Starting phenix.real_space_refine on Sun Jul 27 20:33:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uqy_26702/07_2025/7uqy_26702.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uqy_26702/07_2025/7uqy_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_26702/07_2025/7uqy_26702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uqy_26702/07_2025/7uqy_26702.map" model { file = "/net/cci-nas-00/data/ceres_data/7uqy_26702/07_2025/7uqy_26702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uqy_26702/07_2025/7uqy_26702.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.70, per 1000 atoms: 0.60 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: 2.58 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.07 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: 2.92 Time building geometry restraints manager: 3.01 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.070 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:22.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.570 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (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 TRP 0.013 0.001 TRP B 619 HIS 0.005 0.001 HIS B 88 PHE 0.010 0.001 PHE A 250 TYR 0.018 0.001 TYR B 582 ARG 0.010 0.000 ARG B 383 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 1) link_NAG-ASN : angle 1.16626 ( 3) link_BETA1-4 : bond 0.00274 ( 2) link_BETA1-4 : angle 1.31849 ( 6) hydrogen bonds : bond 0.20549 ( 307) hydrogen bonds : angle 6.86654 ( 834) SS BOND : bond 0.00380 ( 9) SS BOND : angle 1.21526 ( 18) covalent geometry : bond 0.00319 ( 9815) covalent geometry : angle 0.59078 (13339) *********************** 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 : 1.153 Fit side-chains REVERT: A 250 PHE cc_start: 0.6037 (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: 1.0770 time to fit residues: 281.8123 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 : 1.012 ------------------------------------------------------------------------------- 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 97 optimal weight: 0.0980 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 0.0470 chunk 59 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 overall best weight: 0.5882 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.149861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.132614 restraints weight = 13773.369| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.30 r_work: 0.3659 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9827 Z= 0.142 Angle : 0.598 8.616 13366 Z= 0.302 Chirality : 0.045 0.164 1451 Planarity : 0.004 0.060 1694 Dihedral : 8.447 108.740 1377 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.82 % Allowed : 11.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1151 helix: 0.95 (0.28), residues: 362 sheet: -0.30 (0.43), residues: 148 loop : -0.40 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 556 HIS 0.003 0.001 HIS B 88 PHE 0.018 0.001 PHE B 652 TYR 0.020 0.002 TYR B 582 ARG 0.007 0.001 ARG A 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 1) link_NAG-ASN : angle 1.22328 ( 3) link_BETA1-4 : bond 0.00141 ( 2) link_BETA1-4 : angle 2.20868 ( 6) hydrogen bonds : bond 0.04299 ( 307) hydrogen bonds : angle 5.38952 ( 834) SS BOND : bond 0.00472 ( 9) SS BOND : angle 0.72008 ( 18) covalent geometry : bond 0.00329 ( 9815) covalent geometry : angle 0.59541 (13339) *********************** 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 261 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 242 time to evaluate : 1.133 Fit side-chains REVERT: A 105 ASP cc_start: 0.7599 (t0) cc_final: 0.7327 (t0) REVERT: A 115 LYS cc_start: 0.7587 (mmmm) cc_final: 0.7277 (mmmm) REVERT: A 143 PHE cc_start: 0.7852 (m-10) cc_final: 0.7611 (m-10) REVERT: A 265 VAL cc_start: 0.6497 (m) cc_final: 0.4718 (t) REVERT: A 359 MET cc_start: 0.7980 (mpp) cc_final: 0.7653 (mmt) REVERT: A 413 GLU cc_start: 0.7732 (tt0) cc_final: 0.7309 (tt0) REVERT: A 447 LYS cc_start: 0.8197 (tppt) cc_final: 0.7928 (mttp) REVERT: A 664 VAL cc_start: 0.8546 (m) cc_final: 0.8295 (t) REVERT: B 174 MET cc_start: 0.4617 (OUTLIER) cc_final: 0.4098 (mtt) REVERT: B 367 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7536 (mt-10) REVERT: B 573 TRP cc_start: 0.7973 (t-100) cc_final: 0.7409 (t-100) outliers start: 19 outliers final: 2 residues processed: 248 average time/residue: 1.0581 time to fit residues: 283.8540 Evaluate side-chains 226 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 223 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 10 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 