Starting phenix.real_space_refine on Tue Jul 29 10:53:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xul_33473/07_2025/7xul_33473.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xul_33473/07_2025/7xul_33473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xul_33473/07_2025/7xul_33473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xul_33473/07_2025/7xul_33473.map" model { file = "/net/cci-nas-00/data/ceres_data/7xul_33473/07_2025/7xul_33473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xul_33473/07_2025/7xul_33473.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 S 42 5.16 5 Cl 2 4.86 5 C 7346 2.51 5 N 1754 2.21 5 O 1938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11082 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5380 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 30, 'TRANS': 659} Chain breaks: 3 Chain: "B" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5380 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 30, 'TRANS': 659} Chain breaks: 3 Chain: "A" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 161 Unusual residues: {'I2U': 1, 'Y01': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 161 Unusual residues: {'I2U': 1, 'Y01': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 7.69, per 1000 atoms: 0.69 Number of scatterers: 11082 At special positions: 0 Unit cell: (91.545, 128.163, 103.392, 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) Cl 2 17.00 S 42 16.00 O 1938 8.00 N 1754 7.00 C 7346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.6 seconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2584 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 3 sheets defined 61.7% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 46 through 58 removed outlier: 4.085A pdb=" N LYS A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 64 removed outlier: 3.930A pdb=" N TRP A 63 " --> pdb=" O PRO A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 95 removed outlier: 6.275A pdb=" N LEU A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N SER A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 110 through 120 removed outlier: 3.633A pdb=" N LEU A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 147 removed outlier: 3.543A pdb=" N SER A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 196 removed outlier: 4.016A pdb=" N VAL A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.633A pdb=" N TYR A 204 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 removed outlier: 3.848A pdb=" N THR A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 216 " --> pdb=" O GLY A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.904A pdb=" N ILE A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 252 Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 258 through 281 removed outlier: 3.862A pdb=" N THR A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 307 Processing helix chain 'A' and resid 341 through 364 removed outlier: 3.821A pdb=" N GLY A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 removed outlier: 3.639A pdb=" N GLU A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 376 " --> pdb=" O ASN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 406 Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 429 through 433 removed outlier: 3.670A pdb=" N LEU A 432 " --> pdb=" O GLY A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 457 through 463 removed outlier: 3.927A pdb=" N ARG A 463 " --> pdb=" O GLY A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 482 Processing helix chain 'A' and resid 484 through 503 removed outlier: 3.697A pdb=" N LEU A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE A 499 " --> pdb=" O GLN A 495 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 503 " --> pdb=" O ILE A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 563 through 585 Processing helix chain 'A' and resid 612 through 618 removed outlier: 3.786A pdb=" N VAL A 615 " --> pdb=" O GLN A 612 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 617 " --> pdb=" O GLU A 614 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 618 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 677 Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.698A pdb=" N ILE A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG A 696 " --> pdb=" O GLU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 707 No H-bonds generated for 'chain 'A' and resid 705 through 707' Processing helix chain 'A' and resid 713 through 725 removed outlier: 3.590A pdb=" N HIS A 719 " --> pdb=" O ASP A 715 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A 725 " --> pdb=" O LEU A 