Starting phenix.real_space_refine on Sat Aug 23 08:10:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hip_34825/08_2025/8hip_34825.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hip_34825/08_2025/8hip_34825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hip_34825/08_2025/8hip_34825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hip_34825/08_2025/8hip_34825.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hip_34825/08_2025/8hip_34825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hip_34825/08_2025/8hip_34825.map" } resolution = 2.77 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= 0.001 sd= 0.132 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 Zn 2 6.06 5 S 66 5.16 5 C 6788 2.51 5 N 1684 2.21 5 O 1856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10396 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5099 Classifications: {'peptide': 647} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 629} Chain breaks: 3 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5099 Classifications: {'peptide': 647} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 629} Chain breaks: 3 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' ZN': 1, '6OU': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-3': 2, '6OU:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' ZN': 1, '6OU': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-3': 2, '6OU:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 2.35, per 1000 atoms: 0.23 Number of scatterers: 10396 At special positions: 0 Unit cell: (90.48, 86.32, 125.84, 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) Zn 2 29.99 S 66 16.00 O 1856 8.00 N 1684 7.00 C 6788 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 225 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN B 205 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN B 234 " " NAG F 1 " - " ASN A 205 " Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 392.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb=" NE2 HIS A 540 " pdb="ZN ZN A 803 " - pdb=" NE2 HIS A 740 " pdb="ZN ZN A 803 " - pdb=" NE2 HIS A 744 " pdb=" ZN B 803 " pdb="ZN ZN B 803 " - pdb=" NE2 HIS B 540 " pdb="ZN ZN B 803 " - pdb=" NE2 HIS B 740 " pdb="ZN ZN B 803 " - pdb=" NE2 HIS B 744 " 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2488 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 49.5% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.561A pdb=" N SER B 85 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 206 through 210 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 314 through 327 Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 331 through 344 removed outlier: 4.428A pdb=" N ILE B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASN B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE B 339 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG B 344 " --> pdb=" O ILE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 438 through 454 Processing helix chain 'B' and resid 458 through 464 removed outlier: 3.734A pdb=" N GLU B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 471 removed outlier: 3.912A pdb=" N ALA B 471 " --> pdb=" O HIS B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 485 Processing helix chain 'B' and resid 486 through 503 removed outlier: 3.664A pdb=" N THR B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 540 removed outlier: 3.629A pdb=" N SER B 533 " --> pdb=" O MET B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 569 removed outlier: 3.653A pdb=" N GLN B 556 " --> pdb=" O THR B 552 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET B 563 " --> pdb=" O CYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 577 No H-bonds generated for 'chain 'B' and resid 575 through 577' Processing helix chain 'B' and resid 578 through 596 Processing helix chain 'B' and resid 601 through 626 removed outlier: 3.547A pdb=" N GLU B 622 " --> pdb=" O CYS B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 651 removed outlier: 3.638A pdb=" N MET B 637 " --> pdb=" O ARG B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 684 removed outlier: 4.369A pdb=" N ALA B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR B 663 " --> pdb=" O ASN B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 711 Processing helix chain 'B' and resid 720 through 727 removed outlier: 3.845A pdb=" N LEU B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 762 removed outlier: 3.617A pdb=" N ALA B 748 " --> pdb=" O HIS B 744 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP B 762 " --> pdb=" O VAL B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 768 removed outlier: 4.426A pdb=" N ASN B 767 " --> pdb=" O ASP B 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.561A pdb=" N SER A 85 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 314 through 327 Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 331 through 344 removed outlier: 4.428A pdb=" N ILE A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASN A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 340 