Starting phenix.real_space_refine on Fri Jul 3 05:31:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x1u_38002/07_2026/8x1u_38002_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x1u_38002/07_2026/8x1u_38002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x1u_38002/07_2026/8x1u_38002_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x1u_38002/07_2026/8x1u_38002_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x1u_38002/07_2026/8x1u_38002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x1u_38002/07_2026/8x1u_38002.map" } resolution = 2.21 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= 0.005 sd= 0.119 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 40 5.16 5 C 8411 2.51 5 N 1794 2.21 5 O 2060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 127 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12323 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5440 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 670} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 5429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5429 Classifications: {'peptide': 701} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 669} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 718 Unusual residues: {'C14': 4, 'CLR': 1, 'D10': 19, 'D12': 8, 'LPE': 7, 'OXL': 1, 'POV': 2} Classifications: {'undetermined': 42} Link IDs: {None: 41} Chain: "B" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 718 Unusual residues: {'C14': 4, 'CLR': 1, 'D10': 19, 'D12': 8, 'LPE': 7, 'OXL': 1, 'POV': 2} Classifications: {'undetermined': 42} Link IDs: {None: 41} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 2.60, per 1000 atoms: 0.21 Number of scatterers: 12323 At special positions: 0 Unit cell: (102.52, 86.676, 127.684, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 18 15.00 O 2060 8.00 N 1794 7.00 C 8411 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: 1.07 Conformation dependent library (CDL) restraints added in 642.9 milliseconds 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2626 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 5 sheets defined 68.1% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 34 through 43 removed outlier: 3.863A pdb=" N CYS A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 68 through 99 removed outlier: 6.171A pdb=" N LEU A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N SER A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 120 removed outlier: 3.687A pdb=" N LEU A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Proline residue: A 112 - end of helix removed outlier: 3.904A pdb=" N PHE A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 147 Processing helix chain 'A' and resid 169 through 196 Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 206 through 225 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 241 through 253 removed outlier: 3.759A pdb=" N GLN A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 282 Processing helix chain 'A' and resid 291 through 307 removed outlier: 3.514A pdb=" N ILE A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 332 through 339 Processing helix chain 'A' and resid 339 through 366 removed outlier: 3.872A pdb=" N TYR A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 Processing helix chain 'A' and resid 396 through 406 Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 428 through 433 removed outlier: 3.517A pdb=" N LEU A 431 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 453 removed outlier: 3.855A pdb=" N LEU A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N MET A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 465 removed outlier: 3.743A pdb=" N ARG A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 503 removed outlier: 3.614A pdb=" N LEU A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 499 " --> pdb=" O GLN A 495 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 563 through 584 Processing helix chain 'A' and resid 612 through 618 removed outlier: 3.686A 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 697 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 712 through 725 Processing helix chain 'B' and resid 17 through 25 Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 59 through 64 Processing helix chain 'B' and resid 68 through 99 removed outlier: 5.934A pdb=" N LEU B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N SER B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.585A pdb=" N LEU B 106 " --> pdb=" O PRO B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 120 removed outlier: 3.537A pdb=" N ILE B 114 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE B 118 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 147 Processing helix chain 'B' and resid 170 through 196 Processing helix chain 'B' and resid 200 through 205 removed outlier: 3.547A pdb=" N LEU B 205 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 225 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 241 through 253 Processing helix chain 'B' and resid 254 through 257 Processing helix chain 'B' and resid 258 through 282 Processing helix chain 'B' and resid 291 through 307 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 332 through 366 removed outlier: 6.158A pdb=" N GLY B 341 " --> pdb=" O GLN B 337 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASP B 342 " --> pdb=" O ASN B 338 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 396 through 406 Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 436 through 447 removed outlier: 3.642A pdb=" N LEU B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 456 through 465 removed outlier: 3.636A pdb=" N ARG B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 483 Processing helix chain 'B' and resid 483 through 504 removed outlier: 3.546A pdb=" N ALA B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE B 499 " --> pdb=" O GLN B 495 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 563 through 584 removed outlier: 3.537A pdb=" N GLN B 584 " --> pdb=" O LYS B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 618 removed outlier: 3.542A pdb=" N LEU B 616 " --> pdb=" O ILE B 613 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN B 618 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 639 removed outlier: 3.886A pdb=" N ASN B 638 " --> pdb=" O LEU B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 677 Processing helix chain 'B' and resid 687 through 697 removed outlier: 3.558A pdb=" N ILE B 691 " --> pdb=" O ASP B 687 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 709 Processing helix chain 'B' and resid 712 through 725 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.665A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N ASN A 513 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 12.533A pdb=" N VAL A 535 " --> pdb=" O ASN A 513 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LYS A 536 " --> pdb=" O ILE A 650 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASP A 652 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE A 538 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N PHE A 710 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE A 683 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AA4, first strand: chain 'B' and resid 127 through 128 Processing sheet with id=AA5, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.481A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N ASN B 513 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 12.507A pdb=" N VAL B 535 " --> pdb=" O ASN B 513 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LYS B 536 " --> pdb=" O ILE B 650 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ASP B 652 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE B 538 " --> pdb=" O ASP B 652 " (cutoff:3.500A) 686 hydrogen bonds defined for protein. 1983 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: 1.76 Time building geometry restraints manager: 1.39 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: 2085 1.32 - 1.45: 2701 1.45 - 1.57: 7583 1.57 - 1.69: 36 1.69 - 1.82: 60 Bond restraints: 12465 Sorted by residual: bond pdb=" C21 POV B 842 " pdb=" O21 POV B 842 " ideal model delta sigma weight residual 1.330 1.455 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C21 POV A 940 " pdb=" O21 POV A 940 " ideal model delta sigma weight residual 1.330 1.455 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C31 POV B 841 " pdb=" O31 POV B 841 " ideal model delta sigma weight residual 1.327 1.449 -0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" C31 POV A 902 " pdb=" O31 POV A 902 " ideal model delta sigma weight residual 1.327 1.449 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C21 POV B 841 " pdb=" O21 POV B 841 " ideal model delta sigma weight residual 1.330 1.449 -0.119 2.00e-02 2.50e+03 3.52e+01 ... (remaining 12460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.79: 16435 5.79 - 11.58: 103 11.58 - 17.37: 1 17.37 - 23.16: 0 23.16 - 28.95: 2 Bond angle restraints: 16541 Sorted by residual: angle pdb=" C2 LPE B 814 " pdb=" C3 LPE B 814 " pdb=" O3 LPE B 814 " ideal model delta sigma weight residual 103.57 132.52 -28.95 3.00e+00 1.11e-01 9.32e+01 angle pdb=" C15 LPE A 916 " pdb=" C16 LPE A 916 " pdb=" C17 LPE A 916 " ideal model delta