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 43 Processing helix chain 'B' and resid 46 through 58 removed outlier: 4.085A pdb=" N LYS B 51 " --> pdb=" O PRO B 47 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 64 removed outlier: 3.931A pdb=" N TRP B 63 " --> pdb=" O PRO B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 95 removed outlier: 6.276A pdb=" N LEU B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N SER B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 110 through 120 removed outlier: 3.634A pdb=" N LEU B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 118 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 147 removed outlier: 3.543A pdb=" N SER B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 196 removed outlier: 4.015A pdb=" N VAL B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 205 removed outlier: 3.632A pdb=" N TYR B 204 " --> pdb=" O VAL B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 225 removed outlier: 3.847A pdb=" N THR B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 230 removed outlier: 3.904A pdb=" N ILE B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 258 through 281 removed outlier: 3.863A pdb=" N THR B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 307 Processing helix chain 'B' and resid 341 through 364 removed outlier: 3.821A pdb=" N GLY B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 removed outlier: 3.639A pdb=" N GLU B 374 " --> pdb=" O ASP B 370 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 375 " --> pdb=" O GLY B 371 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 376 " --> pdb=" O ASN B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 406 Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 429 through 433 removed outlier: 3.670A pdb=" N LEU B 432 " --> pdb=" O GLY B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 454 through 456 No H-bonds generated for 'chain 'B' and resid 454 through 456' Processing helix chain 'B' and resid 457 through 463 removed outlier: 3.928A pdb=" N ARG B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 482 Processing helix chain 'B' and resid 484 through 503 removed outlier: 3.697A pdb=" N LEU B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE B 499 " --> pdb=" O GLN B 495 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 503 " --> pdb=" O ILE B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 563 through 585 Processing helix chain 'B' and resid 612 through 618 removed outlier: 3.785A pdb=" N VAL B 615 " --> pdb=" O GLN B 612 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP B 617 " --> pdb=" O GLU B 614 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 618 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 677 Processing helix chain 'B' and resid 687 through 696 removed outlier: 3.698A pdb=" N ILE B 691 " --> pdb=" O ASP B 687 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 707 No H-bonds generated for 'chain 'B' and resid 705 through 707' Processing helix chain 'B' and resid 713 through 725 removed outlier: 3.590A pdb=" N HIS B 719 " --> pdb=" O ASP B 715 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP B 725 " --> pdb=" O LEU B 721 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.549A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N ASN A 513 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 12.758A pdb=" N VAL A 535 " --> pdb=" O ASN A 513 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE A 710 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE A 683 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.550A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N ASN B 513 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 12.759A pdb=" N VAL B 535 " --> pdb=" O ASN B 513 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE B 710 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE B 683 " --> pdb=" O PHE B 710 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1584 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: 3.38 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1737 1.32 - 1.44: 2842 1.44 - 1.56: 6687 1.56 - 1.69: 8 1.69 - 1.81: 62 Bond restraints: 11336 Sorted by residual: bond pdb=" C13 I2U B 803 " pdb=" C9 I2U B 803 " ideal model delta sigma weight residual 1.386 1.613 -0.227 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C13 I2U A 801 " pdb=" C9 I2U A 801 " ideal model delta sigma weight residual 1.386 1.612 -0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C12 I2U A 801 " pdb=" C8 I2U A 801 " ideal model delta sigma weight residual 1.393 1.597 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C12 I2U B 