Starting phenix.real_space_refine on Mon Jun 9 16:17:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hip_34825/06_2025/8hip_34825.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hip_34825/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hip_34825/06_2025/8hip_34825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hip_34825/06_2025/8hip_34825.map" model { file = "/net/cci-nas-00/data/ceres_data/8hip_34825/06_2025/8hip_34825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hip_34825/06_2025/8hip_34825.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'ARG:plan': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS: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: {'ARG:plan': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS: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-2': 1, '6OU:plan-3': 2} 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-2': 1, '6OU:plan-3': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 7.39, per 1000 atoms: 0.71 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: 2.72 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.27 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: 3.43 Time building geometry restraints manager: 3.17 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: 0.00 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 30.570 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:12.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.460 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (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 TRP 0.010 0.002 TRP B 717 HIS 0.003 0.001 HIS A 540 PHE 0.014 0.001 PHE B 639 TYR 0.018 0.002 TYR B 650 ARG 0.005 0.000 ARG B 240 Details of bonding type rmsd link_NAG-ASN : bond 0.21408 ( 4) link_NAG-ASN : angle 24.66956 ( 12) link_BETA1-4 : bond 0.06235 ( 4) link_BETA1-4 : angle 4.82669 ( 12) hydrogen bonds : bond 0.23942 ( 570) hydrogen bonds : angle 9.21815 ( 1614) metal coordination : bond 0.08676 ( 6) SS BOND : bond 0.00380 ( 4) SS BOND : angle 1.37271 ( 8) covalent geometry : bond 0.00555 (10622) covalent geometry : angle 0.80499 (14378) *********************** 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 : 1.125 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: 1.0703 time to fit residues: 242.6886 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 : 1.138 ------------------------------------------------------------------------------- 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 108 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 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 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.141319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.109076 restraints weight = 10457.260| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.87 r_work: 0.3119 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 10640 Z= 0.296 Angle : 0.716 8.315 14410 Z= 0.371 Chirality : 0.050 0.184 1714 Planarity : 0.006 0.073 1762 Dihedral : 9.069 88.102 1610 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.76 % Allowed : 9.36 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.22), residues: 1278 helix: -0.61 (0.19), residues: 548 sheet: 1.18 (0.32), residues: 270 loop : -1.22 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 717 HIS 0.005 0.001 HIS B 450 PHE 0.017 0.002 PHE B 528 TYR 0.021 0.002 TYR B 650 ARG 0.004 0.001 ARG B 478 Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 4) link_NAG-ASN : angle 3.08697 ( 12) link_BETA1-4 : bond 0.00259 ( 4) link_BETA1-4 : angle 2.31126 ( 12) hydrogen bonds : bond 0.05301 ( 570) hydrogen bonds : angle 5.29460 ( 1614) metal coordination : bond 0.00235 ( 6) SS BOND : bond 0.01052 ( 4) SS BOND : angle 1.82120 ( 8) covalent geometry : bond 0.00717 (10622) covalent geometry : angle 0.70647 (14378) *********************** 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 175 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 1.307 Fit side-chains REVERT: B 45 LYS cc_start: 0.8024 (mmpt) cc_final: 0.6928 (tptp) REVERT: B 52 GLU cc_start: 0.8017 (mp0) cc_final: 0.7495 (mp0) REVERT: B 237 ILE cc_start: 0.7484 (mt) cc_final: 0.6521 (mt) REVERT: B 449 PHE cc_start: 0.7851 (m-80) cc_final: 0.7031 (t80) REVERT: B 451 LYS cc_start: 0.8757 (tmmt) cc_final: 0.8255 (tmmt) REVERT: B 634 PHE cc_start: 0.7473 (m-80) cc_final: 0.5906 (p90) REVERT: B 637 MET cc_start: 0.7864 (mtm) cc_final: 0.7611 (mtp) REVERT: B 729 LYS cc_start: 0.7892 (mtmm) cc_final: 0.7099 (mmmt) REVERT: A 45 LYS cc_start: 0.8012 (mmpt) cc_final: 0.6932 (tptp) REVERT: A 52 GLU cc_start: 0.8009 (mp0) cc_final: 0.7486 (mp0) REVERT: A 240 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.6050 (ttp-170) REVERT: A 449 PHE cc_start: 0.7888 (m-80) cc_final: 0.7058 (t80) REVERT: A 451 LYS cc_start: 0.8765 (tmmt) cc_final: 0.8260 (tmmt) REVERT: A 634 PHE cc_start: 0.7459 (m-80) cc_final: 0.5895 (p90) REVERT: A 729 LYS cc_start: 0.7900 (mtmm) cc_final: 0.7094 (mmmt) REVERT: A 766 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7478 (tp) outliers start: 31 outliers final: 14 residues processed: 166 average time/residue: 1.1430 time to fit residues: 207.8905 Evaluate side-chains 134 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.333 ------------------------------------------------------------------------------- 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 240 ARG Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 766 ILE 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 30 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 52 optimal weight: 0.0870 chunk 14 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 450 HIS B 728 ASN A 450 HIS A 728 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.144985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.112801 restraints weight = 10454.569| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.87 r_work: 0.3170 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10640 Z= 0.149 Angle : 0.576 7.069 14410 Z= 0.304 Chirality : 0.044 0.168 1714 Planarity : 0.004 0.062 1762 Dihedral : 8.334 75.073 1608 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.76 % Allowed : 10.87 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.23), residues: 1278 helix: 1.05 (0.22), residues: 532 sheet: 1.23 (0.32), residues: 270 loop : -1.09 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 567 HIS 0.004 0.001 HIS A 740 PHE 0.012 0.001 PHE A 528 TYR 0.018 0.001 TYR A 650 ARG 0.002 0.000 ARG B 687 Details of bonding type rmsd link_NAG-ASN : bond 0.00050 ( 4) link_NAG-ASN : angle 2.49450 ( 12) link_BETA1-4 : bond 0.00260 ( 4) link_BETA1-4 : angle 2.04959 ( 12) hydrogen bonds : bond 0.04015 ( 570) hydrogen bonds : angle 4.88174 ( 1614) metal coordination : bond 0.00142 ( 6) SS BOND : bond 0.00172 ( 4) SS BOND : angle 1.41542 ( 8) covalent geometry : bond 0.00335 (10622) covalent geometry : angle 0.56826 (14378) *********************** 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 160 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 1.222 Fit side-chains REVERT: B 45 LYS cc_start: 0.7989 (mmpt) cc_final: 0.6863 (tptp) REVERT: B 52 GLU cc_start: 0.7992 (mp0) cc_final: 0.7429 (mp0) REVERT: B 240 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7496 (ttp-170) REVERT: B 449 PHE cc_start: 0.7719 (m-80) cc_final: 0.6974 (t80) REVERT: B 634 PHE cc_start: 0.7393 (m-80) cc_final: 0.5886 (p90) REVERT: B 729 LYS cc_start: 0.7884 (mtmm) cc_final: 0.7054 (mmmt) REVERT: B 766 ILE cc_start: 0.7739 (tp) cc_final: 0.7487 (tp) REVERT: A 45 LYS cc_start: 0.7972 (mmpt) cc_final: 0.6894 (tptp) REVERT: A 52 GLU cc_start: 0.8021 (mp0) cc_final: 0.7449 (mp0) REVERT: A 449 PHE cc_start: 0.7767 (m-80) cc_final: 0.6998 (t80) REVERT: A 634 PHE cc_start: 0.7407 (m-80) cc_final: 0.5901 (p90) REVERT: A 641 MET cc_start: 0.7910 (mmt) cc_final: 0.7609 (mmt) REVERT: A 729 LYS cc_start: 0.7897 (mtmm) cc_final: 0.7063 (mmmt) REVERT: A 766 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7421 (tp) outliers start: 31 outliers final: 15 residues processed: 149 average time/residue: 1.0047 time to fit residues: 164.5747 Evaluate side-chains 138 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 590 ASN 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 176 ASP 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 766 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.144109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.111618 restraints weight = 10374.603| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.87 r_work: 0.3160 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1940 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= 0.170 Angle : 0.571 7.078 14410 Z= 0.299 Chirality : 0.045 0.160 1714 Planarity : 0.004 0.061 1762 Dihedral : 7.888 62.667 1608 