sigma weight residual 110.73 139.67 -28.94 3.00e+00 1.11e-01 9.30e+01 angle pdb=" N ASP A 366 " pdb=" CA ASP A 366 " pdb=" C ASP A 366 " ideal model delta sigma weight residual 111.52 121.55 -10.03 1.40e+00 5.10e-01 5.14e+01 angle pdb=" CB HIS A 38 " pdb=" CG HIS A 38 " pdb=" CD2 HIS A 38 " ideal model delta sigma weight residual 131.20 122.54 8.66 1.30e+00 5.92e-01 4.44e+01 angle pdb=" CB HIS A 714 " pdb=" CG HIS A 714 " pdb=" CD2 HIS A 714 " ideal model delta sigma weight residual 131.20 122.75 8.45 1.30e+00 5.92e-01 4.22e+01 ... (remaining 16536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.24: 7224 22.24 - 44.48: 502 44.48 - 66.72: 131 66.72 - 88.96: 8 88.96 - 111.20: 14 Dihedral angle restraints: 7879 sinusoidal: 3814 harmonic: 4065 Sorted by residual: dihedral pdb=" C VAL A 241 " pdb=" N VAL A 241 " pdb=" CA VAL A 241 " pdb=" CB VAL A 241 " ideal model delta harmonic sigma weight residual -122.00 -133.94 11.94 0 2.50e+00 1.60e-01 2.28e+01 dihedral pdb=" N VAL A 241 " pdb=" C VAL A 241 " pdb=" CA VAL A 241 " pdb=" CB VAL A 241 " ideal model delta harmonic sigma weight residual 123.40 134.33 -10.93 0 2.50e+00 1.60e-01 1.91e+01 dihedral pdb=" C VAL B 241 " pdb=" N VAL B 241 " pdb=" CA VAL B 241 " pdb=" CB VAL B 241 " ideal model delta harmonic sigma weight residual -122.00 -132.15 10.15 0 2.50e+00 1.60e-01 1.65e+01 ... (remaining 7876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1563 0.075 - 0.149: 227 0.149 - 0.224: 30 0.224 - 0.298: 14 0.298 - 0.372: 4 Chirality restraints: 1838 Sorted by residual: chirality pdb=" CA VAL A 241 " pdb=" N VAL A 241 " pdb=" C VAL A 241 " pdb=" CB VAL A 241 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA ASP A 366 " pdb=" N ASP A 366 " pdb=" C ASP A 366 " pdb=" CB ASP A 366 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA LYS B 678 " pdb=" N LYS B 678 " pdb=" C LYS B 678 " pdb=" CB LYS B 678 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 1835 not shown) Planarity restraints: 1902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 691 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C ILE B 691 " 0.057 2.00e-02 2.50e+03 pdb=" O ILE B 691 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU B 692 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 363 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.05e+00 pdb=" C LEU B 363 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU B 363 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS B 364 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 16 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.88e+00 pdb=" C TYR B 16 " 0.042 2.00e-02 2.50e+03 pdb=" O TYR B 16 " -0.016 2.00e-02 2.50e+03 pdb=" N SER B 17 " -0.014 2.00e-02 2.50e+03 ... (remaining 1899 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1577 2.74 - 3.28: 11744 3.28 - 3.82: 19643 3.82 - 4.36: 25948 4.36 - 4.90: 42233 Nonbonded interactions: 101145 Sorted by model distance: nonbonded pdb=" OD2 ASP A 76 " pdb=" OG1 THR A 410 " model vdw 2.205 3.040 nonbonded pdb=" NZ LYS A 276 " pdb=" OD1 ASN A 447 " model vdw 2.246 3.120 nonbonded pdb=" OH TYR A 116 " pdb=" OE1 GLU A 374 " model vdw 2.253 3.040 nonbonded pdb=" OE1 GLN A 504 " pdb=" OH TYR B 204 " model vdw 2.300 3.040 nonbonded pdb=" OD1 ASP A 525 " pdb=" NH1 ARG B 30 " model vdw 2.305 3.120 ... (remaining 101140 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 30 or (resid 31 and (name N or name CA or name C \ or name O or name CB )) or resid 32 through 168 or resid 170 through 587 or (re \ sid 588 through 589 and (name N or name CA or name C or name O or name CB )) or \ resid 590 through 901 or resid 910 through 911 or resid 915 or resid 917 through \ 919 or resid 922 through 939)) selection = (chain 'B' and (resid 7 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB )) or resid 45 through 596 or (resid 597 and (name N or na \ me CA or name C or name O or name CB )) or resid 598 through 627 or (resid 628 a \ nd (name N or name CA or name C or name O or name CB )) or resid 629 through 801 \ or resid 810 through 811 or resid 815 or resid 817 through 819 or resid 822 thr \ ough 839)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.080 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:8.