399 ASP 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 89 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 157 ILE 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: 0.9980 chunk 87 optimal weight: 2.9990 chunk 98 optimal weight: 0.0020 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 91 optimal weight: 0.0000 chunk 12 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3987 r_free = 0.3987 target = 0.148131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.130836 restraints weight = 13898.371| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.34 r_work: 0.3636 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9827 Z= 0.133 Angle : 0.633 11.501 13366 Z= 0.312 Chirality : 0.044 0.179 1451 Planarity : 0.005 0.066 1694 Dihedral : 4.245 16.601 1282 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.63 % Allowed : 21.96 % Favored : 76.41 % 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: -0.04 (0.25), residues: 1151 helix: 0.98 (0.28), residues: 377 sheet: -0.42 (0.43), residues: 150 loop : -0.50 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 297 TYR 0.023 0.001 TYR B 582 PHE 0.039 0.002 PHE B 551 TRP 0.013 0.001 TRP B 396 HIS 0.014 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 9815) covalent geometry : angle 0.63269 / 0.31 (13339) SS BOND : bond 0.00214 / 0.12 ( 9) SS BOND : angle 0.51886 / 0.29 ( 18) hydrogen bonds : bond 0.03370 / 2.13 ( 307) hydrogen bonds : angle 4.76235 / 3.41 ( 834) link_BETA1-4 : bond 0.00279 / 0.13 ( 2) link_BETA1-4 : angle 1.42747 / 0.78 ( 6) link_NAG-ASN : bond 0.00197 / 0.10 ( 1) link_NAG-ASN : angle 1.16587 / 0.62 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3125.63 seconds wall clock time: 54 minutes 13.37 seconds (3253.37 seconds total)