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.57 % Allowed : 11.68 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.24), residues: 1278 helix: 1.71 (0.22), residues: 534 sheet: 1.23 (0.32), residues: 270 loop : -1.08 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 567 HIS 0.003 0.001 HIS B 450 PHE 0.012 0.001 PHE B 528 TYR 0.018 0.001 TYR A 650 ARG 0.002 0.000 ARG B 478 Details of bonding type rmsd link_NAG-ASN : bond 0.00025 ( 4) link_NAG-ASN : angle 2.18374 ( 12) link_BETA1-4 : bond 0.00287 ( 4) link_BETA1-4 : angle 1.96393 ( 12) hydrogen bonds : bond 0.03920 ( 570) hydrogen bonds : angle 4.73219 ( 1614) metal coordination : bond 0.00155 ( 6) SS BOND : bond 0.00076 ( 4) SS BOND : angle 1.42907 ( 8) covalent geometry : bond 0.00399 (10622) covalent geometry : angle 0.56384 (14378) *********************** 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 164 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 1.168 Fit side-chains REVERT: B 45 LYS cc_start: 0.7952 (mmpt) cc_final: 0.6915 (tptp) REVERT: B 52 GLU cc_start: 0.8010 (mp0) cc_final: 0.7399 (mp0) REVERT: B 240 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7518 (ttp-170) REVERT: B 287 CYS cc_start: 0.7670 (p) cc_final: 0.7282 (p) REVERT: B 449 PHE cc_start: 0.7708 (m-80) cc_final: 0.6962 (t80) REVERT: B 451 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7840 (tttm) REVERT: B 634 PHE cc_start: 0.7355 (m-80) cc_final: 0.5797 (p90) REVERT: B 659 ASN cc_start: 0.7817 (m110) cc_final: 0.7327 (OUTLIER) REVERT: B 712 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7662 (mm110) REVERT: B 729 LYS cc_start: 0.7907 (mtmm) cc_final: 0.7067 (mmmt) REVERT: A 45 LYS cc_start: 0.7968 (mmpt) cc_final: 0.6964 (tptp) REVERT: A 52 GLU cc_start: 0.8048 (mp0) cc_final: 0.7411 (mp0) REVERT: A 287 CYS cc_start: 0.7565 (p) cc_final: 0.7079 (p) REVERT: A 449 PHE cc_start: 0.7788 (m-80) cc_final: 0.6995 (t80) REVERT: A 451 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7867 (tttm) REVERT: A 634 PHE cc_start: 0.7341 (m-80) cc_final: 0.5826 (p90) REVERT: A 712 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7649 (mm110) REVERT: A 729 LYS cc_start: 0.7901 (mtmm) cc_final: 0.7060 (mmmt) outliers start: 40 outliers final: 21 residues processed: 154 average time/residue: 1.0014 time to fit residues: 168.9868 Evaluate side-chains 143 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 1.288 ------------------------------------------------------------------------------- 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 181 LYS 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 663 THR Chi-restraints excluded: chain B residue 712 GLN Chi-restraints excluded: chain A residue 59 LEU 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 659 ASN Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 712 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 105 optimal weight: 0.1980 chunk 88 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 HIS B 466 HIS B 590 ASN B 728 ASN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS A 466 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 = 0.3658 r_free = 0.3658 target = 0.145497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.113354 restraints weight = 10364.585| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.86 r_work: 0.3168 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2052 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= 0.146 Angle : 0.545 6.634 14410 Z= 0.286 Chirality : 0.044 0.161 1714 Planarity : 0.004 0.059 1762 Dihedral : 7.573 59.426 1608 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.21 % Allowed : 12.21 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.24), residues: 1278 helix: 1.95 (0.22), residues: 538 sheet: 1.24 (0.32), residues: 270 loop : -0.90 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 567 HIS 0.003 0.001 HIS B 740 PHE 0.011 0.001 PHE B 528 TYR 0.018 0.001 TYR A 650 ARG 0.002 0.000 ARG A 687 Details of bonding type rmsd link_NAG-ASN : bond 0.00050 ( 4) link_NAG-ASN : angle 2.06435 ( 12) link_BETA1-4 : bond 0.00261 ( 4) link_BETA1-4 : angle 1.89026 ( 12) hydrogen bonds : bond 0.03737 ( 570) hydrogen bonds : angle 4.63571 ( 1614) metal coordination : bond 0.00118 ( 6) SS BOND : bond 0.00044 ( 4) SS BOND : angle 1.13957 ( 8) covalent geometry : bond 0.00337 (10622) covalent geometry : angle 0.53878 (14378) *********************** 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: 