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 : 0.011 0.125 12465 Z= 0.619 Angle : 1.312 28.955 16541 Z= 0.706 Chirality : 0.059 0.372 1838 Planarity : 0.005 0.041 1902 Dihedral : 15.758 111.203 5253 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.27 % Allowed : 8.86 % Favored : 89.87 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.20), residues: 1395 helix: -0.58 (0.16), residues: 909 sheet: 0.75 (0.79), residues: 34 loop : -1.25 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 399 TYR 0.022 0.002 TYR A 9 PHE 0.017 0.002 PHE B 130 TRP 0.014 0.001 TRP A 63 HIS 0.005 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.01074 / 0.62 (12465) covalent geometry : angle 1.31220 / 0.71 (16541) hydrogen bonds : bond 0.16971 / 11.33 ( 686) hydrogen bonds : angle 6.41177 / 4.54 ( 1983) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.335 Fit side-chains REVERT: A 51 LYS cc_start: 0.7707 (tmtt) cc_final: 0.7131 (tptt) REVERT: A 53 ILE cc_start: 0.8426 (mm) cc_final: 0.8208 (mt) REVERT: A 73 LEU cc_start: 0.8131 (tp) cc_final: 0.7901 (tm) REVERT: A 277 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7005 (mm-30) REVERT: A 314 LYS cc_start: 0.8027 (mttt) cc_final: 0.7824 (mmtt) REVERT: A 453 MET cc_start: 0.6846 (ttp) cc_final: 0.6611 (ttp) REVERT: A 589 VAL cc_start: 0.4209 (OUTLIER) cc_final: 0.3907 (p) REVERT: A 612 GLN cc_start: 0.7443 (mt0) cc_final: 0.6897 (pt0) REVERT: B 280 GLN cc_start: 0.7933 (tp40) cc_final: 0.7503 (tp40) REVERT: B 310 LYS cc_start: 0.7656 (ttmt) cc_final: 0.7395 (tttp) REVERT: B 348 MET cc_start: 0.7087 (mmp) cc_final: 0.6346 (tpp) REVERT: B 504 GLN cc_start: 0.8369 (tt0) cc_final: 0.8145 (tt0) REVERT: B 517 THR cc_start: 0.8336 (p) cc_final: 0.8133 (t) REVERT: B 529 MET cc_start: 0.8686 (mtp) cc_final: 0.8230 (mtp) REVERT: B 598 VAL cc_start: 0.7642 (OUTLIER) cc_final: 0.7424 (t) REVERT: B 611 ASN cc_start: 0.7775 (m-40) cc_final: 0.7334 (m-40) REVERT: B 689 ASP cc_start: 0.6933 (m-30) cc_final: 0.6729 (m-30) outliers start: 15 outliers final: 2 residues processed: 186 average time/residue: 0.5620 time to fit residues: 113.5572 Evaluate side-chains 110 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 598 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 GLN A 582 GLN A 672 GLN B 322 ASN B 326 GLN B 337 GLN B 436 GLN B 454 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.153527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110204 restraints weight = 12481.132| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.64 r_work: 0.3246 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12465 Z= 0.130 Angle : 0.544 8.145 16541 Z= 0.280 Chirality : 0.042 0.142 1838 Planarity : 0.004 0.044 1902 Dihedral : 14.725 88.811 2778 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.69 % Allowed : 9.79 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.23), residues: 1395 helix: 1.45 (0.17), residues: 903 sheet: 1.83 (0.80), residues: 34 loop : -0.56 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 173 TYR 0.021 0.002 TYR B 9 PHE 0.016 0.002 PHE B 130 TRP 0.013 0.001 TRP A 63 HIS 0.003 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (12465) covalent geometry : angle 0.54379 / 0.28 (16541) hydrogen bonds : bond 0.04559 / 3.08 ( 686) hydrogen bonds : angle 4.50831 / 3.22 ( 1983) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.464 Fit side-chains REVERT: A 52 ARG cc_start: 0.7647 (tmm160) cc_final: 0.7226 (ttp80) REVERT: A 169 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6148 (tp) REVERT: A 277 GLU cc_start: 0.7686 (mm-30) cc_final: 0.6964 (mm-30) REVERT: A 314 LYS cc_start: 0.8526 (mttt) cc_final: 0.8212 (mmtt) REVERT: A 453 MET cc_start: 0.7798 (ttp) cc_final: 0.7588 (ttp) REVERT: A 609 ASP cc_start: 0.7736 (p0) cc_final: 0.7525 (p0) REVERT: A 612 GLN cc_start: 0.7819 (mt0) cc_final: 0.7420 (pt0) REVERT: A 687 ASP cc_start: 0.7268 (p0) cc_final: 0.7024 (p0) REVERT: B 54 VAL cc_start: 0.8351 (t) cc_final: 0.8055 (t) REVERT: B 280 GLN cc_start: 0.8167 (tp40) cc_final: 0.7631 (tp40) REVERT: B 293 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6720 (mp0) REVERT: B 310 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7954 (tttp) REVERT: B 529 MET cc_start: 0.8964 (mtp) cc_final: 0.8688 (mtp) REVERT: B 607 GLU cc_start: 0.6728 (mm-30) cc_final: 0.6429 (tp30) REVERT: B 611 ASN cc_start: 0.7839 (m-40) cc_final: 0.7630 (m110) REVERT: B 621 ASN cc_start: 0.8903 (t0) cc_final: 0.8415 (t0) outliers start: 20 outliers final: 8 residues processed: 138 average time/residue: 0.5738 time to fit residues: 86.1116 Evaluate side-chains 115 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 293 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 49 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 GLN B 513 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.149509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.105608 restraints weight = 12446.366| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.64 r_work: 0.3179 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12465 