Starting phenix.real_space_refine on Fri Feb 14 23:21:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hip_34825/02_2025/8hip_34825.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hip_34825/02_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_34825/02_2025/8hip_34825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hip_34825/02_2025/8hip_34825.map" model { file = "/net/cci-nas-00/data/ceres_data/8hip_34825/02_2025/8hip_34825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hip_34825/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.84, per 1000 atoms: 0.66 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: 2.63 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: 1.14 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: 3.27 Time building geometry restraints manager: 3.13 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.880 Find NCS groups from input model: 0.290 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: 0.000 Load rotamer database and sin/cos tables:13.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.090 ------------------------------------------------------------------------------- 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 : 0.006 0.129 10622 Z= 0.356 Angle : 0.805 21.187 14378 Z= 0.466 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 *********************** 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 : 1.117 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: 1.1143 time to fit residues: 252.6925 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 : 1.176 ------------------------------------------------------------------------------- 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: 2.9990 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.140641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.108925 restraints weight = 10458.463| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.83 r_work: 0.3107 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.055 10622 Z= 0.550 Angle : 0.754 8.662 14378 Z= 0.392 Chirality : 0.052 0.179 1714 Planarity : 0.006 0.076 1762 Dihedral : 9.222 90.629 1610 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.76 % Allowed : 9.45 % Favored : 87.79 % 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: -0.79 (0.22), residues: 1278 helix: -0.68 (0.19), residues: 558 sheet: 1.20 (0.32), residues: 270 loop : -1.24 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP A 717 HIS 0.005 0.001 HIS B 248 PHE 0.019 0.002 PHE A 528 TYR 0.020 0.002 TYR B 650 ARG 0.005 0.001 ARG A 478 *********************** 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 : 1.199 Fit side-chains REVERT: B 45 LYS cc_start: 0.8021 (mmpt) cc_final: 0.6895 (tptp) REVERT: B 52 GLU cc_start: 0.7963 (mp0) cc_final: 0.7468 (mp0) REVERT: B 237 ILE cc_start: 0.7504 (mt) cc_final: 0.6508 (mt) REVERT: B 240 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.5935 (ttp-170) REVERT: B 449 PHE cc_start: 0.7824 (m-80) cc_final: 0.6973 (t80) REVERT: B 451 LYS cc_start: 0.8738 (tmmt) cc_final: 0.8221 (tmmt) REVERT: B 634 PHE cc_start: 0.7448 (m-80) cc_final: 0.5856 (p90) REVERT: B 729 LYS cc_start: 0.7898 (mtmm) cc_final: 0.7067 (mmmt) REVERT: A 45 LYS cc_start: 0.8031 (mmpt) cc_final: 0.6920 (tptp) REVERT: A 52 GLU cc_start: 0.7993 (mp0) cc_final: 0.7495 (mp0) REVERT: A 237 ILE cc_start: 0.7509 (mt) cc_final: 0.6521 (mt) REVERT: A 240 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.6015 (ttp-170) REVERT: A 449 PHE cc_start: 0.7860 (m-80) cc_final: 0.7007 (t80) REVERT: A 451 LYS cc_start: 0.8762 (tmmt) cc_final: 0.8250 (tmmt) REVERT: A 634 PHE cc_start: 0.7432 (m-80) cc_final: 0.5845 (p90) REVERT: A 675 MET cc_start: 0.9064 (mtm) cc_final: 0.8864 (mtp) REVERT: A 729 LYS cc_start: 0.7897 (mtmm) cc_final: 0.7058 (mmmt) outliers start: 31 outliers final: 12 residues processed: 166 average time/residue: 1.1464 time to fit residues: 206.6619 Evaluate side-chains 130 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 1.385 ------------------------------------------------------------------------------- 