36 poor density : 122 time to evaluate : 1.230 Fit side-chains REVERT: B 45 LYS cc_start: 0.8005 (mmpt) cc_final: 0.6970 (tptp) REVERT: B 240 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7541 (ttp-170) REVERT: B 449 PHE cc_start: 0.7778 (m-80) cc_final: 0.7038 (t80) REVERT: B 451 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7823 (tttm) REVERT: B 634 PHE cc_start: 0.7392 (m-80) cc_final: 0.5794 (p90) REVERT: B 659 ASN cc_start: 0.7815 (m110) cc_final: 0.7370 (OUTLIER) REVERT: B 729 LYS cc_start: 0.7892 (mtmm) cc_final: 0.7074 (mmmt) REVERT: A 45 LYS cc_start: 0.7973 (mmtt) cc_final: 0.7046 (tptp) REVERT: A 449 PHE cc_start: 0.7806 (m-80) cc_final: 0.7047 (t80) REVERT: A 451 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7823 (tttm) REVERT: A 634 PHE cc_start: 0.7328 (m-80) cc_final: 0.5760 (p90) REVERT: A 729 LYS cc_start: 0.7912 (mtmm) cc_final: 0.7084 (mmmt) outliers start: 36 outliers final: 21 residues processed: 144 average time/residue: 0.9739 time to fit residues: 154.3348 Evaluate side-chains 137 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 181 LYS 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 663 THR Chi-restraints excluded: chain A residue 59 LEU 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 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 659 ASN Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 727 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 122 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 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 = 0.3655 r_free = 0.3655 target = 0.144994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.112844 restraints weight = 10425.915| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.87 r_work: 0.3164 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2135 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= 0.167 Angle : 0.556 6.878 14410 Z= 0.292 Chirality : 0.044 0.156 1714 Planarity : 0.004 0.060 1762 Dihedral : 7.455 58.616 1608 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.39 % Allowed : 12.48 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.24), residues: 1278 helix: 2.00 (0.22), residues: 550 sheet: 1.39 (0.33), residues: 262 loop : -0.97 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 567 HIS 0.003 0.001 HIS A 450 PHE 0.013 0.001 PHE A 528 TYR 0.018 0.001 TYR A 650 ARG 0.003 0.000 ARG B 687 Details of bonding type rmsd link_NAG-ASN : bond 0.00061 ( 4) link_NAG-ASN : angle 1.99562 ( 12) link_BETA1-4 : bond 0.00223 ( 4) link_BETA1-4 : angle 1.82645 ( 12) hydrogen bonds : bond 0.03770 ( 570) hydrogen bonds : angle 4.61413 ( 1614) metal coordination : bond 0.00148 ( 6) SS BOND : bond 0.00121 ( 4) SS BOND : angle 1.50091 ( 8) covalent geometry : bond 0.00395 (10622) covalent geometry : angle 0.54980 (14378) *********************** 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 159 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8024 (mmtt) cc_final: 0.6963 (tptp) REVERT: B 240 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7539 (ttp-170) REVERT: B 429 GLN cc_start: 0.7452 (mm110) cc_final: 0.7198 (mm110) REVERT: B 449 PHE cc_start: 0.7795 (m-80) cc_final: 0.7045 (t80) REVERT: B 451 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7787 (tttm) REVERT: B 659 ASN cc_start: 0.7859 (m110) cc_final: 0.7488 (OUTLIER) REVERT: B 712 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7702 (mm110) REVERT: B 729 LYS cc_start: 0.7887 (mtmm) cc_final: 0.7066 (mmmt) REVERT: A 45 LYS cc_start: 0.8008 (mmtt) cc_final: 0.6979 (tptp) REVERT: A 449 PHE cc_start: 0.7849 (m-80) cc_final: 0.7072 (t80) REVERT: A 451 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7799 (tttm) REVERT: A 634 PHE cc_start: 0.7273 (m-80) cc_final: 0.5736 (p90) REVERT: A 712 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7708 (mm110) REVERT: A 729 LYS cc_start: 0.7889 (mtmm) cc_final: 0.7063 (mmmt) outliers start: 38 outliers final: 24 residues processed: 144 average time/residue: 1.0556 time to fit residues: 166.4709 Evaluate side-chains 139 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU 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 181 LYS Chi-restraints excluded: chain B residue 222 ASP 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 712 GLN Chi-restraints excluded: chain A residue 59 LEU 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 