Starting phenix.real_space_refine on Wed Feb 4 14:20:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xul_33473/02_2026/7xul_33473.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xul_33473/02_2026/7xul_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 { model { file = "/net/cci-nas-00/data/ceres_data/7xul_33473/02_2026/7xul_33473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xul_33473/02_2026/7xul_33473.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xul_33473/02_2026/7xul_33473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xul_33473/02_2026/7xul_33473.map" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: 2.63, per 1000 atoms: 0.24 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: 0.91 Conformation dependent library (CDL) restraints added in 513.4 milliseconds 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: 0.36 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: 1.65 Time building geometry restraints manager: 1.20 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: 0.02 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.110 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.940 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.002 0.000 ARG A 52 TYR 0.024 0.002 TYR B 9 PHE 0.021 0.002 PHE B 130 TRP 0.009 0.001 TRP A 63 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00872 (11336) covalent geometry : angle 0.85526 (15432) hydrogen bonds : bond 0.19482 ( 550) hydrogen bonds : angle 6.27475 ( 1584) *********************** 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 : 0.272 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: 0.6891 (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: 0.1183 time to fit residues: 19.3634 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 : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3203 r_free = 0.3203 target = 0.094861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.071887 restraints weight = 18810.248| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.47 r_work: 0.2698 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1069 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= 0.127 Angle : 0.544 6.966 15432 Z= 0.281 Chirality : 0.041 0.134 1846 Planarity : 0.005 0.072 1876 Dihedral : 7.632 54.923 2048 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.69 % Favored : 95.01 % Rotamer: Outliers : 0.84 % Allowed : 10.10 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.22), residues: 1364 helix: -0.05 (0.18), residues: 794 sheet: 1.00 (0.81), residues: 34 loop : -2.69 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 665 TYR 0.012 0.001 TYR B 367 PHE 0.017 0.001 PHE B 130 TRP 0.007 0.001 TRP B 63 HIS 0.003 0.001 HIS B 647 Details of bonding type rmsd covalent geometry : bond 0.00285 (11336) covalent geometry : angle 0.54362 (15432) hydrogen bonds : bond 0.04454 ( 550) hydrogen bonds : angle 4.09423 ( 1584) *********************** 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: 10 poor density : 83 time to evaluate : 0.443 Fit side-chains REVERT: A 449 LYS cc_start: 0.6175 (mmtt) cc_final: 0.5385 (mmtt) REVERT: A 640 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8301 (tm-30) REVERT: B 170 ASP cc_start: 0.8021 (p0) cc_final: 0.7714 (t0) REVERT: B 280 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8420 (tm-30) REVERT: B 638 ASN cc_start: 0.7260 (p0) cc_final: 0.7046 (p0) REVERT: B 640 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8164 (tm-30) outliers start: 10 outliers final: 4 residues processed: 90 average time/residue: 0.0887 time to fit residues: 12.9156 Evaluate side-chains 81 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 B residue 270 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 1 optimal weight: 0.0980 chunk 76 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 126 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 58 optimal weight: 0.4980 chunk 117 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3230 r_free = 0.3230 target = 0.096491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.073513 restraints weight = 18815.371| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.47 r_work: 0.2726 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11336 Z= 0.101 Angle : 0.489 6.904 15432 Z= 0.252 Chirality : 0.040 0.131 1846 Planarity : 0.004 0.073 1876 Dihedral : 7.011 53.412 2048 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.09 % Allowed : 11.70 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.24), residues: 1364 helix: 0.53 (0.19), residues: 816 sheet: 1.78 (0.84), residues: 34 loop : -2.30 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 665 TYR 0.010 0.001 TYR B 367 PHE 0.016 0.001 PHE A 130 TRP 0.006 0.001 TRP B 472 HIS 0.002 0.000 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00221 (11336) covalent geometry : angle 0.48908 (15432) hydrogen bonds : bond 0.03677 ( 550) hydrogen bonds : angle 3.67782 ( 1584) *********************** 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 106 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.477 Fit side-chains REVERT: A 449 LYS cc_start: 0.6032 (mmtt) cc_final: 0.5475 (mmtt) REVERT: A 640 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8185 (tm-30) REVERT: B 170 ASP cc_start: 0.8075 (p0) cc_final: 0.7836 (t0) REVERT: B 640 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7905 (tm-30) outliers start: 13 outliers final: 7 residues processed: 99 average time/residue: 0.0949 time to fit residues: 14.4490 Evaluate side-chains 87 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 ILE 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 51 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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** A 504 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 = 0.3197 r_free = 0.3197 target = 0.094418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.071429 restraints weight = 19117.340| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.47 r_work: 0.2684 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11336 Z= 0.158 Angle : 0.538 7.616 15432 Z= 0.272 Chirality : 0.041 0.152 1846 Planarity : 0.004 0.072 1876 Dihedral : 6.919 50.190 2048 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.85 % Allowed : 11.03 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.24), residues: 1364 helix: 0.98 (0.20), residues: 798 sheet: 2.07 (0.84), residues: 34 loop : -2.09 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 665 TYR 0.015 0.001 TYR A 9 PHE 0.020 0.001 PHE B 130 TRP 0.005 0.001 TRP B 63 HIS 0.003 0.001 HIS A 714 Details of bonding type rmsd covalent geometry : bond 0.00381 (11336) covalent geometry : angle 0.53833 (15432) hydrogen bonds : bond 0.03941 ( 550) hydrogen bonds : angle 3.62200 ( 1584) *********************** 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 98 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.436 Fit side-chains REVERT: A 449 LYS cc_start: 0.6129 (mmtt) cc_final: 0.5359 (mmtt) REVERT: A 640 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8126 (tm-30) REVERT: B 193 PHE cc_start: 0.9115 (m-10) cc_final: 0.8811 (m-80) REVERT: B 640 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7901 (tm-30) outliers start: 22 outliers final: 15 residues processed: 84 average time/residue: 0.0733 time to fit residues: 10.0306 Evaluate side-chains 89 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 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 92 LEU 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 596 CYS 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 137 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 112 optimal weight: 0.0970 chunk 34 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3209 r_free = 0.3209 target = 0.095269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.072257 restraints weight = 18926.328| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.48 r_work: 0.2698 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1775 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= 0.123 Angle : 0.505 7.271 15432 Z= 0.257 Chirality : 0.041 0.148 1846 Planarity : 0.004 0.072 1876 Dihedral : 6.778 48.266 2048 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.27 % Allowed : 11.62 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.24), residues: 1364 helix: 1.17 (0.20), residues: 800 sheet: 2.38 (0.85), residues: 34 loop : -1.97 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 665 TYR 0.010 0.001 TYR B 367 PHE 0.017 0.001 PHE B 130 TRP 0.006 0.001 TRP B 63 HIS 0.002 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00291 (11336) covalent geometry : angle 0.50465 (15432) hydrogen bonds : bond 0.03560 ( 550) hydrogen bonds : angle 3.51753 ( 1584) *********************** 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 105 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.434 Fit side-chains REVERT: A 449 LYS cc_start: 0.6049 (mmtt) cc_final: 0.5269 (mmtt) REVERT: A 640 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8092 (tm-30) REVERT: B 640 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7860 (tm-30) outliers start: 27 outliers final: 20 residues processed: 90 average time/residue: 0.0902 time to fit residues: 12.8091 Evaluate side-chains 93 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 92 LEU 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 457 GLU Chi-restraints excluded: chain B residue 596 CYS 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 63 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 1 optimal weight: 0.0170 chunk 54 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- 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 = 0.3212 r_free = 0.3212 target = 0.095443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.072481 restraints weight = 18990.183| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.47 r_work: 0.2708 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1858 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= 0.121 Angle : 0.505 7.345 15432 Z= 0.257 Chirality : 0.040 0.149 1846 Planarity : 0.004 0.071 1876 Dihedral : 6.716 46.990 2048 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.02 % Allowed : 12.21 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.24), residues: 1364 helix: 1.29 (0.20), residues: 802 sheet: 2.56 (0.85), residues: 34 loop : -1.90 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 