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 240 ARG 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 240 ARG Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 772 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 52 optimal weight: 0.1980 chunk 14 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 54 ASN A 450 HIS A 728 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.144772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.112070 restraints weight = 10477.571| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.92 r_work: 0.3155 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10622 Z= 0.208 Angle : 0.567 6.971 14378 Z= 0.302 Chirality : 0.044 0.165 1714 Planarity : 0.004 0.063 1762 Dihedral : 8.412 77.287 1608 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.58 % Allowed : 11.05 % 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: 0.45 (0.23), residues: 1278 helix: 1.04 (0.22), residues: 532 sheet: 1.27 (0.32), residues: 270 loop : -1.13 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 567 HIS 0.004 0.001 HIS A 740 PHE 0.012 0.001 PHE B 528 TYR 0.019 0.001 TYR B 650 ARG 0.002 0.000 ARG A 687 *********************** 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 161 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.235 Fit side-chains REVERT: B 45 LYS cc_start: 0.8002 (mmpt) cc_final: 0.6859 (tptp) REVERT: B 52 GLU cc_start: 0.7993 (mp0) cc_final: 0.7422 (mp0) REVERT: B 449 PHE cc_start: 0.7721 (m-80) cc_final: 0.6960 (t80) REVERT: B 634 PHE cc_start: 0.7350 (m-80) cc_final: 0.5795 (p90) REVERT: B 729 LYS cc_start: 0.7893 (mtmm) cc_final: 0.7040 (mmmt) REVERT: B 766 ILE cc_start: 0.7687 (tp) cc_final: 0.7465 (tp) REVERT: A 45 LYS cc_start: 0.8008 (mmpt) cc_final: 0.6896 (tptp) REVERT: A 52 GLU cc_start: 0.8022 (mp0) cc_final: 0.7445 (mp0) REVERT: A 449 PHE cc_start: 0.7756 (m-80) cc_final: 0.6963 (t80) REVERT: A 634 PHE cc_start: 0.7401 (m-80) cc_final: 0.5881 (p90) REVERT: A 675 MET cc_start: 0.8978 (mtm) cc_final: 0.8755 (mtp) REVERT: A 729 LYS cc_start: 0.7867 (mtmm) cc_final: 0.7031 (mmmt) outliers start: 29 outliers final: 16 residues processed: 150 average time/residue: 1.0262 time to fit residues: 169.3914 Evaluate side-chains 137 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 104 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 HIS B 466 HIS B 590 ASN B 728 ASN A 450 HIS A 466 HIS A 590 ASN A 660 GLN A 728 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.145732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.113827 restraints weight = 10338.479| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.85 r_work: 0.3179 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10622 Z= 0.203 Angle : 0.534 6.849 14378 Z= 0.283 Chirality : 0.043 0.163 1714 Planarity : 0.004 0.058 1762 Dihedral : 7.734 62.114 1608 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.39 % Allowed : 12.03 % 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: 1.00 (0.24), residues: 1278 helix: 1.70 (0.22), residues: 540 sheet: 1.27 (0.32), residues: 270 loop : -0.96 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 567 HIS 0.003 0.001 HIS B 740 PHE 0.011 0.001 PHE A 528 TYR 0.018 0.001 TYR A 650 ARG 0.002 0.000 ARG B 687 *********************** 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 167 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 1.250 Fit side-chains REVERT: B 45 LYS cc_start: 0.7947 (mmpt) cc_final: 0.6952 (tptp) REVERT: B 52 GLU cc_start: 0.7953 (mp0) cc_final: 0.7455 (mp0) REVERT: B 449 PHE cc_start: 0.7709 (m-80) cc_final: 0.6976 (t80) REVERT: B 451 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7854 (tttm) REVERT: B 634 PHE cc_start: 0.7258 (m-80) cc_final: 0.5759 (p90) REVERT: B 659 ASN cc_start: 0.7816 (m110) cc_final: 0.7353 (OUTLIER) REVERT: B 729 LYS cc_start: 0.7888 (mtmm) cc_final: 0.7063 (mmmt) REVERT: A 45 LYS cc_start: 0.7915 (mmpt) cc_final: 0.6977 (tptp) REVERT: A 52 GLU cc_start: 0.7987 (mp0) cc_final: 0.7483 (mp0) REVERT: A 449 PHE cc_start: 0.7779 (m-80) cc_final: 