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 Chi-restraints excluded: chain A residue 712 GLN 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 76 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3651 r_free = 0.3651 target = 0.144783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.112299 restraints weight = 10510.071| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.89 r_work: 0.3156 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2170 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= 0.170 Angle : 0.558 6.754 14410 Z= 0.293 Chirality : 0.044 0.156 1714 Planarity : 0.004 0.061 1762 Dihedral : 7.428 58.546 1608 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.39 % Allowed : 12.39 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.24), residues: 1278 helix: 2.08 (0.22), residues: 548 sheet: 1.43 (0.33), residues: 262 loop : -0.97 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 567 HIS 0.003 0.001 HIS B 450 PHE 0.011 0.001 PHE B 528 TYR 0.018 0.001 TYR B 650 ARG 0.003 0.000 ARG B 687 Details of bonding type rmsd link_NAG-ASN : bond 0.00065 ( 4) link_NAG-ASN : angle 1.98575 ( 12) link_BETA1-4 : bond 0.00251 ( 4) link_BETA1-4 : angle 1.78765 ( 12) hydrogen bonds : bond 0.03806 ( 570) hydrogen bonds : angle 4.60351 ( 1614) metal coordination : bond 0.00159 ( 6) SS BOND : bond 0.00137 ( 4) SS BOND : angle 1.32176 ( 8) covalent geometry : bond 0.00400 (10622) covalent geometry : angle 0.55267 (14378) *********************** 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 157 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 3.155 Fit side-chains REVERT: B 45 LYS cc_start: 0.8053 (mmtt) cc_final: 0.6996 (tptp) REVERT: B 287 CYS cc_start: 0.7470 (p) cc_final: 0.6969 (p) REVERT: B 429 GLN cc_start: 0.7452 (mm110) cc_final: 0.7195 (mm110) REVERT: B 449 PHE cc_start: 0.7792 (m-80) cc_final: 0.7040 (t80) REVERT: B 451 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7767 (tttm) REVERT: B 659 ASN cc_start: 0.7953 (m110) cc_final: 0.7489 (OUTLIER) REVERT: B 712 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7704 (mm110) REVERT: B 729 LYS cc_start: 0.7880 (mtmm) cc_final: 0.7051 (mmmt) REVERT: A 45 LYS cc_start: 0.8036 (mmtt) cc_final: 0.6992 (tptp) REVERT: A 287 CYS cc_start: 0.7511 (p) cc_final: 0.7004 (p) REVERT: A 449 PHE cc_start: 0.7844 (m-80) cc_final: 0.7071 (t80) REVERT: A 451 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7789 (tttm) REVERT: A 634 PHE cc_start: 0.7181 (m-80) cc_final: 0.5718 (p90) REVERT: A 712 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7691 (mm110) REVERT: A 729 LYS cc_start: 0.7889 (mtmm) cc_final: 0.7053 (mmmt) outliers start: 38 outliers final: 29 residues processed: 144 average time/residue: 1.1090 time to fit residues: 176.8663 Evaluate side-chains 145 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 181 LYS 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 59 LEU 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 451 LYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 590 ASN 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 727 LEU 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 127 optimal weight: 3.9990 chunk 67 optimal weight: 0.2980 chunk 72 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3656 r_free = 0.3656 target = 0.145158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.113030 restraints weight = 10390.338| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.87 r_work: 0.3180 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10640 Z= 0.129 Angle : 0.524 6.851 14410 Z= 0.278 Chirality : 0.043 0.157 1714 Planarity : 0.004 0.058 1762 Dihedral : 7.281 59.738 1608 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.12 % Allowed : 12.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.25), residues: 1278 helix: 2.24 (0.22), residues: 548 sheet: 1.59 (0.33), residues: 256 loop : -0.93 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 567 HIS 0.003 0.001 HIS A 740 PHE 0.010 0.001 PHE A 528 TYR 0.017 0.001 TYR B 650 ARG 0.004 0.000 ARG B 687 Details of bonding type rmsd link_NAG-ASN : bond 0.00076 ( 4) link_NAG-ASN : angle 1.91864 ( 12) link_BETA1-4 : bond 0.00236 ( 4) link_BETA1-4 : angle 1.71332 ( 12) hydrogen bonds : bond 0.03539 ( 570) hydrogen bonds : angle 4.53075 ( 1614) metal coordination : bond 0.00105 ( 6) SS BOND : bond 0.00071 ( 4) SS BOND : angle 1.07230 ( 8) covalent