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 458 through 464 removed outlier: 3.733A pdb=" N GLU A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 removed outlier: 3.912A pdb=" N ALA A 471 " --> pdb=" O HIS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 486 through 503 removed outlier: 3.664A pdb=" N THR A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 540 removed outlier: 3.629A pdb=" N SER A 533 " --> pdb=" O MET A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 569 removed outlier: 3.653A pdb=" N GLN A 556 " --> pdb=" O THR A 552 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET A 563 " --> pdb=" O CYS A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 578 through 596 Processing helix chain 'A' and resid 601 through 626 removed outlier: 3.547A pdb=" N GLU A 622 " --> pdb=" O CYS A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 651 removed outlier: 3.638A pdb=" N MET A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 684 removed outlier: 4.369A pdb=" N ALA A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR A 663 " --> pdb=" O ASN A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 711 Processing helix chain 'A' and resid 720 through 727 removed outlier: 3.845A pdb=" N LEU A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 762 removed outlier: 3.617A pdb=" N ALA A 748 " --> pdb=" O HIS A 744 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP A 762 " --> pdb=" O VAL A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 768 removed outlier: 4.426A pdb=" N ASN A 767 " --> pdb=" O ASP A 764 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 39 Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.686A pdb=" N THR B 72 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AA4, first strand: chain 'B' and resid 186 through 194 removed outlier: 5.270A pdb=" N ILE B 302 " --> pdb=" O ASN B 191 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS B 193 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS B 300 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 213 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 200 through 205 Processing sheet with id=AA6, first strand: chain 'A' and resid 35 through 39 Processing sheet with id=AA7, first strand: chain 'A' and resid 46 through 51 removed outlier: 3.686A pdb=" N THR A 72 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA9, first strand: chain 'A' and resid 186 through 194 removed outlier: 5.270A pdb=" N ILE A 302 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS A 193 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS A 300 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 213 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 200 through 205 570 hydrogen bonds defined for protein. 1614 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: 1.85 Time building geometry restraints manager: 1.00 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: 1626 1.32 - 1.44: 2944 1.44 - 1.56: 5954 1.56 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 10622 Sorted by residual: bond pdb=" C31 6OU B 802 " pdb=" O30 6OU B 802 " ideal model delta sigma weight residual 1.331 1.202 0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" C31 6OU A 802 " pdb=" O30 6OU A 802 " ideal model delta sigma weight residual 1.331 1.203 0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" C ILE B 229 " pdb=" O ILE B 229 " ideal model delta sigma weight residual 1.237 1.197 0.040 1.11e-02 8.12e+03 1.33e+01 bond pdb=" C ILE A 229 " pdb=" O ILE A 229 " ideal model delta sigma weight residual 1.237 1.197 0.040 1.11e-02 8.12e+03 1.33e+01 bond pdb=" C HIS A 740 " pdb=" O HIS A 740 " ideal model delta sigma weight residual 1.237 1.202 0.035 1.19e-02 7.06e+03 8.68e+00 ... (remaining 10617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 14322 4.24 - 8.47: 50 8.47 - 12.71: 1 12.71 - 16.95: 3 16.95 - 21.19: 2 Bond angle restraints: 14378 Sorted by residual: angle pdb=" N TYR A 175 " pdb=" CA TYR A 175 " pdb=" C TYR A 175 " ideal model delta sigma weight residual 109.41 88.22 21.19 1.52e+00 4.33e-01 1.94e+02 angle pdb=" N TYR B 175 " pdb=" CA TYR B 175 " pdb=" C TYR B 175 " ideal model delta sigma weight residual 109.50 88.76 20.74 1.58e+00 4.01e-01 1.72e+02 angle pdb=" C ILE A 237 " pdb=" CA ILE A 237 " pdb=" CB ILE A 237 " ideal model delta sigma weight residual 112.14 99.12 13.02 1.35e+00 5.49e-01 9.30e+01 angle pdb=" C ILE B 237 " pdb=" CA ILE B 237 " pdb=" CB ILE B 237 " ideal model delta sigma weight residual 112.14 99.16 12.98 1.35e+00 5.49e-01 9.25e+01 angle pdb=" N PHE B 177 " pdb=" CA PHE B 177 " pdb=" C PHE B 177 " ideal model delta sigma weight residual 113.88 106.53 7.35 1.23e+00 6.61e-01 3.57e+01 ... (remaining 14373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.07: 6092 23.07 - 46.14: 252 46.14 - 69.21: 37 69.21 - 92.28: 12 92.28 - 115.35: 3 Dihedral angle restraints: 6396 sinusoidal: 2582 harmonic: 3814 Sorted by residual: dihedral pdb=" CB CYS B 225 " pdb=" SG CYS B 225 " pdb=" SG CYS B 287 " pdb=" CB CYS B 287 " ideal model delta sinusoidal sigma weight