0.6993 (t80) REVERT: A 451 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7859 (tttm) REVERT: A 634 PHE cc_start: 0.7258 (m-80) cc_final: 0.5759 (p90) REVERT: A 675 MET cc_start: 0.8997 (mtm) cc_final: 0.8715 (mtp) REVERT: A 729 LYS cc_start: 0.7885 (mtmm) cc_final: 0.7055 (mmmt) outliers start: 38 outliers final: 24 residues processed: 154 average time/residue: 0.9924 time to fit residues: 168.1205 Evaluate side-chains 145 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 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 727 LEU 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 148 ASN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 659 ASN 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: 1.9990 chunk 115 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.143562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.111363 restraints weight = 10400.592| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.86 r_work: 0.3142 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10622 Z= 0.338 Angle : 0.593 7.064 14378 Z= 0.311 Chirality : 0.046 0.158 1714 Planarity : 0.004 0.064 1762 Dihedral : 7.760 57.422 1608 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.30 % Allowed : 12.57 % 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: 1.08 (0.24), residues: 1278 helix: 1.81 (0.22), residues: 538 sheet: 1.42 (0.32), residues: 266 loop : -1.03 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 567 HIS 0.003 0.001 HIS A 450 PHE 0.014 0.002 PHE B 528 TYR 0.018 0.002 TYR B 650 ARG 0.003 0.000 ARG B 687 *********************** 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 160 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 1.151 Fit side-chains REVERT: B 45 LYS cc_start: 0.7993 (mmtt) cc_final: 0.6950 (tptp) REVERT: B 52 GLU cc_start: 0.8051 (mp0) cc_final: 0.7421 (mp0) REVERT: B 240 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7617 (ttp-170) REVERT: B 287 CYS cc_start: 0.7760 (p) cc_final: 0.7353 (p) REVERT: B 449 PHE cc_start: 0.7837 (m-80) cc_final: 0.7075 (t80) REVERT: B 451 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7854 (tttm) REVERT: B 634 PHE cc_start: 0.7412 (m-80) cc_final: 0.5785 (p90) REVERT: B 659 ASN cc_start: 0.7880 (m110) cc_final: 0.7497 (OUTLIER) REVERT: B 729 LYS cc_start: 0.7946 (mtmm) cc_final: 0.7135 (mmmt) REVERT: A 45 LYS cc_start: 0.7983 (mmtt) cc_final: 0.6958 (tptp) REVERT: A 52 GLU cc_start: 0.8074 (mp0) cc_final: 0.7442 (mp0) REVERT: A 287 CYS cc_start: 0.7791 (p) cc_final: 0.7386 (p) REVERT: A 449 PHE cc_start: 0.7849 (m-80) cc_final: 0.7080 (t80) REVERT: A 451 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7879 (tttm) REVERT: A 634 PHE cc_start: 0.7419 (m-80) cc_final: 0.5853 (p90) REVERT: A 675 MET cc_start: 0.9027 (mtm) cc_final: 0.8781 (mtp) REVERT: A 729 LYS cc_start: 0.7957 (mtmm) cc_final: 0.7142 (mmmt) outliers start: 37 outliers final: 22 residues processed: 146 average time/residue: 1.0738 time to fit residues: 171.6169 Evaluate side-chains 140 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 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 170 LEU Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 663 THR 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: 0.5980 chunk 116 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 HIS B 590 ASN B 728 ASN A 192 GLN A 450 HIS A 590 ASN A 728 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.145141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.113025 restraints weight = 10429.545| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.87 r_work: 0.3167 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10622 Z= 0.237 Angle : 0.544 7.076 14378 Z= 0.287 Chirality : 0.044 0.155 1714 Planarity : 0.004 0.061 1762 Dihedral : 7.483 59.361 1608 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.12 % Allowed : 12.75 % 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: 2.01 (0.22), residues: 550 sheet: 1.44 (0.33), residues: 262 loop : -1.00 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 567 HIS 0.003 