geometry : bond 0.00294 (10622) covalent geometry : angle 0.51898 (14378) *********************** 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 154 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 1.330 Fit side-chains REVERT: B 45 LYS cc_start: 0.7928 (mmtt) cc_final: 0.6925 (tptp) REVERT: B 240 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7329 (ttp80) REVERT: B 429 GLN cc_start: 0.7433 (mm110) cc_final: 0.7175 (mm110) REVERT: B 449 PHE cc_start: 0.7736 (m-80) cc_final: 0.6968 (t80) REVERT: B 451 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7655 (tttm) REVERT: B 659 ASN cc_start: 0.7912 (m110) cc_final: 0.7451 (OUTLIER) REVERT: B 712 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7695 (mm110) REVERT: A 45 LYS cc_start: 0.7917 (mmtt) cc_final: 0.6926 (tptp) REVERT: A 287 CYS cc_start: 0.7311 (p) cc_final: 0.6853 (p) REVERT: A 449 PHE cc_start: 0.7784 (m-80) cc_final: 0.6990 (t80) REVERT: A 451 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7663 (tttm) REVERT: A 634 PHE cc_start: 0.7060 (m-80) cc_final: 0.5642 (p90) outliers start: 35 outliers final: 25 residues processed: 142 average time/residue: 0.9896 time to fit residues: 155.2766 Evaluate side-chains 140 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 181 LYS 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 712 GLN 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 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 Chi-restraints excluded: chain A residue 727 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 571 HIS B 590 ASN ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS A 571 HIS A 590 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.145783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.113633 restraints weight = 10427.079| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.87 r_work: 0.3172 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10640 Z= 0.151 Angle : 0.541 7.074 14410 Z= 0.286 Chirality : 0.044 0.162 1714 Planarity : 0.004 0.059 1762 Dihedral : 7.268 59.124 1608 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.58 % Allowed : 13.10 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.25), residues: 1278 helix: 2.22 (0.22), residues: 552 sheet: 1.64 (0.33), residues: 256 loop : -0.88 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 567 HIS 0.003 0.001 HIS A 740 PHE 0.011 0.001 PHE A 528 TYR 0.018 0.001 TYR A 650 ARG 0.004 0.000 ARG A 687 Details of bonding type rmsd link_NAG-ASN : bond 0.00074 ( 4) link_NAG-ASN : angle 1.90759 ( 12) link_BETA1-4 : bond 0.00300 ( 4) link_BETA1-4 : angle 1.70200 ( 12) hydrogen bonds : bond 0.03637 ( 570) hydrogen bonds : angle 4.53155 ( 1614) metal coordination : bond 0.00161 ( 6) SS BOND : bond 0.00155 ( 4) SS BOND : angle 1.36057 ( 8) covalent geometry : bond 0.00354 (10622) covalent geometry : angle 0.53585 (14378) *********************** 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 : 1.492 Fit side-chains revert: symmetry clash REVERT: B 45 LYS cc_start: 0.7947 (mmtt) cc_final: 0.6931 (tptp) REVERT: B 429 GLN cc_start: 0.7445 (mm110) cc_final: 0.7185 (mm110) REVERT: B 449 PHE cc_start: 0.7787 (m-80) cc_final: 0.7038 (t80) REVERT: B 451 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7706 (tttm) REVERT: B 659 ASN cc_start: 0.7915 (m110) cc_final: 0.7493 (OUTLIER) REVERT: B 712 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7727 (mm110) REVERT: B 729 LYS cc_start: 0.7966 (mtmm) cc_final: 0.7032 (mmmt) REVERT: A 45 LYS cc_start: 0.7935 (mmtt) cc_final: 0.6932 (tptp) REVERT: A 449 PHE cc_start: 0.7834 (m-80) cc_final: 0.7052 (t80) REVERT: A 451 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7733 (tttm) REVERT: A 634 PHE cc_start: 0.7084 (m-80) cc_final: 0.5660 (p90) REVERT: A 712 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7702 (mm110) REVERT: A 729 LYS cc_start: 0.7988 (mtmm) cc_final: 0.7101 (mmmt) outliers start: 29 outliers final: 22 residues processed: 135 average time/residue: 1.0032 time to fit residues: 148.8443 Evaluate side-chains 136 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 181 LYS 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 B residue 712 GLN 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 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 Chi-restraints excluded: chain A residue 712 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 8 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 98 optimal weight: 0.0870 chunk 71 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.146989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.114617 restraints weight = 10482.954| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.90 r_work: 0.3192 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10640 Z= 0.121 Angle : 0.523 7.077 14410 Z= 0.276 Chirality : 0.043 0.157 1714 Planarity : 0.004 0.058 1762 Dihedral : 7.131 60.104 1608 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.41 % Allowed : 13.