803 " pdb=" C8 I2U B 803 " ideal model delta sigma weight residual 1.393 1.597 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C21 I2U B 803 " pdb=" S2 I2U B 803 " ideal model delta sigma weight residual 1.705 1.521 0.184 2.00e-02 2.50e+03 8.45e+01 ... (remaining 11331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 15271 3.23 - 6.46: 151 6.46 - 9.69: 6 9.69 - 12.92: 2 12.92 - 16.15: 2 Bond angle restraints: 15432 Sorted by residual: angle pdb=" C18 I2U B 803 " pdb=" S2 I2U B 803 " pdb=" C21 I2U B 803 " ideal model delta sigma weight residual 91.76 107.91 -16.15 3.00e+00 1.11e-01 2.90e+01 angle pdb=" C18 I2U A 801 " pdb=" S2 I2U A 801 " pdb=" C21 I2U A 801 " ideal model delta sigma weight residual 91.76 107.88 -16.12 3.00e+00 1.11e-01 2.89e+01 angle pdb=" N ILE A 549 " pdb=" CA ILE A 549 " pdb=" C ILE A 549 " ideal model delta sigma weight residual 111.81 108.55 3.26 8.60e-01 1.35e+00 1.44e+01 angle pdb=" N ILE B 549 " pdb=" CA ILE B 549 " pdb=" C ILE B 549 " ideal model delta sigma weight residual 111.81 108.57 3.24 8.60e-01 1.35e+00 1.42e+01 angle pdb=" C LEU B 637 " pdb=" N ASN B 638 " pdb=" CA ASN B 638 " ideal model delta sigma weight residual 121.54 128.00 -6.46 1.91e+00 2.74e-01 1.14e+01 ... (remaining 15427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.44: 6247 15.44 - 30.88: 683 30.88 - 46.32: 160 46.32 - 61.76: 30 61.76 - 77.20: 12 Dihedral angle restraints: 7132 sinusoidal: 3136 harmonic: 3996 Sorted by residual: dihedral pdb=" CA PRO B 240 " pdb=" C PRO B 240 " pdb=" N VAL B 241 " pdb=" CA VAL B 241 " ideal model delta harmonic sigma weight residual 180.00 -120.11 -59.89 0 5.00e+00 4.00e-02 1.43e+02 dihedral pdb=" CA PRO A 240 " pdb=" C PRO A 240 " pdb=" N VAL A 241 " pdb=" CA VAL A 241 " ideal model delta harmonic sigma weight residual -180.00 -120.16 -59.84 0 5.00e+00 4.00e-02 1.43e+02 dihedral pdb=" CA ASP B 239 " pdb=" C ASP B 239 " pdb=" N PRO B 240 " pdb=" CA PRO B 240 " ideal model delta harmonic sigma weight residual 180.00 148.27 31.73 0 5.00e+00 4.00e-02 4.03e+01 ... (remaining 7129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1328 0.053 - 0.105: 433 0.105 - 0.158: 71 0.158 - 0.211: 6 0.211 - 0.263: 8 Chirality restraints: 1846 Sorted by residual: chirality pdb=" CG LEU A 671 " pdb=" CB LEU A 671 " pdb=" CD1 LEU A 671 " pdb=" CD2 LEU A 671 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CG LEU B 671 " pdb=" CB LEU B 671 " pdb=" CD1 LEU B 671 " pdb=" CD2 LEU B 671 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB THR A 238 " pdb=" CA THR A 238 " pdb=" OG1 THR A 238 " pdb=" CG2 THR A 238 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1843 not shown) Planarity restraints: 1876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 240 " -0.017 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C PRO B 240 " 0.058 2.00e-02 2.50e+03 pdb=" O PRO B 240 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL B 241 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 240 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C PRO A 240 " -0.058 2.00e-02 2.50e+03 pdb=" O PRO A 240 " 0.022 2.00e-02 2.50e+03 pdb=" N VAL A 241 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 239 " -0.053 5.00e-02 4.00e+02 8.04e-02 1.04e+01 pdb=" N PRO B 240 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 240 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 240 " -0.044 5.00e-02 4.00e+02 ... (remaining 1873 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3653 2.84 - 3.36: 9905 3.36 - 3.87: 17478 3.87 - 4.39: 20042 4.39 - 4.90: 35203 Nonbonded interactions: 86281 Sorted by model distance: nonbonded pdb=" OG1 THR A 503 " pdb=" OH TYR A 545 " model vdw 2.330 3.040 nonbonded pdb=" OG1 THR B 503 " pdb=" OH TYR B 545 " model vdw 2.330 3.040 nonbonded pdb=" OG SER A 75 " pdb=" O GLY A 407 " model vdw 2.337 3.040 nonbonded pdb=" OG SER B 75 " pdb=" O GLY B 407 " model vdw 2.337 3.040 nonbonded pdb=" OH TYR B 116 " pdb=" OE1 GLU B 374 " model vdw 2.350 3.040 ... (remaining 86276 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 725 or resid 802 or resid 804 through 805)) selection = (chain 'B' and (resid 8 through 725 or resid 802 or resid 804 through 805)) } 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: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 29.430 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 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 : 0.009 0.227 11336 Z= 0.422 Angle : 0.855 16.155 15432 Z= 0.461 Chirality : 0.052 0.263 1846 Planarity : 0.008 0.080 1876 Dihedral : 13.639 77.198 4548 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.45 % Favored : 93.40 % Rotamer: Outliers : 0.34 % Allowed : 6.73 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.15 % 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: -3.95 (0.18), residues: 1364 helix: -2.26 (0.14), residues: 810 sheet: 0.07 (0.80), residues: 34 loop : -3.27 (0.22), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.003 0.001 HIS A 220 PHE 0.021 0.002 PHE B 130 TYR 0.024 0.002 TYR B 9 ARG 0.002 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.19482 ( 550) hydrogen bonds : angle 6.27475 ( 1584) covalent geometry : bond 0.00872 (11336) covalent geometry : angle 0.85526 (15432) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 1.205 Fit side-chains REVERT: A 280 GLN cc_start: 0.8402 (tm-30) cc_final: 0.8136 (tm-30) REVERT: A 449 LYS cc_start: 0.5934 (mmtt) cc_final: 0.5329 (mmtt) REVERT: A 545 TYR cc_start: 0.8642 (p90) cc_final: 0.8376 (p90) REVERT: A 640 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7874 (tm-30) REVERT: B 280 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8251 (tm-30) REVERT: B 474 MET cc_start: 0.8928 (mmm) cc_final: 0.8722 (mmt) REVERT: B 545 TYR cc_start: 0.8898 (p90) cc_final: 0.8655 (p90) REVERT: B 638 ASN cc_start: 0.6890 (p0) cc_final: 0.6525 (p0) REVERT: B 640 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7810 (tm-30) outliers start: 4 outliers final: 0 residues processed: 117 average time/residue: 0.2440 time to fit residues: 40.3620 Evaluate side-chains 73 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 58 optimal weight: 0.0570 chunk 35 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 504 GLN B 90 GLN B 225 GLN B 504 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.094965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.072056 restraints weight = 18664.218| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.45 r_work: 0.2698 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11336 Z= 0.125 Angle : 0.546 6.935 15432 Z= 0.283 Chirality : 0.041 0.133 1846 Planarity : 0.005 0.071 1876 Dihedral : 7.666 55.231 2048 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.84 % Favored : 94.87 % Rotamer: Outliers : 0.76 % Allowed : 10.35 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.61 (0.22), residues: 1364 helix: -0.12 (0.18), residues: 794 sheet: 0.99 (0.80), residues: 34 loop : -2.70 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 63 HIS 0.003 0.001 HIS A 647 PHE 0.018 0.001 PHE B 130 TYR 0.012 0.001 TYR B 367 ARG 0.003 0.000 ARG A 665 Details of bonding type rmsd hydrogen bonds : bond 0.04565 ( 550) hydrogen bonds : angle 4.12651 ( 1584) covalent geometry : bond 0.00276 (11336) covalent geometry : angle 0.54601 (15432) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 1.401 Fit side-chains REVERT: A 449 LYS cc_start: 0.6152 (mmtt) cc_final: 0.5380 (mmtt) REVERT: A 640 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8269 (tm-30) REVERT: B 170 ASP cc_start: 0.8033 (p0) cc_final: 0.7707 (t0) REVERT: B 280 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8402 (tm-30) REVERT: B 545 TYR cc_start: 0.9222 (p90) cc_final: 0.9020 (p90) REVERT: B 638 ASN cc_start: 0.7241 (p0) cc_final: 0.7028 (p0) REVERT: B 640 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8152 (tm-30) outliers start: 9 outliers final: 3 residues processed: 91 average time/residue: 0.1862 time to fit residues: 27.4407 Evaluate side-chains 79 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 270 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 7 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.092812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.069951 restraints weight = 19220.405| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.47 r_work: 0.2657 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 11336 Z= 0.194 Angle : 0.569 7.337 15432 Z= 0.289 Chirality : 0.042 0.140 1846 Planarity : 0.005 0.072 1876 Dihedral : 7.275 51.908 2048 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.38 % Favored : 93.48 % Rotamer: Outliers : 1.60 % Allowed : 11.36 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.73 (0.24), residues: 1364 helix: 0.65 (0.20), residues: 800 sheet: 1.64 (0.82), residues: 34 loop : -2.48 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 63 HIS 0.004 0.001 HIS A 714 PHE 0.017 0.001 PHE A 130 TYR 0.018 0.001 TYR A 9 ARG 0.003 0.000 ARG A 665 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 550) hydrogen bonds : angle 3.76683 ( 1584) covalent geometry : bond 0.00474 (11336) covalent geometry : angle 0.56933 (15432) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 1.655 Fit side-chains REVERT: A 449 LYS cc_start: 0.6136 (mmtt) cc_final: 0.5525 (mmtt) REVERT: A 453 MET cc_start: 0.9231 (mmm) cc_final: 0.9023 (mmm) REVERT: A 640 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8109 (tm-30) REVERT: B 640 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7916 (tm-30) outliers start: 19 outliers final: 10 residues processed: 84 average time/residue: 0.1886 time to fit residues: 25.8520 Evaluate side-chains 79 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 97 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 136 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.094390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.071585 restraints weight = 18794.735| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.46 r_work: 0.2682 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11336 Z= 0.133 Angle : 0.516 7.143 15432 Z= 0.265 Chirality : 0.041 0.154 1846 Planarity : 0.004 0.072 1876 Dihedral : 7.035 49.974 2048 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.19 % Allowed : 11.36 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.28 (0.24), residues: 1364 helix: 0.97 (0.20), residues: 798 sheet: 1.92 (0.85), residues: 34 loop : -2.20 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.002 0.001 HIS A 647 PHE 0.016 0.001 PHE B 130 TYR 0.011 0.001 TYR A 9 ARG 0.002 0.000 ARG B 665 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 550) hydrogen bonds : angle 3.62620 ( 1584) covalent geometry : bond 0.00315 (11336) covalent geometry : angle 0.51574 (15432) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 1.318 Fit side-chains REVERT: A 449 LYS cc_start: 0.6129 (mmtt) cc_final: 0.5545 (mmtt) REVERT: A 640 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8119 (tm-30) REVERT: B 640 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7906 (tm-30) outliers start: 26 outliers final: 19 residues processed: 93 average time/residue: 0.1917 time to fit residues: 28.2384 Evaluate side-chains 93 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 39 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 126 optimal weight: 0.0070 chunk 68 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 119 optimal weight: 0.0470 chunk 8 optimal weight: 0.1980 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.096890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.074471 restraints weight = 18706.459| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.36 r_work: 0.2747 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11336 Z= 0.092 Angle : 0.477 6.913 15432 Z= 0.245 Chirality : 0.040 0.160 1846 Planarity : 0.004 0.071 1876 Dihedral : 6.725 47.495 2048 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.19 % Allowed : 12.46 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 (0.24), residues: 1364 helix: 1.21 (0.20), residues: 800 sheet: 2.31 (0.87), residues: 34 loop : -1.98 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.001 0.000 HIS A 647 PHE 0.015 0.001 PHE B 130 TYR 0.010 0.001 TYR B 367 ARG 0.003 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.03164 ( 550) hydrogen bonds : angle 3.46353 ( 1584) covalent geometry : bond 0.00194 (11336) covalent geometry : angle 0.47679 (15432) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 1.401 Fit side-chains REVERT: A 257 THR cc_start: 0.9133 (m) cc_final: 0.8868 (m) REVERT: A 449 LYS cc_start: 0.6069 (mmtt) cc_final: 0.5342 (mmtt) REVERT: A 640 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8068 (tm-30) REVERT: A 660 ASP cc_start: 0.8409 (p0) cc_final: 0.8176 (p0) REVERT: B 257 THR cc_start: 0.9172 (m) cc_final: 0.8895 (m) REVERT: B 640 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7878 (tm-30) outliers start: 26 outliers final: 15 residues processed: 107 average time/residue: 0.2053 time to fit residues: 34.2199 Evaluate side-chains 100 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 97 optimal weight: 0.0770 chunk 74 optimal weight: 0.4980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN ** B 403 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 = 0.3224 r_free = 0.3224 target = 0.096189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.073579 restraints weight = 18739.649| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.45 r_work: 0.2724 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11336 Z= 0.110 Angle : 0.490 6.334 15432 Z= 0.251 Chirality : 0.040 0.153 1846 Planarity : 0.004 0.070 1876 Dihedral : 6.646 46.605 2048 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.85 % Allowed : 13.55 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.30 (0.24), residues: 1364 helix: 1.37 (0.20), residues: 800 sheet: 2.43 (0.87), residues: 34 loop : -1.86 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.002 