0.001 HIS A 740 PHE 0.013 0.001 PHE A 528 TYR 0.018 0.001 TYR B 650 ARG 0.002 0.000 ARG A 687 *********************** 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 151 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 1.361 Fit side-chains REVERT: B 45 LYS cc_start: 0.8002 (mmtt) cc_final: 0.6950 (tptp) REVERT: B 449 PHE cc_start: 0.7839 (m-80) cc_final: 0.7067 (t80) REVERT: B 451 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7795 (tttm) REVERT: B 634 PHE cc_start: 0.7270 (m-80) cc_final: 0.5728 (p90) REVERT: B 659 ASN cc_start: 0.7854 (m110) cc_final: 0.7486 (OUTLIER) REVERT: B 729 LYS cc_start: 0.7882 (mtmm) cc_final: 0.7059 (mmmt) REVERT: B 766 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7446 (tp) REVERT: A 45 LYS cc_start: 0.7992 (mmtt) cc_final: 0.6963 (tptp) REVERT: A 449 PHE cc_start: 0.7837 (m-80) cc_final: 0.7066 (t80) REVERT: A 451 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7808 (tttm) REVERT: A 634 PHE cc_start: 0.7283 (m-80) cc_final: 0.5741 (p90) REVERT: A 675 MET cc_start: 0.9014 (mtm) cc_final: 0.8782 (mtp) REVERT: A 729 LYS cc_start: 0.7915 (mtmm) cc_final: 0.7093 (mmmt) outliers start: 35 outliers final: 25 residues processed: 138 average time/residue: 0.9865 time to fit residues: 150.3562 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 : 1.164 ------------------------------------------------------------------------------- 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 225 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 766 ILE 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 181 LYS Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 772 SER 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: 0.8980 chunk 122 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 52 optimal weight: 0.2980 chunk 34 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 GLN B 450 HIS B 590 ASN B 728 ASN A 450 HIS A 590 ASN A 728 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.145191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.112389 restraints weight = 10558.451| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.92 r_work: 0.3161 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10622 Z= 0.222 Angle : 0.538 6.985 14378 Z= 0.284 Chirality : 0.044 0.161 1714 Planarity : 0.004 0.059 1762 Dihedral : 7.383 59.586 1608 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.39 % Allowed : 12.66 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.37 (0.24), residues: 1278 helix: 2.13 (0.22), residues: 550 sheet: 1.57 (0.33), residues: 256 loop : -1.00 (0.29), residues: 472 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 A 528 TYR 0.018 0.001 TYR A 650 ARG 0.004 0.000 ARG A 687 *********************** 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 154 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8009 (mmtt) cc_final: 0.6923 (tptp) REVERT: B 449 PHE cc_start: 0.7760 (m-80) cc_final: 0.6978 (t80) REVERT: B 451 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7714 (tttm) REVERT: B 659 ASN cc_start: 0.7927 (m110) cc_final: 0.7453 (OUTLIER) REVERT: B 729 LYS cc_start: 0.7862 (mtmm) cc_final: 0.7015 (mmmt) REVERT: B 766 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7398 (tp) REVERT: A 45 LYS cc_start: 0.8004 (mmtt) cc_final: 0.6938 (tptp) REVERT: A 449 PHE cc_start: 0.7788 (m-80) cc_final: 0.6989 (t80) REVERT: A 451 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7719 (tttm) REVERT: A 675 MET cc_start: 0.9042 (mtm) cc_final: 0.8809 (mtp) REVERT: A 729 LYS cc_start: 0.7867 (mtmm) cc_final: 0.7014 (mmmt) outliers start: 38 outliers final: 26 residues processed: 141 average time/residue: 0.9936 time to fit residues: 153.9640 Evaluate side-chains 141 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 225 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain B residue 766 ILE 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 181 LYS Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 663 THR 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: 0.0060 