Z= 0.135 Angle : 0.504 7.771 16541 Z= 0.267 Chirality : 0.042 0.145 1838 Planarity : 0.004 0.043 1902 Dihedral : 13.326 88.646 2773 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.27 % Allowed : 10.46 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.23), residues: 1395 helix: 1.85 (0.18), residues: 904 sheet: 2.23 (0.77), residues: 34 loop : -0.20 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 312 TYR 0.021 0.002 TYR B 9 PHE 0.015 0.002 PHE A 130 TRP 0.012 0.001 TRP B 63 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (12465) covalent geometry : angle 0.50381 / 0.27 (16541) hydrogen bonds : bond 0.04809 / 3.27 ( 686) hydrogen bonds : angle 4.39199 / 3.14 ( 1983) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.443 Fit side-chains REVERT: A 52 ARG cc_start: 0.7683 (tmm160) cc_final: 0.7237 (ttp80) REVERT: A 277 GLU cc_start: 0.7665 (mm-30) cc_final: 0.6916 (mm-30) REVERT: A 314 LYS cc_start: 0.8561 (mttt) cc_final: 0.8239 (mmtt) REVERT: A 320 ASP cc_start: 0.8787 (m-30) cc_final: 0.8564 (m-30) REVERT: A 530 TYR cc_start: 0.8963 (t80) cc_final: 0.8619 (t80) REVERT: A 609 ASP cc_start: 0.8022 (p0) cc_final: 0.7763 (p0) REVERT: A 612 GLN cc_start: 0.7966 (mt0) cc_final: 0.7538 (pt0) REVERT: B 293 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6780 (mp0) REVERT: B 310 LYS cc_start: 0.8348 (ttmt) cc_final: 0.7955 (tttp) REVERT: B 451 MET cc_start: 0.8679 (mtm) cc_final: 0.8328 (mtm) REVERT: B 529 MET cc_start: 0.8963 (mtp) cc_final: 0.8618 (mtp) REVERT: B 607 GLU cc_start: 0.6759 (mm-30) cc_final: 0.6459 (tp30) REVERT: B 621 ASN cc_start: 0.8946 (t0) cc_final: 0.8446 (t0) outliers start: 15 outliers final: 8 residues processed: 125 average time/residue: 0.5505 time to fit residues: 74.9589 Evaluate side-chains 113 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 590 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 128 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 GLN A 621 ASN B 280 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.144995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.100482 restraints weight = 12269.429| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.65 r_work: 0.3090 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12465 Z= 0.208 Angle : 0.585 10.642 16541 Z= 0.308 Chirality : 0.046 0.235 1838 Planarity : 0.005 0.060 1902 Dihedral : 13.941 81.788 2773 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.77 % Allowed : 9.70 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.23), residues: 1395 helix: 1.69 (0.17), residues: 908 sheet: 2.30 (0.77), residues: 34 loop : -0.24 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 566 TYR 0.026 0.002 TYR A 9 PHE 0.015 0.002 PHE A 130 TRP 0.012 0.002 TRP B 63 HIS 0.007 0.002 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (12465) covalent geometry : angle 0.58540 / 0.31 (16541) hydrogen bonds : bond 0.05749 / 3.92 ( 686) hydrogen bonds : angle 4.58607 / 3.27 ( 1983) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.479 Fit side-chains REVERT: A 169 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6546 (tp) REVERT: A 277 GLU cc_start: 0.7677 (mm-30) cc_final: 0.6873 (mm-30) REVERT: A 314 LYS cc_start: 0.8539 (mttt) cc_final: 0.8218 (mmtt) REVERT: A 553 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.7896 (ttt180) REVERT: A 609 ASP cc_start: 0.8015 (p0) cc_final: 0.7733 (p0) REVERT: A 612 GLN cc_start: 0.8011 (mt0) cc_final: 0.7535 (pt0) REVERT: B 266 LEU cc_start: 0.8188 (mt) cc_final: 0.7769 (mp) REVERT: B 293 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6825 (mp0) REVERT: B 310 LYS cc_start: 0.8427 (ttmt) cc_final: 0.8021 (tttp) REVERT: B 312 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7880 (ttt-90) outliers start: 21 outliers final: 9 residues processed: 116 average time/residue: 0.6036 time to fit residues: 76.1511 Evaluate side-chains 113 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 590 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 16 optimal weight: 2.9990 chunk 118 optimal weight: 0.0870 chunk 119 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 57 optimal weight: 20.0000 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 621 ASN B 280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.148398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.104405 restraints weight = 12297.681| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.65 r_work: 0.3151 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12465 Z= 0.106 Angle : 0.464 9.633 16541 Z= 0.247 Chirality : 0.041 0.238 1838 Planarity : 0.004 0.053 1902 Dihedral : 12.664 79.997 2771 