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 = 0.3997 r_free = 0.3997 target = 0.149610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.132221 restraints weight = 13748.817| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.30 r_work: 0.3649 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9827 Z= 0.135 Angle : 0.579 10.414 13366 Z= 0.288 Chirality : 0.044 0.164 1451 Planarity : 0.004 0.054 1694 Dihedral : 6.986 59.041 1375 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.59 % Allowed : 13.71 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1151 helix: 1.10 (0.28), residues: 364 sheet: -0.44 (0.42), residues: 154 loop : -0.37 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 374 HIS 0.003 0.001 HIS A 285 PHE 0.015 0.001 PHE B 91 TYR 0.020 0.001 TYR B 582 ARG 0.016 0.001 ARG B 149 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 1) link_NAG-ASN : angle 1.35779 ( 3) link_BETA1-4 : bond 0.00261 ( 2) link_BETA1-4 : angle 2.29694 ( 6) hydrogen bonds : bond 0.03902 ( 307) hydrogen bonds : angle 5.04076 ( 834) SS BOND : bond 0.00259 ( 9) SS BOND : angle 0.65112 ( 18) covalent geometry : bond 0.00314 ( 9815) covalent geometry : angle 0.57678 (13339) *********************** 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 : 1.027 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7565 (t0) cc_final: 0.7309 (t0) REVERT: A 147 ASP cc_start: 0.7862 (t0) cc_final: 0.7659 (t0) REVERT: A 265 VAL cc_start: 0.6593 (m) cc_final: 0.4844 (t) REVERT: A 295 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7353 (mt) REVERT: A 413 GLU cc_start: 0.7693 (tt0) cc_final: 0.7404 (tt0) REVERT: A 447 LYS cc_start: 0.8144 (tppt) cc_final: 0.7931 (mmtp) REVERT: A 549 ARG cc_start: 0.7748 (ptp90) cc_final: 0.7525 (ptm160) REVERT: A 664 VAL cc_start: 0.8607 (m) cc_final: 0.8377 (t) REVERT: B 270 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6988 (mm-30) REVERT: B 367 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7595 (mt-10) REVERT: B 512 VAL cc_start: 0.8148 (t) cc_final: 0.7937 (m) REVERT: B 558 GLU cc_start: 0.6766 (mt-10) cc_final: 0.6482 (mt-10) REVERT: B 573 TRP cc_start: 0.7995 (t-100) cc_final: 0.7656 (t-100) outliers start: 27 outliers final: 6 residues processed: 241 average time/residue: 1.0042 time to fit residues: 262.0226 Evaluate side-chains 227 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 220 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 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 0 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 328 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.145635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.128052 restraints weight = 13760.927| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.33 r_work: 0.3598 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9827 Z= 0.221 Angle : 0.633 8.912 13366 Z= 0.317 Chirality : 0.047 0.160 1451 Planarity : 0.005 0.064 1694 Dihedral : 6.781 57.272 1375 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.16 % Allowed : 15.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.25), residues: 1151 helix: 0.99 (0.28), residues: 365 sheet: -0.50 (0.43), residues: 150 loop : -0.44 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 374 HIS 0.005 0.001 HIS B 575 PHE 0.030 0.002 PHE B 400 TYR 0.020 0.002 TYR B 582 ARG 0.008 0.001 ARG A 280 Details of bonding type rmsd link_NAG-ASN : bond 0.00713 ( 1) link_NAG-ASN : angle 1.59888 ( 3) link_BETA1-4 : bond 0.00261 ( 2) link_BETA1-4 : angle 2.49336 ( 6) hydrogen bonds : bond 0.04209 ( 307) hydrogen bonds : angle 5.04085 ( 834) SS BOND : bond 0.00427 ( 9) SS BOND : angle 0.66957 ( 18) covalent geometry : bond 0.00513 ( 9815) covalent geometry : angle 0.63066 (13339) *********************** 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 269 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 236 time to evaluate : 1.059 Fit side-chains REVERT: A 105 ASP cc_start: 0.7620 (t0) cc_final: 0.7377 (t0) REVERT: A 115 LYS cc_start: 0.7771 (mmmm) cc_final: 0.7410 (mmmm) REVERT: A 147 ASP cc_start: 0.7886 (t0) cc_final: 0.7588 (t0) REVERT: A 248 ARG cc_start: 0.7359 (mmm160) cc_final: 0.7069 (mmm160) REVERT: A 265 VAL cc_start: 0.6782 (m) cc_final: 0.5142 (t) REVERT: A 295 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7417 (mt) REVERT: A 609 THR cc_start: 0.8269 (m) cc_final: 0.7849 (p) REVERT: B 129 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6554 (mm-30) REVERT: B 174 MET cc_start: 0.4946 (OUTLIER) cc_final: 0.4218 (mtt) REVERT: B 270 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7074 (mm-30) REVERT: B 280 VAL cc_start: 0.8406 (t) cc_final: 0.8176 (p) REVERT: B 310 GLN cc_start: 0.7958 (mp10) cc_final: 0.7376 (mp10) REVERT: B 367 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7539 (mt-10) REVERT: B 428 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7316 (tm-30) REVERT: B 512 VAL cc_start: 0.8198 (t) cc_final: 0.7964 (m) outliers start: 33 outliers final: 9 residues processed: 251 average time/residue: 0.9977 time to fit residues: 272.0827 Evaluate side-chains 234 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 223 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 295 LEU 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 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 5 optimal weight: 0.9980 chunk 58 optimal weight: 0.0670 chunk 81 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- 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 131 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.147341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.129665 restraints weight = 13817.752| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.36 r_work: 0.3614 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2035 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= 0.146 Angle : 0.591 7.963 13366 Z= 0.295 Chirality : 0.044 0.181 1451 Planarity : 0.005 0.072 1694 Dihedral : 6.442 55.040 1375 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.16 % Allowed : 16.78 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1151 helix: 1.16 (0.28), residues: 365 sheet: -0.59 (0.42), residues: 151 loop : -0.47 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 396 HIS 0.003 0.001 HIS A 285 PHE 0.029 0.002 PHE B 400 TYR 0.020 0.002 TYR B 582 ARG 0.007 0.000 ARG B 149 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 1) link_NAG-ASN : angle 1.31294 ( 3) link_BETA1-4 : bond 0.00329 ( 2) link_BETA1-4 : angle 2.43883 ( 6) hydrogen bonds : bond 0.03681 ( 307) hydrogen bonds : angle 4.87601 ( 834) SS BOND : bond 0.00206 ( 9) SS BOND : angle 0.56609 ( 18) covalent geometry : bond 0.00341 ( 9815) covalent geometry : angle 0.58888 (13339) *********************** 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 262 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7649 (t0) cc_final: 0.7343 (t0) REVERT: A 115 LYS cc_start: 0.7742 (mmmm) cc_final: 0.7384 (mmmm) REVERT: A 132 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6843 (mp-120) REVERT: A 143 PHE cc_start: 0.7972 (m-10) cc_final: 0.7543 (m-10) REVERT: A 147 ASP cc_start: 0.7934 (t0) cc_final: 0.7632 (t0) REVERT: A 169 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7968 (mp10) REVERT: A 265 VAL cc_start: 0.6792 (m) cc_final: 0.5098 (t) REVERT: A 359 MET cc_start: 0.8223 (mpp) cc_final: 0.7654 (mmt) REVERT: A 413 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7357 (mt-10) REVERT: A 549 ARG cc_start: 0.7827 (ptp90) cc_final: 0.7507 (ptm160) REVERT: A 609 THR cc_start: 0.8243 (m) cc_final: 0.7814 (p) REVERT: A 664 VAL cc_start: 0.8594 (m) cc_final: 0.8378 (t) REVERT: B 109 TYR cc_start: 0.7859 (m-80) cc_final: 0.7625 (m-80) REVERT: B 129 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6377 (mm-30) REVERT: B 270 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7040 (mm-30) REVERT: B 428 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7279 (tm-30) REVERT: B 473 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.7198 (tp) REVERT: B 512 VAL cc_start: 0.8199 (t) cc_final: 0.7967 (m) REVERT: B 516 GLU cc_start: 0.6709 (mp0) cc_final: 0.6098 (mp0) REVERT: B 558 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6429 (mt-10) outliers start: 33 outliers final: 12 residues processed: 243 average time/residue: 1.0391 time to fit residues: 273.2503 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 : 0.991 ------------------------------------------------------------------------------- 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 413 GLU Chi-restraints excluded: chain A residue 420 GLU 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 473 ILE Chi-restraints excluded: chain B residue 558 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 77 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 316 ASN ** A 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.146162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.128603 restraints weight = 13817.574| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.33 r_work: 0.3608 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9827 Z= 0.185 Angle : 0.620 9.627 13366 Z= 0.309 Chirality : 0.046 0.163 1451 Planarity : 0.005 0.061 1694 Dihedral : 6.401 53.711 1375 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.45 % Allowed : 17.