residual -86.00 -131.13 45.13 1 1.00e+01 1.00e-02 2.83e+01 dihedral pdb=" CB CYS A 225 " pdb=" SG CYS A 225 " pdb=" SG CYS A 287 " pdb=" CB CYS A 287 " ideal model delta sinusoidal sigma weight residual -86.00 -131.13 45.13 1 1.00e+01 1.00e-02 2.83e+01 dihedral pdb=" C ASN A 234 " pdb=" N ASN A 234 " pdb=" CA ASN A 234 " pdb=" CB ASN A 234 " ideal model delta harmonic sigma weight residual -122.60 -135.46 12.86 0 2.50e+00 1.60e-01 2.65e+01 ... (remaining 6393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.405: 1707 0.405 - 0.811: 5 0.811 - 1.216: 0 1.216 - 1.621: 0 1.621 - 2.027: 2 Chirality restraints: 1714 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-02 2.50e+03 5.03e+02 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.37 -2.03 2.00e-01 2.50e+01 1.03e+02 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.41 -1.99 2.00e-01 2.50e+01 9.87e+01 ... (remaining 1711 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 205 " 0.161 2.00e-02 2.50e+03 1.66e-01 3.45e+02 pdb=" CG ASN B 205 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN B 205 " -0.048 2.00e-02 2.50e+03 pdb=" ND2 ASN B 205 " -0.258 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " 0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 205 " -0.159 2.00e-02 2.50e+03 1.63e-01 3.31e+02 pdb=" CG ASN A 205 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN A 205 " 0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN A 205 " 0.254 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.195 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.130 2.00e-02 2.50e+03 1.07e-01 1.42e+02 pdb=" C7 NAG E 2 " -0.037 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.098 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.169 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.022 2.00e-02 2.50e+03 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 65 2.49 - 3.09: 6830 3.09 - 3.69: 15273 3.69 - 4.30: 25038 4.30 - 4.90: 40918 Nonbonded interactions: 88124 Sorted by model distance: nonbonded pdb=" OG SER B 244 " pdb=" CE1 HIS A 248 " model vdw 1.885 3.260 nonbonded pdb=" CE1 HIS B 248 " pdb=" OG SER A 244 " model vdw 1.889 3.260 nonbonded pdb=" N TYR A 175 " pdb=" O TYR A 175 " model vdw 2.080 2.496 nonbonded pdb=" N TYR B 175 " pdb=" O TYR B 175 " model vdw 2.145 2.496 nonbonded pdb=" O VAL B 648 " pdb=" OG1 THR B 652 " model vdw 2.240 3.040 ... (remaining 88119 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.020 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.170 Find NCS groups from input model: 0.180 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:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 : 0.007 0.268 10640 Z= 0.369 Angle : 1.083 40.456 14410 Z= 0.525 Chirality : 0.089 2.027 1714 Planarity : 0.008 0.107 1762 Dihedral : 13.364 115.353 3896 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.81 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: -3.00 (0.20), residues: 1278 helix: -3.54 (0.12), residues: 550 sheet: 0.84 (0.31), residues: 266 loop : -1.42 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 240 TYR 0.018 0.002 TYR B 650 PHE 0.014 0.001 PHE B 639 TRP 0.010 0.002 TRP B 717 HIS 0.003 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00555 (10622) covalent geometry : angle 0.80499 (14378) SS BOND : bond 0.00380 ( 4) SS BOND : angle 1.37271 ( 8) hydrogen bonds : bond 0.23942 ( 570) hydrogen bonds : angle 9.21815 ( 1614) metal coordination : bond 0.08676 ( 6) link_BETA1-4 : bond 0.06235 ( 4) link_BETA1-4 : angle 4.82669 ( 12) link_NAG-ASN : bond 0.21408 ( 4) link_NAG-ASN : angle 24.66956 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.404 Fit side-chains REVERT: B 52 GLU cc_start: 0.7505 (mp0) cc_final: 0.7211 (mp0) REVERT: B 312 GLN cc_start: 0.8158 (pt0) cc_final: 0.7954 (pt0) REVERT: B 449 PHE cc_start: 0.7552 (m-80) cc_final: 0.7086 (t80) REVERT: B 451 LYS cc_start: 0.8341 (tmmt) cc_final: 0.7955 (tmmt) REVERT: B 522 ASP cc_start: 0.8179 (m-30) cc_final: 0.7859 (m-30) REVERT: B 634 PHE cc_start: 0.7374 (m-80) cc_final: 0.6129 (p90) REVERT: B 641 MET cc_start: 0.7236 (mmp) cc_final: 0.6979 (mmt) REVERT: B 675 MET cc_start: 0.8527 (mtm) cc_final: 0.8311 (mtp) REVERT: B 729 LYS cc_start: 0.7659 (mtmm) cc_final: 0.7041 (mmtt) REVERT: A 52 GLU cc_start: 0.7525 (mp0) cc_final: 0.7218 (mp0) REVERT: A 312 GLN cc_start: 0.8161 (pt0) cc_final: 0.7908 (pt0) REVERT: A 449 PHE cc_start: 0.7551 (m-80) cc_final: 0.7073 (t80) REVERT: A 451 LYS cc_start: 0.8355 (tmmt) cc_final: 0.7973 (tmmt) REVERT: A 522 ASP cc_start: 0.8127 (m-30) cc_final: 0.7843 (m-30) REVERT: A 634 PHE cc_start: 0.7339 (m-80) cc_final: 0.6130 (p90) REVERT: A 675 MET cc_start: 0.8518 (mtm) cc_final: 0.8290 (mtp) REVERT: A 729 LYS cc_start: 0.7667 (mtmm) cc_final: 0.7047 (mmtt) outliers start: 1 outliers final: 1 residues processed: 209 average time/residue: 0.4612 time to fit residues: 104.7738 Evaluate side-chains 146 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 659 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN B 57 HIS B 154 GLN B 342 ASN B 432 GLN B 450 