Starting phenix.real_space_refine on Sun Dec 29 03:06:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uqy_26702/12_2024/7uqy_26702.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uqy_26702/12_2024/7uqy_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_26702/12_2024/7uqy_26702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uqy_26702/12_2024/7uqy_26702.map" model { file = "/net/cci-nas-00/data/ceres_data/7uqy_26702/12_2024/7uqy_26702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uqy_26702/12_2024/7uqy_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-5532/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: 5.93, per 1000 atoms: 0.62 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: 2.44 Conformation dependent library (CDL) restraints added in 1.2 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: 1.17 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: 2.88 Time building geometry restraints manager: 2.82 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: 0.750 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.580 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: 0.000 Load rotamer database and sin/cos tables:13.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.660 ------------------------------------------------------------------------------- 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 9815 Z= 0.201 Angle : 0.591 7.160 13339 Z= 0.321 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 *********************** 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 : 1.096 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: 1.0854 time to fit residues: 283.6452 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 : 1.084 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 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 9815 Z= 0.211 Angle : 0.595 8.616 13339 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 *********************** 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 : 1.061 Fit side-chains REVERT: A 265 VAL cc_start: 0.6303 (m) cc_final: 0.4446 (t) REVERT: A 413 GLU cc_start: 0.6713 (tt0) cc_final: 0.6311 (tt0) REVERT: A 664 VAL cc_start: 0.8227 (m) cc_final: 0.7973 (t) REVERT: B 174 MET cc_start: 0.4736 (OUTLIER) cc_final: 0.4147 (mtt) REVERT: B 573 TRP cc_start: 0.7782 (t-100) cc_final: 0.7448 (t-100) outliers start: 19 outliers final: 2 residues processed: 248 average time/residue: 1.1018 time to fit residues: 295.2310 Evaluate side-chains 224 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 221 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 58 optimal weight: 0.0050 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 412 GLN B 623 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9815 Z= 0.209 Angle : 0.582 10.145 13339 Z= 0.290 Chirality : 0.045 0.164 1451 Planarity : 0.004 0.054 1694 Dihedral : 7.075 58.722 1375 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.59 % Allowed : 14.00 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.09 (0.28), residues: 362 sheet: -0.47 (0.41), residues: 161 loop : -0.37 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 0.015 0.001 ARG B 149 *********************** 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 253 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 226 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 265 VAL cc_start: 0.6301 (m) cc_final: 0.4514 (t) REVERT: A 295 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.7034 (mt) REVERT: A 413 GLU cc_start: 0.6728 (tt0) cc_final: 0.6449 (tt0) REVERT: B 572 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7212 (mm) REVERT: B 573 TRP cc_start: 0.7825 (t-100) cc_final: 0.7598 (t-100) outliers start: 27 outliers final: 6 residues processed: 237 average time/residue: 1.1030 time to fit residues: 282.3007 Evaluate side-chains 228 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 220 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 572 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 30 optimal weight: 0.0050 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9815 Z= 0.207 Angle : 0.574 7.397 13339 Z= 0.286 Chirality : 0.044 0.141 1451 Planarity : 0.004 0.063 1694 Dihedral : 6.490 59.224 1375 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.78 % Allowed : 15.05 % Favored : 82.17 % 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: 1.14 (0.28), residues: 362 sheet: -0.48 (0.41), residues: 165 loop : -0.38 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 374 HIS 0.003 0.001 HIS A 285 PHE 0.019 0.001 PHE A 345 TYR 0.022 0.002 TYR B 582 ARG 0.012 0.001 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 1.056 Fit side-chains REVERT: A 265 VAL cc_start: 0.6299 (m) cc_final: 0.4505 (t) REVERT: A 295 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.7043 (mt) REVERT: A 413 GLU cc_start: 0.6695 (tt0) cc_final: 0.6465 (tt0) REVERT: B 174 MET cc_start: 0.4711 (OUTLIER) cc_final: 0.4070 (mtt) REVERT: B 473 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7436 (tp) REVERT: B 572 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7174 (mm) outliers start: 29 outliers final: 11 residues processed: 239 average time/residue: 1.0977 time to fit residues: 285.8299 