0.000 HIS B 220 PHE 0.017 0.001 PHE A 130 TYR 0.010 0.001 TYR B 545 ARG 0.008 0.000 ARG A 665 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 550) hydrogen bonds : angle 3.44038 ( 1584) covalent geometry : bond 0.00255 (11336) covalent geometry : angle 0.49002 (15432) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 1.236 Fit side-chains REVERT: A 257 THR cc_start: 0.9153 (m) cc_final: 0.8884 (m) REVERT: A 449 LYS cc_start: 0.6383 (mmtt) cc_final: 0.5540 (mmtt) REVERT: A 640 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8077 (tm-30) REVERT: A 660 ASP cc_start: 0.8425 (p0) cc_final: 0.8201 (p0) REVERT: B 257 THR cc_start: 0.9173 (m) cc_final: 0.8899 (m) REVERT: B 640 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7875 (tm-30) outliers start: 22 outliers final: 18 residues processed: 92 average time/residue: 0.1693 time to fit residues: 25.3815 Evaluate side-chains 95 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.072906 restraints weight = 19085.654| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.48 r_work: 0.2711 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11336 Z= 0.123 Angle : 0.497 6.331 15432 Z= 0.254 Chirality : 0.040 0.149 1846 Planarity : 0.004 0.070 1876 Dihedral : 6.619 46.208 2048 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.02 % Allowed : 13.80 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.44 (0.24), residues: 1364 helix: 1.47 (0.20), residues: 800 sheet: 2.55 (0.87), residues: 34 loop : -1.79 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.002 0.001 HIS A 714 PHE 0.017 0.001 PHE A 130 TYR 0.010 0.001 TYR B 367 ARG 0.006 0.000 ARG A 665 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 550) hydrogen bonds : angle 3.42932 ( 1584) covalent geometry : bond 0.00291 (11336) covalent geometry : angle 0.49670 (15432) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 1.386 Fit side-chains REVERT: A 257 THR cc_start: 0.9180 (m) cc_final: 0.8922 (m) REVERT: A 449 LYS cc_start: 0.6422 (mmtt) cc_final: 0.5578 (mmtt) REVERT: A 612 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8332 (tt0) REVERT: A 640 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8002 (tm-30) REVERT: A 660 ASP cc_start: 0.8473 (p0) cc_final: 0.8255 (p0) REVERT: B 257 THR cc_start: 0.9189 (m) cc_final: 0.8912 (m) REVERT: B 640 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7867 (tm-30) outliers start: 24 outliers final: 18 residues processed: 90 average time/residue: 0.2226 time to fit residues: 32.8239 Evaluate side-chains 96 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 612 GLN Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 112 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.095724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.072974 restraints weight = 18824.293| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.45 r_work: 0.2716 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11336 Z= 0.117 Angle : 0.497 6.219 15432 Z= 0.255 Chirality : 0.040 0.157 1846 Planarity : 0.004 0.070 1876 Dihedral : 6.570 45.956 2048 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.60 % Allowed : 14.56 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.54 (0.25), residues: 1364 helix: 1.55 (0.20), residues: 800 sheet: 2.60 (0.87), residues: 34 loop : -1.76 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.002 0.001 HIS B 220 PHE 0.017 0.001 PHE B 130 TYR 0.010 0.001 TYR A 367 ARG 0.005 0.000 ARG A 665 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 550) hydrogen bonds : angle 3.40468 ( 1584) covalent geometry : bond 0.00277 (11336) covalent geometry : angle 0.49674 (15432) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 1.278 Fit side-chains REVERT: A 257 THR cc_start: 0.9181 (m) cc_final: 0.8913 (m) REVERT: A 449 LYS cc_start: 0.6439 (mmtt) cc_final: 0.5584 (mmtt) REVERT: A 640 GLU cc_start: 0.8418 (tm-30) cc_final: 0.7990 (tm-30) REVERT: A 660 ASP cc_start: 0.8468 (p0) cc_final: 0.8246 (p0) REVERT: B 257 THR cc_start: 0.9192 (m) cc_final: 0.8922 (m) REVERT: B 640 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7854 (tm-30) outliers start: 19 outliers final: 16 residues processed: 91 average time/residue: 0.1991 time to fit residues: 29.5132 Evaluate side-chains 91 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 52 optimal weight: 0.3980 chunk 100 optimal weight: 0.7980 chunk 135 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 28 optimal weight: 0.0980 chunk 131 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.096137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.073654 restraints weight = 