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.25), residues: 1151 helix: 0.98 (0.27), residues: 371 sheet: -0.62 (0.43), residues: 143 loop : -0.47 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 374 HIS 0.003 0.001 HIS A 285 PHE 0.032 0.002 PHE B 400 TYR 0.021 0.002 TYR B 582 ARG 0.009 0.001 ARG A 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 1) link_NAG-ASN : angle 1.46541 ( 3) link_BETA1-4 : bond 0.00288 ( 2) link_BETA1-4 : angle 2.62168 ( 6) hydrogen bonds : bond 0.03846 ( 307) hydrogen bonds : angle 4.87563 ( 834) SS BOND : bond 0.00514 ( 9) SS BOND : angle 0.70622 ( 18) covalent geometry : bond 0.00432 ( 9815) covalent geometry : angle 0.61694 (13339) *********************** 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 264 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 228 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7681 (t0) cc_final: 0.7368 (t0) REVERT: A 115 LYS cc_start: 0.7762 (mmmm) cc_final: 0.7395 (mmmm) REVERT: A 132 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6896 (mp-120) REVERT: A 143 PHE cc_start: 0.7973 (m-10) cc_final: 0.7632 (m-10) REVERT: A 147 ASP cc_start: 0.7934 (t0) cc_final: 0.7634 (t0) REVERT: A 248 ARG cc_start: 0.7435 (mmm160) cc_final: 0.7150 (mmm-85) REVERT: A 250 PHE cc_start: 0.7042 (t80) cc_final: 0.6512 (t80) REVERT: A 265 VAL cc_start: 0.6877 (m) cc_final: 0.5210 (t) REVERT: A 359 MET cc_start: 0.8184 (mpp) cc_final: 0.7708 (mmt) REVERT: A 549 ARG cc_start: 0.7850 (ptp90) cc_final: 0.7609 (ptm160) REVERT: A 609 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.7844 (p) REVERT: A 653 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6633 (pt0) REVERT: A 664 VAL cc_start: 0.8602 (m) cc_final: 0.8367 (t) REVERT: B 109 TYR cc_start: 0.7891 (m-80) cc_final: 0.7601 (m-80) REVERT: B 129 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6617 (mm-30) REVERT: B 270 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7064 (mm-30) REVERT: B 428 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7245 (tm-30) REVERT: B 473 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7272 (tp) REVERT: B 512 VAL cc_start: 0.8272 (t) cc_final: 0.8039 (m) REVERT: B 516 GLU cc_start: 0.6758 (mp0) cc_final: 0.6170 (mp0) REVERT: B 558 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6461 (tt0) REVERT: B 675 GLU cc_start: 0.7747 (tp30) cc_final: 0.7507 (tp30) outliers start: 36 outliers final: 17 residues processed: 244 average time/residue: 1.0486 time to fit residues: 277.2407 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 : 1.084 ------------------------------------------------------------------------------- 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 420 GLU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 609 THR 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 558 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 91 optimal weight: 0.0060 chunk 7 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 21 optimal weight: 0.0870 chunk 37 optimal weight: 0.9980 overall best weight: 0.4574 ------------------------------------------------------------------------------- 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 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.148169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.130957 restraints weight = 13883.681| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.32 r_work: 0.3640 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2273 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= 0.121 Angle : 0.589 11.307 13366 Z= 0.292 Chirality : 0.044 0.199 1451 Planarity : 0.004 0.056 1694 Dihedral : 6.051 51.652 1375 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.97 % Allowed : 18.50 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.25), residues: 1151 helix: 1.16 (0.28), residues: 365 sheet: -0.43 (0.43), residues: 150 loop : -0.54 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 396 HIS 0.002 0.000 HIS A 285 PHE 0.029 0.001 PHE B 400 TYR 0.023 0.001 TYR B 582 ARG 0.005 0.000 ARG B 149 Details of bonding type rmsd link_NAG-ASN : bond 0.00103 ( 1) link_NAG-ASN : angle 1.17073 ( 3) link_BETA1-4 : bond 0.00417 ( 2) link_BETA1-4 : angle 2.41512 ( 6) hydrogen bonds : bond 0.03382 ( 307) hydrogen bonds : angle 4.77069 ( 834) SS BOND : bond 0.00353 ( 9) SS BOND : angle 0.55782 ( 18) covalent geometry : bond 0.00285 ( 9815) covalent geometry : angle 0.58639 (13339) *********************** 