Evaluate side-chains 231 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 216 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 391 SER 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 174 MET Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 616 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 100 optimal weight: 0.0040 chunk 28 optimal weight: 0.6980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9815 Z= 0.199 Angle : 0.575 8.236 13339 Z= 0.286 Chirality : 0.044 0.181 1451 Planarity : 0.004 0.053 1694 Dihedral : 6.225 57.622 1375 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.07 % Allowed : 16.01 % Favored : 80.92 % 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: 1.21 (0.28), residues: 362 sheet: -0.44 (0.41), residues: 165 loop : -0.44 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 374 HIS 0.019 0.001 HIS B 88 PHE 0.027 0.002 PHE B 551 TYR 0.021 0.001 TYR B 582 ARG 0.006 0.000 ARG A 248 *********************** 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 257 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 1.116 Fit side-chains REVERT: A 169 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7645 (mp10) REVERT: A 265 VAL cc_start: 0.6372 (m) cc_final: 0.4594 (t) REVERT: A 413 GLU cc_start: 0.6717 (tt0) cc_final: 0.6442 (tt0) REVERT: A 549 ARG cc_start: 0.7236 (ptp90) cc_final: 0.6941 (ptm160) REVERT: B 177 LEU cc_start: 0.5330 (tt) cc_final: 0.5109 (tt) REVERT: B 473 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7518 (tp) outliers start: 32 outliers final: 14 residues processed: 239 average time/residue: 1.1152 time to fit residues: 287.9231 Evaluate side-chains 231 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 572 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 93 optimal weight: 0.0060 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 0.0370 chunk 108 optimal weight: 0.5980 overall best weight: 0.4074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9815 Z= 0.178 Angle : 0.581 8.854 13339 Z= 0.287 Chirality : 0.043 0.144 1451 Planarity : 0.004 0.050 1694 Dihedral : 5.950 55.963 1375 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.68 % Allowed : 17.83 % Favored : 79.48 % 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: 0.12 (0.25), residues: 1151 helix: 1.36 (0.28), residues: 359 sheet: -0.40 (0.40), residues: 165 loop : -0.50 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 619 HIS 0.013 0.001 HIS B 88 PHE 0.030 0.002 PHE B 551 TYR 0.022 0.001 TYR B 582 ARG 0.007 0.000 ARG A 248 *********************** 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 247 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 250 PHE cc_start: 0.6186 (t80) cc_final: 0.5755 (t80) REVERT: A 265 VAL cc_start: 0.6333 (m) cc_final: 0.4567 (t) REVERT: A 413 GLU cc_start: 0.6685 (tt0) cc_final: 0.6459 (tt0) REVERT: B 129 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6648 (mm-30) REVERT: B 177 LEU cc_start: 0.5311 (tt) cc_final: 0.5102 (tt) outliers start: 28 outliers final: 13 residues processed: 231 average time/residue: 1.0693 time to fit residues: 267.3076 Evaluate side-chains 224 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 211 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 572 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 4.9990 chunk 63 optimal weight: 0.0770 chunk 81 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 69 optimal weight: 0.0570 chunk 68 optimal weight: 0.9990 chunk 51 optimal weight: 0.0670 chunk 44 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9815 Z= 0.170 Angle : 0.584 9.736 13339 Z= 0.287 Chirality : 0.043 0.157 1451 Planarity : 0.004 0.055 1694 Dihedral : 5.724 55.590 1375 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.21 % Allowed : 18.98 % Favored : 78.81 % 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: 0.15 (0.25), residues: 1151 helix: 1.30 (0.28), residues: 366 sheet: -0.22 (0.42), residues: 154 loop : -0.50 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 619 HIS 0.012 0.001 HIS B 88 PHE 0.027 0.002 PHE B 400 TYR 0.023 0.001 TYR B 582 ARG 0.007 0.000 ARG A 142 *********************** 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 243 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 VAL cc_start: 0.6373 (m) cc_final: 0.4635 (t) REVERT: A 413 GLU cc_start: 0.6692 (tt0) cc_final: 0.6454 (tt0) REVERT: A 564 LEU cc_start: 0.6319 (tp) cc_final: 0.5967 (tp) REVERT: A 664 VAL cc_start: 0.8241 (m) cc_final: 0.8022 (t) outliers start: 23 outliers final: 16 residues processed: 230 average time/residue: 1.0884 time to fit residues: 270.6588 Evaluate side-chains 227 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 242 LEU 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 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 104 optimal weight: 0.3980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9815 Z= 0.232 Angle : 0.616 10.106 13339 Z= 0.304 Chirality : 0.044 0.176 1451 Planarity : 0.004 0.064 1694 Dihedral : 5.811 53.295 1375 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.59 % Allowed : 19.75 % 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: 0.01 (0.25), residues: 1151 helix: 1.13 (0.28), residues: 371 sheet: -0.42 (0.42), residues: 150 loop : -0.52 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 619 HIS 0.011 0.001 HIS B 88 PHE 0.026 0.002 PHE B 400 TYR 0.021 0.001 TYR B 582 ARG 0.009 0.001 ARG A 142 *********************** 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 246 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 VAL cc_start: 0.6485 (m) cc_final: 0.4727 (t) REVERT: A 413 GLU cc_start: 0.6723 (tt0) cc_final: 0.6455 (tt0) REVERT: A 564 LEU cc_start: 0.6375 (tp) cc_final: 0.6013 (tp) REVERT: A 653 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6124 (pt0) REVERT: A 664 VAL cc_start: 0.8268 (m) cc_final: 0.8029 (t) REVERT: B 129 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6732 (mm-30) outliers start: 27 outliers final: 17 residues processed: 231 average time/residue: 1.0640 time to fit residues: 265.9154 Evaluate side-chains 232 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 452 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 572 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9815 Z= 0.235 Angle : 0.630 12.107 13339 Z= 0.313 Chirality : 0.045 0.186 1451 Planarity : 0.004 0.056 1694 Dihedral : 5.874 51.679 1375 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.68 % Allowed : 20.61 % Favored : 76.70 % 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: -0.02 (0.25), residues: 1151 helix: 1.14 (0.28), residues: 371 sheet: -0.52 (0.42), residues: 143 loop : -0.55 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 374 HIS 0.010 0.001 HIS B 88 PHE 0.039 0.002 PHE B 551 TYR 0.021 0.001 TYR B 582 ARG 0.009 0.001 ARG A 142 *********************** 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 248 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: A 265 VAL cc_start: 0.6500 (m) cc_final: 0.4739 (t) REVERT: A 413 GLU cc_start: 0.6727 (tt0) cc_final: 0.6474 (tt0) REVERT: A 653 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6213 (pt0) REVERT: A 664 VAL cc_start: 0.8262 (m) cc_final: 0.8024 (t) REVERT: B 321 LEU cc_start: 0.8480 (mm) cc_final: 0.8279 (mm) REVERT: B 516 GLU cc_start: 0.6053 (mp0) cc_final: 0.5704 (mp0) REVERT: B 558 GLU cc_start: 0.6139 (mt-10) cc_final: 0.5928 (mt-10) outliers start: 28 outliers final: 21 residues processed: 234 average time/residue: 1.0672 time to fit residues: 270.8771 Evaluate side-chains 236 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 297 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 572 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 92 optimal weight: 0.0000 chunk 9 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 98 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9815 Z= 0.203 Angle : 0.642 12.152 13339 Z= 0.316 Chirality : 0.044 0.165 1451 Planarity : 0.005 0.058 1694 Dihedral : 5.812 50.940 1375 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.30 % Allowed : 21.38 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.21 (0.28), residues: 365 sheet: -0.40 (0.42), residues: 150 loop : -0.59 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 619 HIS 0.010 0.001 HIS B 88 PHE 0.039 0.002 PHE B 551 TYR 0.022 0.001 TYR B 582 ARG 0.017 0.001 ARG A 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 265 VAL cc_start: 0.6497 (m) cc_final: 0.4741 (t) REVERT: A 413 GLU cc_start: 0.6719 (tt0) cc_final: 0.6456 (tt0) REVERT: A 653 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6183 (pt0) REVERT: A 664 VAL cc_start: 0.8240 (m) cc_final: 0.8004 (t) REVERT: B 393 ARG cc_start: 0.6913 (tpt170) cc_final: 0.6682 (tmt-80) REVERT: B 516 GLU cc_start: 0.6053 (mp0) cc_final: 0.5685 (mp0) outliers start: 24 outliers final: 17 residues processed: 228 average time/residue: 1.0338 time to fit residues: 255.8905 Evaluate side-chains 230 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 212 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 508 GLN Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 725 ASP 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 512 VAL Chi-restraints excluded: chain B residue 572 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 0.0770 chunk 38 optimal weight: 0.0570 chunk 94 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 66 optimal weight: 4.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- 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 623 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.150787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.133448 restraints weight = 13776.927| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.34 r_work: 0.3667 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9815 Z= 0.185 Angle : 0.625 13.033 13339 Z= 0.310 Chirality : 0.044 0.156 1451 Planarity : 0.005 0.056 1694 Dihedral : 5.686 50.315 1375 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.01 % Allowed : 22.15 % Favored : 75.84 % 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: 1.27 (0.28), residues: 365 sheet: -0.30 (0.46), residues: 126 loop : -0.59 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 619 HIS 0.011 0.001 HIS B 88 PHE 0.041 0.002 PHE B 551 TYR 0.024 0.001 TYR B 582 ARG 0.011 0.001 ARG A 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4362.89 seconds wall clock time: 78 minutes 40.70 seconds (4720.70 seconds total)