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.01 % Allowed : 10.63 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.23), residues: 1395 helix: 2.04 (0.18), residues: 910 sheet: 2.72 (0.77), residues: 34 loop : -0.12 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 173 TYR 0.017 0.001 TYR A 9 PHE 0.014 0.001 PHE A 130 TRP 0.014 0.001 TRP B 63 HIS 0.003 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (12465) covalent geometry : angle 0.46440 / 0.25 (16541) hydrogen bonds : bond 0.04200 / 2.85 ( 686) hydrogen bonds : angle 4.27053 / 3.06 ( 1983) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.380 Fit side-chains REVERT: A 169 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6512 (tp) REVERT: A 277 GLU cc_start: 0.7591 (mm-30) cc_final: 0.6895 (mm-30) REVERT: A 314 LYS cc_start: 0.8552 (mttt) cc_final: 0.8228 (mmtt) REVERT: A 584 GLN cc_start: 0.7038 (mt0) cc_final: 0.6670 (mt0) REVERT: A 609 ASP cc_start: 0.8107 (p0) cc_final: 0.7625 (p0) REVERT: A 612 GLN cc_start: 0.7962 (mt0) cc_final: 0.7484 (pt0) REVERT: B 266 LEU cc_start: 0.8139 (mt) cc_final: 0.7726 (mp) REVERT: B 277 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7388 (tp30) REVERT: B 293 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6804 (mp0) REVERT: B 310 LYS cc_start: 0.8398 (ttmt) cc_final: 0.8003 (tttp) REVERT: B 607 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6394 (tp30) REVERT: B 621 ASN cc_start: 0.8972 (t0) cc_final: 0.8468 (t0) outliers start: 12 outliers final: 7 residues processed: 114 average time/residue: 0.6314 time to fit residues: 77.7765 Evaluate side-chains 112 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 340 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 62 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 621 ASN B 280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.146089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.101652 restraints weight = 12311.331| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.66 r_work: 0.3108 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12465 Z= 0.158 Angle : 0.522 10.574 16541 Z= 0.276 Chirality : 0.043 0.222 1838 Planarity : 0.004 0.054 1902 Dihedral : 12.951 76.716 2771 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.35 % Allowed : 11.31 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.23), residues: 1395 helix: 1.95 (0.18), residues: 910 sheet: 2.65 (0.79), residues: 34 loop : -0.13 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 173 TYR 0.024 0.002 TYR A 9 PHE 0.015 0.002 PHE A 130 TRP 0.013 0.001 TRP B 63 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (12465) covalent geometry : angle 0.52169 / 0.28 (16541) hydrogen bonds : bond 0.05069 / 3.45 ( 686) hydrogen bonds : angle 4.40372 / 3.15 ( 1983) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.509 Fit side-chains REVERT: A 169 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6497 (tp) REVERT: A 277 GLU cc_start: 0.7672 (mm-30) cc_final: 0.6885 (mm-30) REVERT: A 314 LYS cc_start: 0.8552 (mttt) cc_final: 0.8230 (mmtt) REVERT: A 584 GLN cc_start: 0.7041 (mt0) cc_final: 0.6695 (mt0) REVERT: A 609 ASP cc_start: 0.8082 (p0) cc_final: 0.7851 (p0) REVERT: A 612 GLN cc_start: 0.7971 (mt0) cc_final: 0.7509 (pt0) REVERT: B 39 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6351 (mt) REVERT: B 266 LEU cc_start: 0.8143 (mt) cc_final: 0.7772 (mp) REVERT: B 277 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7427 (tp30) REVERT: B 293 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6773 (mp0) REVERT: B 607 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6421 (tp30) REVERT: B 621 ASN cc_start: 0.8985 (t0) cc_final: 0.8468 (t0) outliers start: 16 outliers final: 10 residues processed: 114 average time/residue: 0.6323 time to fit residues: 77.9968 Evaluate side-chains 115 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 613 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 88 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 GLN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN A 621 ASN B 280 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.140809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.097532 restraints weight = 12020.819| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.63 r_work: 0.3077 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 12465 Z= 0.228 Angle : 0.602 11.795 16541 Z= 0.318 Chirality : 0.047 0.231 1838 Planarity : 0.005 0.057 1902 Dihedral : 14.473 76.786 2771 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.94 % Allowed : 10.63 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.23), residues: 1395 helix: 1.70 (0.17), residues: 