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.25), residues: 1278 helix: 2.30 (0.22), residues: 554 sheet: 1.54 (0.33), residues: 262 loop : -0.77 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 567 HIS 0.003 0.001 HIS A 740 PHE 0.009 0.001 PHE A 528 TYR 0.017 0.001 TYR A 650 ARG 0.004 0.000 ARG A 687 Details of bonding type rmsd link_NAG-ASN : bond 0.00089 ( 4) link_NAG-ASN : angle 1.84694 ( 12) link_BETA1-4 : bond 0.00286 ( 4) link_BETA1-4 : angle 1.64591 ( 12) hydrogen bonds : bond 0.03423 ( 570) hydrogen bonds : angle 4.46996 ( 1614) metal coordination : bond 0.00098 ( 6) SS BOND : bond 0.00074 ( 4) SS BOND : angle 1.37511 ( 8) covalent geometry : bond 0.00276 (10622) covalent geometry : angle 0.51789 (14378) ********************** 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: 27 poor density : 113 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.7938 (mmtt) cc_final: 0.6963 (tptp) REVERT: B 429 GLN cc_start: 0.7435 (mm110) cc_final: 0.7162 (mm110) REVERT: B 449 PHE cc_start: 0.7773 (m-80) cc_final: 0.7028 (t80) REVERT: B 451 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7697 (tttm) REVERT: B 659 ASN cc_start: 0.7910 (m110) cc_final: 0.7498 (OUTLIER) REVERT: B 712 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7773 (mm110) REVERT: B 729 LYS cc_start: 0.7935 (mtmm) cc_final: 0.7066 (mmmt) REVERT: A 45 LYS cc_start: 0.7924 (mmtt) cc_final: 0.6884 (tptp) REVERT: A 52 GLU cc_start: 0.8012 (mp0) cc_final: 0.7341 (mp0) REVERT: A 449 PHE cc_start: 0.7843 (m-80) cc_final: 0.7063 (t80) REVERT: A 451 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7719 (tttm) REVERT: A 634 PHE cc_start: 0.7047 (m-80) cc_final: 0.5655 (p90) REVERT: A 712 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7730 (mm110) outliers start: 27 outliers final: 23 residues processed: 132 average time/residue: 1.5174 time to fit residues: 219.6189 Evaluate side-chains 136 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 3.092 ------------------------------------------------------------------------------- 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 181 LYS 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 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 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 Chi-restraints excluded: chain A residue 712 GLN 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 72 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 chunk 127 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3659 r_free = 0.3659 target = 0.145620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.113429 restraints weight = 10363.676| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.87 r_work: 0.3190 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.188 10640 Z= 0.222 Angle : 0.885 59.200 14410 Z= 0.534 Chirality : 0.054 1.173 1714 Planarity : 0.006 0.128 1762 Dihedral : 7.181 60.068 1608 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.41 % Allowed : 13.37 % Favored : 84.22 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.25), residues: 1278 helix: 2.29 (0.22), residues: 554 sheet: 1.55 (0.33), residues: 262 loop : -0.80 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 567 HIS 0.002 0.001 HIS A 740 PHE 0.032 0.001 PHE B 634 TYR 0.017 0.001 TYR A 650 ARG 0.003 0.000 ARG B 687 Details of bonding type rmsd link_NAG-ASN : bond 0.00087 ( 4) link_NAG-ASN : angle 1.82030 ( 12) link_BETA1-4 : bond 0.00442 ( 4) link_BETA1-4 : angle 1.77842 ( 12) hydrogen bonds : bond 0.03478 ( 570) hydrogen bonds : angle 4.46864 ( 1614) metal coordination : bond 0.00126 ( 6) SS BOND : bond 0.00096 ( 4) SS BOND : angle 1.28408 ( 8) covalent geometry : bond 0.00461 (10622) covalent geometry : angle 0.88258 (14378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7737.66 seconds wall clock time: 138 minutes 32.98 seconds (8312.98 seconds total)