19021.700| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.37 r_work: 0.2731 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11336 Z= 0.109 Angle : 0.495 7.781 15432 Z= 0.252 Chirality : 0.040 0.161 1846 Planarity : 0.004 0.069 1876 Dihedral : 6.537 45.771 2048 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.85 % Allowed : 14.48 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.61 (0.25), residues: 1364 helix: 1.60 (0.20), residues: 802 sheet: 2.60 (0.87), residues: 34 loop : -1.72 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.002 0.000 HIS B 220 PHE 0.017 0.001 PHE A 130 TYR 0.010 0.001 TYR A 367 ARG 0.005 0.000 ARG B 665 Details of bonding type rmsd hydrogen bonds : bond 0.03247 ( 550) hydrogen bonds : angle 3.39278 ( 1584) covalent geometry : bond 0.00254 (11336) covalent geometry : angle 0.49534 (15432) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 1.800 Fit side-chains REVERT: A 257 THR cc_start: 0.9146 (m) cc_final: 0.8871 (m) REVERT: A 449 LYS cc_start: 0.6410 (mmtt) cc_final: 0.5580 (mmtt) REVERT: A 640 GLU cc_start: 0.8398 (tm-30) cc_final: 0.7967 (tm-30) REVERT: A 660 ASP cc_start: 0.8453 (p0) cc_final: 0.8241 (p0) REVERT: B 257 THR cc_start: 0.9181 (m) cc_final: 0.8899 (m) REVERT: B 640 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7839 (tm-30) outliers start: 22 outliers final: 16 residues processed: 91 average time/residue: 0.1999 time to fit residues: 29.6762 Evaluate side-chains 93 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 119 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 57 optimal weight: 0.1980 chunk 84 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 55 optimal weight: 0.2980 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 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.073151 restraints weight = 18838.449| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.46 r_work: 0.2721 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11336 Z= 0.118 Angle : 0.505 7.703 15432 Z= 0.260 Chirality : 0.040 0.152 1846 Planarity : 0.004 0.066 1876 Dihedral : 6.496 45.446 2048 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.84 % Favored : 95.01 % Rotamer: Outliers : 1.43 % Allowed : 14.73 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.65 (0.25), residues: 1364 helix: 1.60 (0.20), residues: 810 sheet: 2.62 (0.86), residues: 34 loop : -1.70 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 63 HIS 0.002 0.000 HIS B 220 PHE 0.017 0.001 PHE A 130 TYR 0.010 0.001 TYR A 367 ARG 0.005 0.000 ARG B 665 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 550) hydrogen bonds : angle 3.38399 ( 1584) covalent geometry : bond 0.00276 (11336) covalent geometry : angle 0.50459 (15432) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 1.321 Fit side-chains REVERT: A 257 THR cc_start: 0.9151 (m) cc_final: 0.8877 (m) REVERT: A 449 LYS cc_start: 0.6378 (mmtt) cc_final: 0.5516 (mmtt) REVERT: A 640 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7977 (tm-30) REVERT: A 660 ASP cc_start: 0.8469 (p0) cc_final: 0.8251 (p0) REVERT: B 257 THR cc_start: 0.9183 (m) cc_final: 0.8911 (m) REVERT: B 640 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7827 (tm-30) outliers start: 17 outliers final: 16 residues processed: 84 average time/residue: 0.1892 time to fit residues: 26.0206 Evaluate side-chains 91 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 106 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 42 optimal weight: 0.0370 chunk 108 optimal weight: 0.0770 chunk 117 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.096962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.074488 restraints weight = 18823.434| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.37 r_work: 0.2750 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11336 Z= 0.101 Angle : 0.494 8.268 15432 Z= 0.254 Chirality : 0.040 0.154 1846 Planarity : 0.004 0.070 1876 Dihedral : 6.442 45.365 2048 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.77 % Favored : 95.16 % Rotamer: Outliers : 1.35 % Allowed : 14.65 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.67 (0.25), residues: 1364 helix: 1.57 (0.20), residues: 814 sheet: 2.64 (0.87), residues: 34 loop : -1.63 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.000 HIS B 220 PHE 0.016 0.001 PHE B 130 TYR 0.010 0.001 TYR B 367 ARG 0.005 0.000 ARG B 665 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 550) hydrogen bonds : angle 3.35892 ( 1584) covalent geometry : bond 0.00229 (11336) covalent geometry : angle 0.49446 (15432) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5530.06 seconds wall clock time: 97 minutes 50.06 seconds (5870.06 seconds total)