HIS B 468 HIS B 482 ASN B 566 GLN B 590 ASN B 728 ASN A 54 ASN A 57 HIS A 342 ASN A 432 GLN A 450 HIS A 468 HIS A 482 ASN A 566 GLN A 590 ASN A 728 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.144956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.112794 restraints weight = 10448.431| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.88 r_work: 0.3168 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10640 Z= 0.175 Angle : 0.620 7.686 14410 Z= 0.325 Chirality : 0.046 0.163 1714 Planarity : 0.005 0.063 1762 Dihedral : 8.746 89.011 1610 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.50 % Allowed : 9.36 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: -0.55 (0.22), residues: 1278 helix: -0.36 (0.20), residues: 536 sheet: 1.10 (0.31), residues: 268 loop : -1.12 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 623 TYR 0.021 0.002 TYR B 650 PHE 0.012 0.001 PHE A 528 TRP 0.009 0.002 TRP A 717 HIS 0.005 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00406 (10622) covalent geometry : angle 0.60923 (14378) SS BOND : bond 0.00022 ( 4) SS BOND : angle 1.58318 ( 8) hydrogen bonds : bond 0.04782 ( 570) hydrogen bonds : angle 5.19306 ( 1614) metal coordination : bond 0.00283 ( 6) link_BETA1-4 : bond 0.00485 ( 4) link_BETA1-4 : angle 2.28557 ( 12) link_NAG-ASN : bond 0.00373 ( 4) link_NAG-ASN : angle 3.24582 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.369 Fit side-chains REVERT: B 45 LYS cc_start: 0.7944 (mmpt) cc_final: 0.6884 (tptp) REVERT: B 52 GLU cc_start: 0.7930 (mp0) cc_final: 0.7483 (mp0) REVERT: B 312 GLN cc_start: 0.8353 (pt0) cc_final: 0.8099 (pt0) REVERT: B 449 PHE cc_start: 0.7737 (m-80) cc_final: 0.6924 (t80) REVERT: B 451 LYS cc_start: 0.8703 (tmmt) cc_final: 0.8199 (tmmt) REVERT: B 634 PHE cc_start: 0.7412 (m-80) cc_final: 0.5811 (p90) REVERT: B 729 LYS cc_start: 0.7867 (mtmm) cc_final: 0.7050 (mmmt) REVERT: A 45 LYS cc_start: 0.7938 (mmpt) cc_final: 0.6890 (tptp) REVERT: A 52 GLU cc_start: 0.7980 (mp0) cc_final: 0.7526 (mp0) REVERT: A 312 GLN cc_start: 0.8346 (pt0) cc_final: 0.8098 (pt0) REVERT: A 449 PHE cc_start: 0.7753 (m-80) cc_final: 0.6945 (t80) REVERT: A 451 LYS cc_start: 0.8719 (tmmt) cc_final: 0.8210 (tmmt) REVERT: A 634 PHE cc_start: 0.7397 (m-80) cc_final: 0.5861 (p90) REVERT: A 641 MET cc_start: 0.7815 (mmt) cc_final: 0.7508 (mmt) REVERT: A 675 MET cc_start: 0.9048 (mtm) cc_final: 0.8841 (mtp) REVERT: A 729 LYS cc_start: 0.7887 (mtmm) cc_final: 0.7056 (mmmt) outliers start: 28 outliers final: 15 residues processed: 168 average time/residue: 0.4588 time to fit residues: 84.1063 Evaluate side-chains 138 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 772 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 127 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.0470 chunk 105 optimal weight: 0.0870 chunk 8 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 HIS B 466 HIS B 728 ASN A 450 HIS A 466 HIS A 728 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.146505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.114636 restraints weight = 10516.315| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.84 r_work: 0.3197 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10640 Z= 0.127 Angle : 0.546 7.139 14410 Z= 0.289 Chirality : 0.043 0.171 1714 Planarity : 0.004 0.057 1762 Dihedral : 8.060 80.241 1610 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.23 % Allowed : 10.96 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 0.55 (0.23), residues: 1278 helix: 1.06 (0.21), residues: 542 sheet: 1.24 (0.32), residues: 270 loop : -0.99 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 687 TYR 0.018 0.001 TYR B 650 PHE 0.010 0.001 PHE A 528 TRP 0.010 0.001 TRP B 567 HIS 0.003 0.001 HIS A 740 Details of bonding type rmsd covalent geometry : bond 0.00277 (10622) covalent geometry : angle 0.53710 (14378) SS BOND : bond 0.00748 ( 4) SS BOND : angle 1.44233 ( 8) hydrogen bonds : bond 0.03813 ( 570) hydrogen bonds : angle 4.80627 ( 1614) metal coordination : bond 0.00114 ( 6) link_BETA1-4 : bond 0.00390 ( 4) link_BETA1-4 : angle 2.03459 ( 12) link_NAG-ASN : bond 0.00077 ( 4) link_NAG-ASN : angle 2.53259 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.399 Fit side-chains REVERT: B 45 LYS cc_start: 0.7874 (mmpt) cc_final: 0.6877 (tptp) REVERT: B 52 GLU cc_start: 0.7922 (mp0) cc_final: 0.7429 (mp0) REVERT: B 449 PHE cc_start: 0.7722 (m-80) cc_final: 0.7006 (t80) REVERT: B 634 PHE cc_start: 0.7319 (m-80) cc_final: 0.5784 (p90) REVERT: B 729 LYS cc_start: 0.7863 (mtmm) cc_final: 0.7061 (mmmt) REVERT: B 766 ILE cc_start: 0.7670 (tp) cc_final: 0.7288 (mm) REVERT: A 45 LYS cc_start: 0.7861 (mmpt) cc_final: 0.6874 (tptp) REVERT: A 52 GLU cc_start: 0.7956 (mp0) cc_final: 0.7455 (mp0) REVERT: A 312 GLN cc_start: 0.8308 (pt0) cc_final: 0.8049 (pt0) REVERT: A 449 PHE cc_start: 0.7691 (m-80) cc_final: 0.6971 (t80) REVERT: A 634 PHE cc_start: 0.7313 (m-80) cc_final: 0.5803 (p90) REVERT: A 641 MET cc_start: 0.7904 (mmt) cc_final: 0.7595 (mmt) REVERT: A 675 MET cc_start: 0.8966 (mtm) cc_final: 0.8719 (mtp) REVERT: A 729 LYS cc_start: 0.7871 (mtmm) cc_final: 0.7058 (mmmt) outliers start: 25 outliers final: 14 residues processed: 145 average time/residue: 0.4877 time to fit residues: 77.1396 Evaluate side-chains 134 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 659 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 121 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.0050 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 HIS B 590 ASN B 728 ASN A 450 HIS A 590 ASN A 660 GLN A 728 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.144243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.111998 restraints weight = 10450.883| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.87 r_work: 0.3154 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10640 Z= 0.190 Angle : 0.588 7.570 14410 Z= 0.307 Chirality : 0.045 0.160 1714 Planarity : 0.004 0.062 1762 Dihedral : 7.766 54.860 1610 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.21 % Allowed : 11.85 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 0.96 (0.24), residues: 1278 helix: 1.69 (0.22), residues: 536 sheet: 1.30 (0.32), residues: 270 loop : -1.03 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 687 TYR 0.018 0.002 TYR A 650 PHE 0.013 0.002 PHE B 528 TRP 0.010 0.002 TRP A 567 HIS 0.004 0.001 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00452 (10622) covalent geometry : angle 0.58173 (14378) SS BOND : bond 0.00113 ( 4) SS BOND : angle 1.58634 ( 8) hydrogen bonds : bond 0.04081 ( 570) hydrogen bonds : angle 4.74340 ( 1614) metal coordination : bond 0.00161 ( 6) link_BETA1-4 : bond 0.00307 ( 4) link_BETA1-4 : angle 1.97420 ( 12) link_NAG-ASN : bond 0.00029 ( 4) link_NAG-ASN : angle 2.18521 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.399 Fit side-chains REVERT: B 45 LYS cc_start: 0.7963 (mmpt) cc_final: 0.7014 (tptp) REVERT: B 52 GLU cc_start: 0.8007 (mp0) cc_final: 0.7512 (mp0) REVERT: B 287 CYS cc_start: 0.7738 (p) cc_final: 0.7351 (p) REVERT: B 449 PHE cc_start: 0.7763 (m-80) cc_final: 0.7033 (t80) REVERT: B 451 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7833 (tttm) REVERT: B 634 PHE cc_start: 0.7418 (m-80) cc_final: 0.5781 (p90) REVERT: B 659 ASN cc_start: 0.7828 (m110) cc_final: 0.7340 (OUTLIER) REVERT: B 729 LYS cc_start: 0.7902 (mtmm) cc_final: 0.7090 (mmmt) REVERT: A 45 LYS cc_start: 0.7934 (mmpt) cc_final: 0.6907 (tptp) REVERT: A 287 CYS cc_start: 0.7622 (p) cc_final: 0.7135 (p) REVERT: A 449 PHE cc_start: 0.7765 (m-80) cc_final: 0.7037 (t80) REVERT: A 451 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7852 (tttm) REVERT: A 675 MET cc_start: 0.9027 (mtm) cc_final: 0.8806 (mtp) REVERT: A 729 LYS cc_start: 0.7918 (mtmm) cc_final: 0.7098 (mmmt) outliers start: 36 outliers final: 17 residues processed: 153 average time/residue: 0.4276 time to fit residues: 71.5258 Evaluate side-chains 135 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 634 PHE Chi-restraints excluded: chain A residue 663 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 91 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 HIS B 590 ASN B 728 ASN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS A 590 ASN A 728 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.144879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.112511 restraints weight = 10476.420| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.88 r_work: 0.3162 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10640 Z= 0.166 Angle : 0.559 7.224 14410 Z= 0.293 Chirality : 0.044 0.158 1714 Planarity : 0.004 0.061 1762 Dihedral : 7.551 56.910 1608 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.12 % Allowed : 11.94 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.20 (0.24), residues: 1278 helix: 1.96 (0.22), residues: 536 sheet: 1.40 (0.32), residues: 266 loop : -0.95 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 687 TYR 0.018 0.001 TYR B 650 PHE 0.012 0.001 PHE A 528 TRP 0.010 0.002 TRP B 567 HIS 0.003 0.001 HIS A 740 Details of bonding type rmsd covalent geometry : bond 0.00388 (10622) covalent geometry : angle 0.55250 (14378) SS BOND : bond 0.00131 ( 4) SS BOND : angle 1.17262 ( 8) hydrogen bonds : bond 0.03877 ( 570) hydrogen bonds : angle 4.67114 ( 1614) metal coordination : bond 0.00157 ( 6) link_BETA1-4 : bond 0.00264 ( 4) link_BETA1-4 : angle 1.90993 ( 12) link_NAG-ASN : bond 0.00048 ( 4) link_NAG-ASN : angle 2.09933 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.317 Fit side-chains REVERT: B 45 LYS cc_start: 0.7959 (mmtt) cc_final: 0.6938 (tptp) REVERT: B 52 GLU cc_start: 0.7999 (mp0) cc_final: 0.7490 (mp0) REVERT: B 240 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7569 (ttp-170) REVERT: B 449 PHE cc_start: 0.7753 (m-80) cc_final: 0.7019 (t80) REVERT: B 451 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7806 (tttm) REVERT: B 634 PHE cc_start: 0.7398 (m-80) cc_final: 0.5790 (p90) REVERT: B 659 ASN cc_start: 0.7913 (m110) cc_final: 0.7372 (OUTLIER) REVERT: B 729 LYS cc_start: 0.7879 (mtmm) cc_final: 0.7062 (mmmt) REVERT: A 45 LYS cc_start: 0.7947 (mmtt) cc_final: 