906 sheet: 2.37 (0.79), residues: 34 loop : -0.17 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 173 TYR 0.026 0.003 TYR A 9 PHE 0.015 0.002 PHE B 251 TRP 0.013 0.002 TRP B 63 HIS 0.006 0.002 HIS B 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.23 (12465) covalent geometry : angle 0.60237 / 0.32 (16541) hydrogen bonds : bond 0.06040 / 4.12 ( 686) hydrogen bonds : angle 4.62748 / 3.31 ( 1983) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.475 Fit side-chains REVERT: A 169 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6528 (tp) REVERT: A 277 GLU cc_start: 0.7702 (mm-30) cc_final: 0.6917 (mm-30) REVERT: A 314 LYS cc_start: 0.8520 (mttt) cc_final: 0.8199 (mmtt) REVERT: A 609 ASP cc_start: 0.8104 (p0) cc_final: 0.7733 (p0) REVERT: A 612 GLN cc_start: 0.7984 (mt0) cc_final: 0.7506 (pt0) REVERT: B 39 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6385 (mt) REVERT: B 277 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7458 (tp30) REVERT: B 293 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: B 312 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7861 (ttt-90) REVERT: B 611 ASN cc_start: 0.8252 (m-40) cc_final: 0.8029 (m110) outliers start: 23 outliers final: 9 residues processed: 119 average time/residue: 0.6279 time to fit residues: 81.3663 Evaluate side-chains 113 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 590 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 25 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 GLN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.146308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.102324 restraints weight = 12208.159| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.64 r_work: 0.3119 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12465 Z= 0.132 Angle : 0.500 9.543 16541 Z= 0.266 Chirality : 0.042 0.203 1838 Planarity : 0.004 0.057 1902 Dihedral : 13.357 76.614 2771 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.43 % Allowed : 11.31 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.23), residues: 1395 helix: 1.96 (0.18), residues: 908 sheet: 2.57 (0.80), residues: 34 loop : -0.10 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 173 TYR 0.020 0.002 TYR A 9 PHE 0.015 0.001 PHE A 130 TRP 0.015 0.001 TRP B 63 HIS 0.003 0.001 HIS B 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (12465) covalent geometry : angle 0.50037 / 0.27 (16541) hydrogen bonds : bond 0.04762 / 3.24 ( 686) hydrogen bonds : angle 4.39255 / 3.14 ( 1983) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.481 Fit side-chains REVERT: A 169 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6648 (tp) REVERT: A 277 GLU cc_start: 0.7645 (mm-30) cc_final: 0.6836 (mm-30) REVERT: A 314 LYS cc_start: 0.8563 (mttt) cc_final: 0.8245 (mmtt) REVERT: A 584 GLN cc_start: 0.6989 (mt0) cc_final: 0.6697 (mt0) REVERT: A 609 ASP cc_start: 0.8145 (p0) cc_final: 0.7744 (p0) REVERT: A 612 GLN cc_start: 0.8007 (mt0) cc_final: 0.7589 (pt0) REVERT: B 39 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6390 (mt) REVERT: B 277 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7529 (tp30) REVERT: B 293 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6813 (mp0) REVERT: B 611 ASN cc_start: 0.8294 (m-40) cc_final: 0.8076 (m110) REVERT: B 621 ASN cc_start: 0.8963 (t0) cc_final: 0.8462 (t0) outliers start: 17 outliers final: 8 residues processed: 111 average time/residue: 0.6585 time to fit residues: 79.3138 Evaluate side-chains 111 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 340 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 62 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 GLN A 337 GLN B 280 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.145459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.101509 restraints weight = 12006.231| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.66 r_work: 0.3137 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12465 Z= 0.117 Angle : 0.475 8.079 16541 Z= 0.253 Chirality : 0.041 0.173 1838 Planarity : 0.004 0.056 1902 Dihedral : 12.462 76.227 2771 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.27 % Allowed : 11.81 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.23), residues: 1395 helix: 2.10 (0.18), residues: 909 sheet: 2.76 (0.81), residues: 34 loop : -0.02 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 173 TYR 0.019 0.001 TYR A 9 PHE 0.014 0.001 PHE B 130 TRP 0.015 0.001 TRP B 63 HIS 0.003 0.001 HIS B 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (12465) covalent geometry : angle 0.47475 / 0.25 (16541) hydrogen bonds : bond 0.04395 / 2.98 ( 686) hydrogen bonds : angle 