665 TYR 0.010 0.001 TYR B 367 PHE 0.017 0.001 PHE A 130 TRP 0.006 0.001 TRP B 63 HIS 0.002 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00285 (11336) covalent geometry : angle 0.50466 (15432) hydrogen bonds : bond 0.03486 ( 550) hydrogen bonds : angle 3.48513 ( 1584) *********************** 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 100 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.514 Fit side-chains REVERT: A 449 LYS cc_start: 0.6036 (mmtt) cc_final: 0.5605 (mmtt) REVERT: A 640 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8094 (tm-30) REVERT: B 640 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7876 (tm-30) outliers start: 24 outliers final: 17 residues processed: 89 average time/residue: 0.0771 time to fit residues: 11.1807 Evaluate side-chains 93 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 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 45 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 66 optimal weight: 0.2980 chunk 46 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3217 r_free = 0.3217 target = 0.095795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.072911 restraints weight = 18928.622| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.47 r_work: 0.2715 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1952 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= 0.115 Angle : 0.498 6.839 15432 Z= 0.255 Chirality : 0.040 0.148 1846 Planarity : 0.004 0.071 1876 Dihedral : 6.646 46.620 2048 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.02 % Allowed : 12.79 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.24), residues: 1364 helix: 1.44 (0.20), residues: 800 sheet: 2.65 (0.85), residues: 34 loop : -1.83 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 665 TYR 0.010 0.001 TYR B 367 PHE 0.017 0.001 PHE A 130 TRP 0.006 0.001 TRP A 63 HIS 0.002 0.000 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00267 (11336) covalent geometry : angle 0.49807 (15432) hydrogen bonds : bond 0.03368 ( 550) hydrogen bonds : angle 3.44441 ( 1584) *********************** 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 104 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.439 Fit side-chains REVERT: A 257 THR cc_start: 0.9167 (m) cc_final: 0.8906 (m) REVERT: A 640 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8034 (tm-30) REVERT: B 257 THR cc_start: 0.9193 (m) cc_final: 0.8914 (m) REVERT: B 640 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7828 (tm-30) outliers start: 24 outliers final: 17 residues processed: 92 average time/residue: 0.0744 time to fit residues: 11.2219 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 : 0.261 ------------------------------------------------------------------------------- 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 92 LEU Chi-restraints excluded: chain B residue 98 VAL 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 596 CYS 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 107 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 69 optimal weight: 0.0970 chunk 28 optimal weight: 0.0870 chunk 137 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 = 0.3234 r_free = 0.3234 target = 0.096779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.073920 restraints weight = 18795.576| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.46 r_work: 0.2733 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11336 Z= 0.100 Angle : 0.487 7.238 15432 Z= 0.251 Chirality : 0.040 0.155 1846 Planarity : 0.004 0.069 1876 Dihedral : 6.530 46.356 2048 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.62 % Favored : 95.31 % Rotamer: Outliers : 1.85 % Allowed : 13.13 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.25), residues: 1364 helix: 1.41 (0.20), residues: 816 sheet: 2.76 (0.85), residues: 34 loop : -1.79 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 665 TYR 0.010 0.001 TYR A 204 PHE 0.015 0.001 PHE A 130 TRP 0.007 0.001 TRP A 63 HIS 0.002 0.000 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00224 (11336) covalent geometry : angle 0.48724 (15432) hydrogen bonds : bond 0.03164 ( 550) hydrogen bonds : angle 3.40231 ( 1584) *********************** 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 103 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.432 Fit side-chains REVERT: A 257 THR cc_start: 0.9130 (m) cc_final: 0.8848 (m) REVERT: A 640 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8008 (tm-30) REVERT: A 660 ASP cc_start: 0.8450 (p0) cc_final: 0.8229 (p0) REVERT: B 257 THR cc_start: 0.9176 (m) cc_final: 0.8892 (m) REVERT: B 640 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7835 (tm-30) outliers start: 22 outliers final: 15 residues processed: 94 average time/residue: 0.0685 time to fit residues: 10.8744 Evaluate side-chains 91 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 56 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 118 optimal weight: 0.0070 chunk 72 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 71 optimal weight: 0.0770 chunk 105 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 overall best weight: 0.4556 ------------------------------------------------------------------------------- 