0.6980 (tptp) REVERT: A 240 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7557 (ttp-170) REVERT: A 449 PHE cc_start: 0.7769 (m-80) cc_final: 0.7030 (t80) REVERT: A 451 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7795 (tttm) REVERT: A 675 MET cc_start: 0.9013 (mtm) cc_final: 0.8792 (mtp) REVERT: A 729 LYS cc_start: 0.7894 (mtmm) cc_final: 0.7067 (mmmt) outliers start: 35 outliers final: 19 residues processed: 146 average time/residue: 0.4416 time to fit residues: 70.4430 Evaluate side-chains 139 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 240 ARG Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 634 PHE Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 772 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 53 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 HIS B 590 ASN B 728 ASN A 192 GLN A 450 HIS A 590 ASN A 728 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.146504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.114335 restraints weight = 10510.655| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.89 r_work: 0.3184 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10640 Z= 0.129 Angle : 0.520 6.957 14410 Z= 0.274 Chirality : 0.043 0.157 1714 Planarity : 0.004 0.058 1762 Dihedral : 7.247 59.233 1608 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.58 % Allowed : 13.46 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.46 (0.24), residues: 1278 helix: 2.24 (0.22), residues: 538 sheet: 1.37 (0.32), residues: 266 loop : -0.82 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 687 TYR 0.018 0.001 TYR B 650 PHE 0.012 0.001 PHE A 528 TRP 0.010 0.001 TRP B 567 HIS 0.003 0.001 HIS A 740 Details of bonding type rmsd covalent geometry : bond 0.00293 (10622) covalent geometry : angle 0.51396 (14378) SS BOND : bond 0.00053 ( 4) SS BOND : angle 1.31996 ( 8) hydrogen bonds : bond 0.03486 ( 570) hydrogen bonds : angle 4.53456 ( 1614) metal coordination : bond 0.00100 ( 6) link_BETA1-4 : bond 0.00265 ( 4) link_BETA1-4 : angle 1.78152 ( 12) link_NAG-ASN : bond 0.00062 ( 4) link_NAG-ASN : angle 1.98096 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.7955 (mmtt) cc_final: 0.6985 (tptp) REVERT: B 52 GLU cc_start: 0.7941 (mp0) cc_final: 0.7396 (mp0) REVERT: B 449 PHE cc_start: 0.7771 (m-80) cc_final: 0.7021 (t80) REVERT: B 451 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7749 (tttm) REVERT: B 659 ASN cc_start: 0.7885 (m110) cc_final: 0.7395 (OUTLIER) REVERT: A 45 LYS cc_start: 0.7939 (mmtt) cc_final: 0.7087 (tptp) REVERT: A 449 PHE cc_start: 0.7753 (m-80) cc_final: 0.7016 (t80) REVERT: A 451 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7710 (tttm) REVERT: A 675 MET cc_start: 0.9039 (mtm) cc_final: 0.8829 (mtp) outliers start: 29 outliers final: 22 residues processed: 139 average time/residue: 0.4095 time to fit residues: 62.6335 Evaluate side-chains 139 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 634 PHE Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 634 PHE Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 727 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 26 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 GLN B 450 HIS B 590 ASN B 728 ASN A 450 HIS A 590 ASN A 728 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.145237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.112833 restraints weight = 10423.511| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.88 r_work: 0.3161 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10640 Z= 0.173 Angle : 0.554 7.104 14410 Z= 0.290 Chirality : 0.044 0.155 1714 Planarity : 0.004 0.059 1762 Dihedral : 7.319 58.773 1608 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.58 % Allowed : 13.37 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.42 (0.24), residues: 1278 helix: 2.17 (0.22), residues: 550 sheet: 1.43 (0.33), residues: 262 loop : -0.91 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 687 TYR 0.018 0.001 TYR B 650 PHE 0.012 0.001 PHE B 528 TRP 0.009 0.002 TRP A 567 HIS 0.003 0.001 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00409 (10622) covalent geometry : angle 0.54850 (14378) SS BOND : bond 0.00136 ( 4) SS BOND : angle 1.28234 ( 8) hydrogen bonds : bond 0.03761 ( 570) hydrogen bonds : angle 4.56621 ( 1614) metal coordination : bond 0.00175 ( 6) link_BETA1-4 : bond 0.00228 ( 4) link_BETA1-4 : angle 1.79565 ( 12) link_NAG-ASN : bond 0.00050 ( 4) link_NAG-ASN : angle 1.97136 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.391 Fit side-chains REVERT: B 45 LYS cc_start: 0.7988 (mmtt) cc_final: 0.6989 (tptp) REVERT: B 52 GLU cc_start: 0.7968 (mp0) cc_final: 0.7417 (mp0) REVERT: B 240 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7544 (ttp-170) REVERT: B 287 CYS cc_start: 0.7416 (p) cc_final: 0.6928 (p) REVERT: B 449 PHE cc_start: 0.7779 (m-80) cc_final: 0.7009 (t80) REVERT: B 451 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7725 (tttm) REVERT: B 659 ASN cc_start: 0.7953 (m110) cc_final: 0.7507 (OUTLIER) REVERT: A 45 LYS cc_start: 0.7986 (mmtt) cc_final: 0.6960 (tptp) REVERT: A 287 