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: 31 poor density : 226 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7621 (t0) cc_final: 0.7323 (t0) REVERT: A 115 LYS cc_start: 0.7728 (mmmm) cc_final: 0.7381 (mmmm) REVERT: A 132 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6835 (mp-120) REVERT: A 143 PHE cc_start: 0.7868 (m-10) cc_final: 0.7587 (m-10) REVERT: A 147 ASP cc_start: 0.7872 (t0) cc_final: 0.7581 (t0) REVERT: A 250 PHE cc_start: 0.7037 (t80) cc_final: 0.6381 (t80) REVERT: A 265 VAL cc_start: 0.6813 (m) cc_final: 0.5159 (t) REVERT: A 609 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.7779 (p) REVERT: A 664 VAL cc_start: 0.8551 (m) cc_final: 0.8337 (t) REVERT: B 109 TYR cc_start: 0.7849 (m-80) cc_final: 0.7631 (m-80) REVERT: B 129 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6459 (mm-30) REVERT: B 270 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7045 (mm-30) REVERT: B 428 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7247 (tm-30) REVERT: B 512 VAL cc_start: 0.8266 (t) cc_final: 0.8026 (m) REVERT: B 516 GLU cc_start: 0.6731 (mp0) cc_final: 0.6146 (mp0) REVERT: B 556 TRP cc_start: 0.8330 (t60) cc_final: 0.8110 (t60) REVERT: B 558 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6442 (mt-10) REVERT: B 675 GLU cc_start: 0.7789 (tp30) cc_final: 0.7518 (tp30) outliers start: 31 outliers final: 16 residues processed: 239 average time/residue: 1.0008 time to fit residues: 259.4331 Evaluate side-chains 242 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 223 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 609 THR 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 488 VAL Chi-restraints excluded: chain B residue 558 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 100 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 112 optimal weight: 0.3980 chunk 85 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 106 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 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN ** A 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN B 412 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.147606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.130145 restraints weight = 13969.422| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.35 r_work: 0.3628 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2321 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= 0.143 Angle : 0.603 11.855 13366 Z= 0.300 Chirality : 0.044 0.142 1451 Planarity : 0.004 0.065 1694 Dihedral : 5.961 49.652 1375 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.07 % Allowed : 19.46 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.25), residues: 1151 helix: 1.19 (0.28), residues: 359 sheet: -0.40 (0.43), residues: 150 loop : -0.49 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 396 HIS 0.022 0.001 HIS B 88 PHE 0.037 0.002 PHE B 551 TYR 0.022 0.001 TYR B 582 ARG 0.006 0.000 ARG B 297 Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 1) link_NAG-ASN : angle 1.23568 ( 3) link_BETA1-4 : bond 0.00320 ( 2) link_BETA1-4 : angle 2.47576 ( 6) hydrogen bonds : bond 0.03488 ( 307) hydrogen bonds : angle 4.77209 ( 834) SS BOND : bond 0.00211 ( 9) SS BOND : angle 0.60252 ( 18) covalent geometry : bond 0.00339 ( 9815) covalent geometry : angle 0.60107 (13339) *********************** 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 262 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 230 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7653 (t0) cc_final: 0.7358 (t0) REVERT: A 115 LYS cc_start: 0.7742 (mmmm) cc_final: 0.7385 (mmmm) REVERT: A 132 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6896 (mp-120) REVERT: A 143 PHE cc_start: 0.7845 (m-10) cc_final: 0.7635 (m-10) REVERT: A 147 ASP cc_start: 0.7897 (t0) cc_final: 0.7609 (t0) REVERT: A 169 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7920 (mp10) REVERT: A 265 VAL cc_start: 0.6837 (m) cc_final: 0.5189 (t) REVERT: A 609 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.7808 (p) REVERT: B 129 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6569 (mm-30) REVERT: B 270 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7051 (mm-30) REVERT: B 428 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7272 (tm-30) REVERT: B 512 VAL cc_start: 0.8266 (t) cc_final: 0.8029 (m) REVERT: B 516 GLU cc_start: 0.6740 (mp0) cc_final: 0.6160 (mp0) REVERT: B 556 TRP cc_start: 0.8328 (t60) cc_final: 0.8091 (t60) REVERT: B 558 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6542 (tt0) REVERT: B 612 MET cc_start: 0.7054 (OUTLIER) cc_final: 0.6724 (ttp) REVERT: B 675 GLU cc_start: 0.7803 (tp30) cc_final: 0.7507 (tp30) outliers start: 32 outliers final: 18 residues processed: 244 average time/residue: 1.0571 time to fit residues: 278.8489 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 : 0.979 ------------------------------------------------------------------------------- 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 609 THR 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 Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 612 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 53 optimal weight: 0.9980 chunk 92 optimal weight: 0.0370 chunk 77 optimal weight: 5.9990 chunk 15 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 84 optimal weight: 0.0980 chunk 35 optimal weight: 0.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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 330 ASN ** A 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.149103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.131751 restraints weight = 13860.146| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.33 r_work: 0.3652 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9827 Z= 0.123 Angle : 0.601 10.381 13366 Z= 0.298 Chirality : 0.044 0.280 1451 Planarity : 0.004 0.063 1694 Dihedral : 5.806 48.637 1375 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.68 % Allowed : 19.85 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.25), residues: 1151 helix: 1.14 (0.28), residues: 365 sheet: -0.26 (0.43), residues: 148 loop : -0.57 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 396 HIS 0.019 0.001 HIS B 88 PHE 0.038 0.002 PHE B 551 TYR 0.023 0.001 TYR B 582 ARG 0.008 0.000 ARG B 297 Details of bonding type rmsd link_NAG-ASN : bond 0.00053 ( 1) link_NAG-ASN : angle 1.08857 ( 3) link_BETA1-4 : bond 0.00376 ( 2) link_BETA1-4 : angle 2.38195 ( 6) hydrogen bonds : bond 0.03292 ( 307) hydrogen bonds : angle 4.74654 ( 834) SS BOND : bond 0.00159 ( 9) SS BOND : angle 0.48105 ( 18) covalent geometry : bond 0.00298 ( 9815) covalent geometry : angle 0.59886 (13339) *********************** 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 244 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7655 (t0) cc_final: 0.7355 (t0) REVERT: A 115 LYS cc_start: 0.7719 (mmmm) cc_final: 0.7367 (mmmm) REVERT: A 132 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6843 (mp-120) REVERT: A 147 ASP cc_start: 0.7938 (t0) cc_final: 0.7649 (t0) REVERT: A 169 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: A 250 PHE cc_start: 0.6960 (t80) cc_final: 0.6488 (t80) REVERT: A 265 VAL cc_start: 0.6810 (m) cc_final: 0.5136 (t) REVERT: A 549 ARG cc_start: 0.7716 (ptp-170) cc_final: 0.7466 (ptm160) REVERT: A 609 THR cc_start: 0.8279 (OUTLIER) cc_final: 0.7826 (p) REVERT: A 664 VAL cc_start: 0.8551 (m) cc_final: 0.8304 (t) REVERT: B 104 ILE cc_start: 0.8145 (mm) cc_final: 0.7878 (tp) REVERT: B 129 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6560 (mm-30) REVERT: B 270 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7036 (mm-30) REVERT: B 428 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7254 (tm-30) REVERT: B 512 VAL cc_start: 0.8246 (t) cc_final: 0.8014 (m) REVERT: B 516 GLU cc_start: 0.6739 (mp0) cc_final: 0.6166 (mp0) REVERT: B 556 TRP cc_start: 0.8264 (t60) cc_final: 0.8064 (t60) REVERT: B 558 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6405 (mt-10) REVERT: B 589 GLU cc_start: 0.7136 (mp0) cc_final: 0.6832 (mp0) REVERT: B 612 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6717 (ttp) REVERT: B 675 GLU cc_start: 0.7763 (tp30) cc_final: 0.7467 (tp30) outliers start: 28 outliers final: 20 residues processed: 229 average time/residue: 0.9787 time to fit residues: 243.2692 Evaluate side-chains 239 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 214 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 297 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 587 GLU Chi-restraints excluded: chain A residue 609 THR 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 Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 612 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 62 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 91 optimal weight: 0.0040 chunk 101 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 88 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 330 ASN ** A 697 HIS ** 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 623 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.148621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.131374 restraints weight = 