4.28901 / 3.07 ( 1983) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.422 Fit side-chains REVERT: A 169 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6557 (tp) REVERT: A 277 GLU cc_start: 0.7631 (mm-30) cc_final: 0.6801 (mm-30) REVERT: A 314 LYS cc_start: 0.8546 (mttt) cc_final: 0.8219 (mmtt) REVERT: A 609 ASP cc_start: 0.8112 (p0) cc_final: 0.7742 (p0) REVERT: A 612 GLN cc_start: 0.7935 (mt0) cc_final: 0.7531 (pt0) REVERT: B 39 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6227 (mt) REVERT: B 266 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7800 (mp) REVERT: B 277 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7563 (tp30) REVERT: B 293 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6725 (mp0) REVERT: B 607 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6478 (tp30) REVERT: B 611 ASN cc_start: 0.8259 (m-40) cc_final: 0.8042 (m110) REVERT: B 621 ASN cc_start: 0.8929 (t0) cc_final: 0.8448 (t0) outliers start: 15 outliers final: 7 residues processed: 109 average time/residue: 0.6423 time to fit residues: 75.9334 Evaluate side-chains 108 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 613 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 101 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 87 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 GLN A 337 GLN B 7 ASN B 280 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.148801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.105073 restraints weight = 12316.143| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.65 r_work: 0.3161 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12465 Z= 0.105 Angle : 0.458 8.197 16541 Z= 0.244 Chirality : 0.041 0.182 1838 Planarity : 0.004 0.054 1902 Dihedral : 11.883 75.767 2771 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.43 % Allowed : 11.56 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.23), residues: 1395 helix: 2.21 (0.18), residues: 909 sheet: 2.97 (0.79), residues: 35 loop : 0.07 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 173 TYR 0.017 0.001 TYR A 9 PHE 0.014 0.001 PHE A 130 TRP 0.015 0.001 TRP B 63 HIS 0.002 0.001 HIS B 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (12465) covalent geometry : angle 0.45755 / 0.24 (16541) hydrogen bonds : bond 0.04061 / 2.76 ( 686) hydrogen bonds : angle 4.20189 / 3.01 ( 1983) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.553 Fit side-chains REVERT: A 169 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6364 (tp) REVERT: A 277 GLU cc_start: 0.7555 (mm-30) cc_final: 0.6874 (mm-30) REVERT: A 314 LYS cc_start: 0.8549 (mttt) cc_final: 0.8223 (mmtt) REVERT: A 609 ASP cc_start: 0.8021 (p0) cc_final: 0.7571 (p0) REVERT: A 612 GLN cc_start: 0.7940 (mt0) cc_final: 0.7552 (pt0) REVERT: B 39 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6313 (mt) REVERT: B 277 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7574 (tp30) REVERT: B 607 GLU cc_start: 0.6721 (mm-30) cc_final: 0.6447 (tp30) REVERT: B 609 ASP cc_start: 0.8286 (p0) cc_final: 0.7784 (p0) REVERT: B 611 ASN cc_start: 0.8251 (m-40) cc_final: 0.8013 (m110) REVERT: B 621 ASN cc_start: 0.8972 (t0) cc_final: 0.8483 (t0) outliers start: 17 outliers final: 8 residues processed: 118 average time/residue: 0.6592 time to fit residues: 84.4515 Evaluate side-chains 111 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 340 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 107 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 GLN A 337 GLN B 7 ASN B 280 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.145898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.101751 restraints weight = 12191.213| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.64 r_work: 0.3111 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12465 Z= 0.170 Angle : 0.532 9.148 16541 Z= 0.283 Chirality : 0.044 0.194 1838 Planarity : 0.004 0.053 1902 Dihedral : 12.401 76.135 2771 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.18 % Allowed : 12.41 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.23), residues: 1395 helix: 2.02 (0.18), residues: 908 sheet: 2.71 (0.81), residues: 34 loop : 0.03 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 173 TYR 0.025 0.002 TYR A 9 PHE 0.015 0.002 PHE A 130 TRP 0.013 0.001 TRP A 63 HIS 0.004 0.001 HIS B 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (12465) covalent geometry : angle 0.53175 / 0.28 (16541) hydrogen bonds : bond 0.05091 / 3.47 ( 686) hydrogen bonds : angle 4.38105 / 3.13 ( 1983) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5154.51 seconds wall clock time: 88 minutes 30.12 seconds (5310.12 seconds total)