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 = 0.3234 r_free = 0.3234 target = 0.096987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.074555 restraints weight = 18692.646| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.36 r_work: 0.2751 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11336 Z= 0.102 Angle : 0.497 8.032 15432 Z= 0.254 Chirality : 0.040 0.158 1846 Planarity : 0.004 0.068 1876 Dihedral : 6.477 45.987 2048 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.69 % Favored : 95.23 % Rotamer: Outliers : 1.68 % Allowed : 13.80 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.25), residues: 1364 helix: 1.51 (0.20), residues: 814 sheet: 2.76 (0.85), residues: 34 loop : -1.74 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 665 TYR 0.010 0.001 TYR A 367 PHE 0.016 0.001 PHE A 130 TRP 0.007 0.001 TRP A 63 HIS 0.002 0.000 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00230 (11336) covalent geometry : angle 0.49733 (15432) hydrogen bonds : bond 0.03137 ( 550) hydrogen bonds : angle 3.38904 ( 1584) *********************** 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: 20 poor density : 78 time to evaluate : 0.338 Fit side-chains REVERT: A 257 THR cc_start: 0.9126 (m) cc_final: 0.8845 (m) REVERT: A 640 GLU cc_start: 0.8414 (tm-30) cc_final: 0.7981 (tm-30) REVERT: A 660 ASP cc_start: 0.8428 (p0) cc_final: 0.8224 (p0) REVERT: B 257 THR cc_start: 0.9158 (m) cc_final: 0.8878 (m) REVERT: B 640 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7805 (tm-30) REVERT: B 660 ASP cc_start: 0.8455 (p0) cc_final: 0.8244 (p0) outliers start: 20 outliers final: 16 residues processed: 89 average time/residue: 0.0730 time to fit residues: 10.5152 Evaluate side-chains 92 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 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 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 596 CYS 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: 0.9990 chunk 76 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 82 optimal weight: 0.0060 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.3228 r_free = 0.3228 target = 0.096550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.074059 restraints weight = 18937.543| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.37 r_work: 0.2743 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11336 Z= 0.113 Angle : 0.503 8.309 15432 Z= 0.258 Chirality : 0.040 0.149 1846 Planarity : 0.004 0.066 1876 Dihedral : 6.454 46.097 2048 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.62 % Favored : 95.31 % Rotamer: Outliers : 1.52 % Allowed : 13.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.25), residues: 1364 helix: 1.49 (0.20), residues: 824 sheet: 2.76 (0.85), residues: 34 loop : -1.75 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.010 0.001 TYR A 367 PHE 0.017 0.001 PHE A 130 TRP 0.007 0.001 TRP A 63 HIS 0.002 0.000 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00262 (11336) covalent geometry : angle 0.50293 (15432) hydrogen bonds : bond 0.03215 ( 550) hydrogen bonds : angle 3.37946 ( 1584) ********************** 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 93 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.358 Fit side-chains REVERT: A 257 THR cc_start: 0.9133 (m) cc_final: 0.8852 (m) REVERT: A 640 GLU cc_start: 0.8417 (tm-30) cc_final: 0.7972 (tm-30) REVERT: A 660 ASP cc_start: 0.8456 (p0) cc_final: 0.8249 (p0) REVERT: B 257 THR cc_start: 0.9168 (m) cc_final: 0.8887 (m) REVERT: B 640 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7787 (tm-30) outliers start: 18 outliers final: 16 residues processed: 84 average time/residue: 0.0776 time to fit residues: 10.6575 Evaluate side-chains 90 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 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 596 CYS 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 102 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 137 optimal weight: 0.0030 chunk 107 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.3232 r_free = 0.3232 target = 0.096746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.074205 restraints weight = 18813.757| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.36 r_work: 0.2751 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11336 Z= 0.109 Angle : 0.500 8.291 15432 Z= 0.256 Chirality : 0.040 0.156 1846 Planarity : 0.004 0.066 1876 Dihedral : 6.430 46.822 2048 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.62 % Favored : 95.31 % Rotamer: Outliers : 1.43 % Allowed : 13.89 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.25), residues: 1364 helix: 1.53 (0.20), residues: 824 sheet: 2.78 (0.85), residues: 34 loop : -1.71 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 68 TYR 0.010 0.001 TYR A 367 PHE 0.016 0.001 PHE A 130 TRP 0.007 0.001 TRP A 63 HIS 0.002 0.000 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00253 (11336) covalent geometry : angle 0.50036 (15432) hydrogen bonds : bond 0.03168 ( 550) hydrogen bonds : angle 3.36720 ( 1584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2513.85 seconds wall clock time: 43 minutes 52.26 seconds (2632.26 seconds total)