CYS cc_start: 0.7474 (p) cc_final: 0.6978 (p) REVERT: A 449 PHE cc_start: 0.7766 (m-80) cc_final: 0.7008 (t80) REVERT: A 451 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7671 (tttm) REVERT: A 675 MET cc_start: 0.9047 (mtm) cc_final: 0.8760 (mtp) REVERT: A 729 LYS cc_start: 0.7909 (mtmm) cc_final: 0.7135 (mmpt) outliers start: 29 outliers final: 25 residues processed: 143 average time/residue: 0.4119 time to fit residues: 64.4423 Evaluate side-chains 141 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 240 ARG Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 634 PHE Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 634 PHE Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 728 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 57 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 HIS B 571 HIS B 590 ASN B 728 ASN A 450 HIS A 571 HIS A 590 ASN A 728 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.144797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.112482 restraints weight = 10389.240| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.87 r_work: 0.3151 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10640 Z= 0.184 Angle : 0.567 7.142 14410 Z= 0.296 Chirality : 0.045 0.154 1714 Planarity : 0.004 0.061 1762 Dihedral : 7.358 60.497 1608 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.94 % Allowed : 13.37 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.40 (0.24), residues: 1278 helix: 2.15 (0.22), residues: 550 sheet: 1.45 (0.33), residues: 262 loop : -0.92 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 687 TYR 0.018 0.002 TYR A 650 PHE 0.012 0.001 PHE A 528 TRP 0.008 0.002 TRP A 567 HIS 0.003 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00437 (10622) covalent geometry : angle 0.56133 (14378) SS BOND : bond 0.00168 ( 4) SS BOND : angle 1.27844 ( 8) hydrogen bonds : bond 0.03842 ( 570) hydrogen bonds : angle 4.58793 ( 1614) metal coordination : bond 0.00190 ( 6) link_BETA1-4 : bond 0.00222 ( 4) link_BETA1-4 : angle 1.75946 ( 12) link_NAG-ASN : bond 0.00073 ( 4) link_NAG-ASN : angle 1.99150 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.368 Fit side-chains REVERT: B 45 LYS cc_start: 0.7973 (mmtt) cc_final: 0.6958 (tptp) REVERT: B 287 CYS cc_start: 0.7407 (p) cc_final: 0.6952 (p) REVERT: B 449 PHE cc_start: 0.7785 (m-80) cc_final: 0.7005 (t80) REVERT: B 451 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7722 (tttm) REVERT: B 659 ASN cc_start: 0.7961 (m110) cc_final: 0.7505 (OUTLIER) REVERT: B 712 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7668 (mm110) REVERT: A 45 LYS cc_start: 0.7997 (mmtt) cc_final: 0.6929 (tptp) REVERT: A 287 CYS cc_start: 0.7393 (p) cc_final: 0.6941 (p) REVERT: A 449 PHE cc_start: 0.7787 (m-80) cc_final: 0.7015 (t80) REVERT: A 451 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7670 (tttm) REVERT: A 675 MET cc_start: 0.9018 (mtm) cc_final: 0.8795 (mtp) REVERT: A 712 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7656 (mm110) REVERT: A 729 LYS cc_start: 0.7980 (mtmm) cc_final: 0.7098 (mmpt) outliers start: 33 outliers final: 26 residues processed: 140 average time/residue: 0.3864 time to fit residues: 59.2778 Evaluate side-chains 140 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 634 PHE Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 712 GLN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 634 PHE Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 712 GLN Chi-restraints excluded: chain A residue 728 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 17 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 68 optimal weight: 0.0030 chunk 50 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 HIS B 590 ASN B 728 ASN A 450 HIS A 590 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.145510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.113308 restraints weight = 10410.207| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.87 r_work: 0.3167 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10640 Z= 0.149 Angle : 0.542 7.131 14410 Z= 0.286 Chirality : 0.044 0.154 1714 Planarity : 0.004 0.059 1762 Dihedral : 7.289 61.472 1608 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.58 % Allowed : 13.55 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.47 (0.25), residues: 1278 helix: 2.22 (0.22), residues: 550 sheet: 1.43 (0.33), residues: 262 loop : -0.88 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 687 TYR 0.018 0.001 TYR A 650 PHE 0.011 0.001 PHE B 528 TRP 0.009 0.002 TRP B 567 HIS 0.003 0.001 HIS A 740 Details of bonding type rmsd covalent geometry : bond 0.00346 (10622) covalent geometry : angle 0.53690 (14378) SS BOND : bond 0.00117 ( 4) SS BOND : angle 1.13185 ( 8) hydrogen bonds : bond 0.03652 ( 570) hydrogen bonds : angle 4.55048 ( 1614) metal coordination : bond 0.00137 ( 6) link_BETA1-4 : bond 0.00256 ( 4) link_BETA1-4 : angle 1.71487 ( 12) link_NAG-ASN : bond 0.00063 ( 4) link_NAG-ASN : angle 1.94694 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.291 Fit side-chains REVERT: B 45 LYS cc_start: 0.7982 (mmtt) cc_final: 0.6970 (tptp) REVERT: B 449 PHE cc_start: 0.7794 (m-80) cc_final: 0.7041 (t80) REVERT: B 451 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7703 (tttm) REVERT: B 659 ASN cc_start: 0.7943 (m110) cc_final: 0.7508 (OUTLIER) REVERT: B 729 LYS cc_start: 0.7954 (mtmm) cc_final: 0.7070 (mmmt) REVERT: A 45 LYS cc_start: 0.7981 (mmtt) cc_final: 0.6984 (tptp) REVERT: A 449 PHE cc_start: 0.7792 (m-80) cc_final: 0.7043 (t80) REVERT: A 451 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7668 (tttm) REVERT: A 675 MET cc_start: 0.9047 (mtm) cc_final: 0.8763 (mtp) REVERT: A 729 LYS cc_start: 0.7946 (mtmm) cc_final: 0.7027 (mmmt) outliers start: 29 outliers final: 24 residues processed: 135 average time/residue: 0.4390 time to fit residues: 64.9227 Evaluate side-chains 139 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 634 PHE Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 663 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 85 optimal weight: 0.9980 chunk 41 optimal weight: 0.0030 chunk 102 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 98 optimal weight: 0.0020 chunk 49 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 HIS B 590 ASN A 450 HIS A 590 ASN A 728 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.146869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.114722 restraints weight = 10304.907| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.87 r_work: 0.3188 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10640 Z= 0.119 Angle : 0.517 7.115 14410 Z= 0.274 Chirality : 0.043 0.156 1714 Planarity : 0.004 0.058 1762 Dihedral : 7.137 62.197 1608 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.14 % Allowed : 14.26 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.60 (0.25), residues: 1278 helix: 2.31 (0.22), residues: 554 sheet: 1.45 (0.33), residues: 262 loop : -0.78 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 687 TYR 0.017 0.001 TYR A 650 PHE 0.010 0.001 PHE B 528 TRP 0.010 0.001 TRP A 567 HIS 0.003 0.001 HIS A 740 Details of bonding type rmsd covalent geometry : bond 0.00264 (10622) covalent geometry : angle 0.51105 (14378) SS BOND : bond 0.00088 ( 4) SS BOND : angle 1.54557 ( 8) hydrogen bonds : bond 0.03423 ( 570) hydrogen bonds : angle 4.47200 ( 1614) metal coordination : bond 0.00098 ( 6) link_BETA1-4 : bond 0.00249 ( 4) link_BETA1-4 : angle 1.64802 ( 12) link_NAG-ASN : bond 0.00093 ( 4) link_NAG-ASN : angle 1.87043 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.7865 (mmtt) cc_final: 0.6959 (tptp) REVERT: B 52 GLU cc_start: 0.7980 (mp0) cc_final: 0.7428 (mp0) REVERT: B 431 LEU cc_start: 0.8273 (mt) cc_final: 0.8030 (mm) REVERT: B 449 PHE cc_start: 0.7784 (m-80) cc_final: 0.7036 (t80) REVERT: B 451 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7703 (tttm) REVERT: B 659 ASN cc_start: 0.7907 (m110) cc_final: 0.7493 (OUTLIER) REVERT: B 729 LYS cc_start: 0.7912 (mtmm) cc_final: 0.6988 (mmmt) REVERT: A 45 LYS cc_start: 0.7869 (mmtt) cc_final: 0.6960 (tptp) REVERT: A 449 PHE cc_start: 0.7782 (m-80) cc_final: 0.7041 (t80) REVERT: A 675 MET cc_start: 0.9038 (mtm) cc_final: 0.8833 (mtp) REVERT: A 729 LYS cc_start: 0.7922 (mtmm) cc_final: 0.7042 (mmmt) outliers start: 24 outliers final: 22 residues processed: 133 average time/residue: 0.4566 time to fit residues: 66.5551 Evaluate side-chains 135 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 634 PHE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 728 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 77 optimal weight: 0.1980 chunk 82 optimal weight: 0.5980 chunk 127 optimal weight: 0.0970 chunk 85 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 HIS A 450 HIS A 728 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.146865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.114565 restraints weight = 10412.801| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.88 r_work: 0.3191 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.193 10640 Z= 0.209 Angle : 0.876 59.041 14410 Z= 0.529 Chirality : 0.053 1.150 1714 Planarity : 0.006 0.124 1762 Dihedral : 7.181 62.241 1608 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.14 % Allowed : 14.17 % Favored : 83.69 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 1.59 (0.25), residues: 1278 helix: 2.32 (0.22), residues: 554 sheet: 1.45 (0.33), residues: 262 loop : -0.80 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 687 TYR 0.017 0.001 TYR A 650 PHE 0.031 0.001 PHE A 634 TRP 0.010 0.001 TRP A 567 HIS 0.003 0.001 HIS A 740 Details of bonding type rmsd covalent geometry : bond 0.00421 (10622) covalent geometry : angle 0.87295 (14378) SS BOND : bond 0.00053 ( 4) SS BOND : angle 1.44489 ( 8) hydrogen bonds : bond 0.03435 ( 570) hydrogen bonds : angle 4.47224 ( 1614) metal coordination : bond 0.00105 ( 6) link_BETA1-4 : bond 0.00386 ( 4) link_BETA1-4 : angle 1.77828 ( 12) link_NAG-ASN : bond 0.00091 ( 4) link_NAG-ASN : angle 1.86067 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2887.48 seconds wall clock time: 50 minutes 12.25 seconds (3012.25 seconds total)