13962.188| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.32 r_work: 0.3646 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9827 Z= 0.141 Angle : 0.621 11.646 13366 Z= 0.305 Chirality : 0.045 0.203 1451 Planarity : 0.004 0.065 1694 Dihedral : 5.802 49.010 1375 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.78 % Allowed : 19.56 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.25), residues: 1151 helix: 0.99 (0.28), residues: 371 sheet: -0.30 (0.43), residues: 148 loop : -0.55 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 374 HIS 0.018 0.001 HIS B 88 PHE 0.042 0.002 PHE B 551 TYR 0.023 0.002 TYR B 582 ARG 0.010 0.000 ARG A 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00164 ( 1) link_NAG-ASN : angle 1.16822 ( 3) link_BETA1-4 : bond 0.00285 ( 2) link_BETA1-4 : angle 2.41243 ( 6) hydrogen bonds : bond 0.03416 ( 307) hydrogen bonds : angle 4.77415 ( 834) SS BOND : bond 0.00224 ( 9) SS BOND : angle 0.54159 ( 18) covalent geometry : bond 0.00338 ( 9815) covalent geometry : angle 0.61890 (13339) ********************** 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 251 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 222 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7676 (t0) cc_final: 0.7393 (t0) REVERT: A 115 LYS cc_start: 0.7760 (mmmm) cc_final: 0.7396 (mmmm) REVERT: A 132 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6866 (mp-120) REVERT: A 143 PHE cc_start: 0.7930 (m-10) cc_final: 0.7677 (m-10) REVERT: A 147 ASP cc_start: 0.7924 (t0) cc_final: 0.7640 (t0) REVERT: A 169 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7890 (mp10) REVERT: A 248 ARG cc_start: 0.7258 (mmm-85) cc_final: 0.7038 (mmm160) REVERT: A 250 PHE cc_start: 0.6978 (t80) cc_final: 0.6350 (t80) REVERT: A 265 VAL cc_start: 0.6818 (m) cc_final: 0.5190 (t) REVERT: A 549 ARG cc_start: 0.7726 (ptp-170) cc_final: 0.7517 (ptm160) REVERT: A 609 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.7857 (p) REVERT: A 664 VAL cc_start: 0.8567 (m) cc_final: 0.8326 (t) REVERT: B 104 ILE cc_start: 0.8191 (mm) cc_final: 0.7925 (tp) REVERT: B 129 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6661 (mm-30) REVERT: B 270 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7046 (mm-30) REVERT: B 428 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7282 (tm-30) REVERT: B 512 VAL cc_start: 0.8244 (t) cc_final: 0.8014 (m) REVERT: B 516 GLU cc_start: 0.6748 (mp0) cc_final: 0.6189 (mp0) REVERT: B 558 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6382 (mt-10) REVERT: B 589 GLU cc_start: 0.7137 (mp0) cc_final: 0.6834 (mp0) REVERT: B 612 MET cc_start: 0.7070 (OUTLIER) cc_final: 0.6758 (ttp) REVERT: B 675 GLU cc_start: 0.7798 (tp30) cc_final: 0.7495 (tp30) outliers start: 29 outliers final: 19 residues processed: 236 average time/residue: 1.0058 time to fit residues: 257.4364 Evaluate side-chains 243 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 219 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 297 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 609 THR 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 Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 612 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 330 ASN ** A 697 HIS ** 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 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 = 0.147360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.130147 restraints weight = 13966.941| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.32 r_work: 0.3632 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9827 Z= 0.165 Angle : 0.635 9.709 13366 Z= 0.315 Chirality : 0.045 0.201 1451 Planarity : 0.005 0.072 1694 Dihedral : 5.925 46.653 1375 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.40 % Allowed : 20.81 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.25), residues: 1151 helix: 0.99 (0.28), residues: 371 sheet: -0.49 (0.42), residues: 162 loop : -0.55 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 374 HIS 0.017 0.001 HIS B 88 PHE 0.040 0.002 PHE B 551 TYR 0.022 0.002 TYR B 582 ARG 0.011 0.001 ARG B 297 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 1) link_NAG-ASN : angle 1.27514 ( 3) link_BETA1-4 : bond 0.00277 ( 2) link_BETA1-4 : angle 2.46023 ( 6) hydrogen bonds : bond 0.03586 ( 307) hydrogen bonds : angle 4.81826 ( 834) SS BOND : bond 0.00266 ( 9) SS BOND : angle 0.57825 ( 18) covalent geometry : bond 0.00394 ( 9815) covalent geometry : angle 0.63272 (13339) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6433.87 seconds wall clock time: 110 minutes 33.63 seconds (6633.63 seconds total)