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 HIS B 571 HIS B 590 ASN 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 = 0.3662 r_free = 0.3662 target = 0.145824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.112983 restraints weight = 10423.732| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.92 r_work: 0.3162 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10622 Z= 0.209 Angle : 0.528 6.821 14378 Z= 0.280 Chirality : 0.043 0.158 1714 Planarity : 0.004 0.059 1762 Dihedral : 7.301 59.817 1608 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.94 % Allowed : 12.75 % 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: 1.48 (0.25), residues: 1278 helix: 2.21 (0.22), residues: 550 sheet: 1.62 (0.33), residues: 256 loop : -0.94 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 567 HIS 0.003 0.001 HIS B 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 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 1.125 Fit side-chains REVERT: B 45 LYS cc_start: 0.7912 (mmtt) cc_final: 0.6896 (tptp) REVERT: B 287 CYS cc_start: 0.7341 (p) cc_final: 0.6835 (p) REVERT: B 429 GLN cc_start: 0.7463 (mm110) cc_final: 0.7234 (mm110) REVERT: B 449 PHE cc_start: 0.7753 (m-80) cc_final: 0.6967 (t80) REVERT: B 451 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7679 (tttm) REVERT: B 659 ASN cc_start: 0.7921 (m110) cc_final: 0.7452 (OUTLIER) REVERT: A 45 LYS cc_start: 0.7909 (mmtt) cc_final: 0.6905 (tptp) REVERT: A 287 CYS cc_start: 0.7373 (p) cc_final: 0.6863 (p) REVERT: A 449 PHE cc_start: 0.7786 (m-80) cc_final: 0.6976 (t80) REVERT: A 451 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7686 (tttm) REVERT: A 634 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.5685 (p90) REVERT: A 675 MET cc_start: 0.9039 (mtm) cc_final: 0.8811 (mtp) REVERT: A 729 LYS cc_start: 0.7959 (mtmm) cc_final: 0.7048 (mmpt) outliers start: 33 outliers final: 22 residues processed: 135 average time/residue: 1.0364 time to fit residues: 153.2513 Evaluate side-chains 134 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 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 181 LYS Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 634 PHE Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 663 THR 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: 0.7980 chunk 30 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 HIS B 590 ASN B 728 ASN A 450 HIS A 571 HIS A 590 ASN A 728 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.144478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.112336 restraints weight = 10429.825| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.87 r_work: 0.3173 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10622 Z= 0.234 Angle : 0.535 6.997 14378 Z= 0.284 Chirality : 0.044 0.157 1714 Planarity : 0.004 0.059 1762 Dihedral : 7.281 59.153 1608 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.03 % Allowed : 13.10 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.51 (0.25), residues: 1278 helix: 2.20 (0.22), residues: 554 sheet: 1.64 (0.33), residues: 256 loop : -0.90 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 567 HIS 0.003 0.001 HIS A 571 PHE 0.011 0.001 PHE A 528 TYR 0.018 0.001 TYR A 650 ARG 0.004 0.000 ARG A 687 *********************** 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 150 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 1.178 Fit side-chains REVERT: B 45 LYS cc_start: 0.7919 (mmtt) cc_final: 0.6895 (tptp) REVERT: B 48 GLU cc_start: 0.8206 (tt0) cc_final: 0.7992 (tt0) REVERT: B 287 CYS cc_start: 0.7418 (p) cc_final: 0.6906 (p) REVERT: B 429 GLN cc_start: 0.7472 (mm110) cc_final: 0.7245 (mm110) REVERT: B 449 PHE cc_start: 0.7765 (m-80) cc_final: 0.6992 (t80) REVERT: B 451 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7702 (tttm) REVERT: B 659 ASN cc_start: 0.7896 (m110) cc_final: 0.7453 (OUTLIER) REVERT: B 729 LYS cc_start: 0.7938 (mtmm) cc_final: 0.7024 (mmmt) REVERT: A 45 LYS cc_start: 0.7922 (mmtt) cc_final: 0.6896 (tptp) REVERT: A 287 CYS cc_start: 0.7362 (p) cc_final: 0.6873 (p) REVERT: A 449 PHE cc_start: 0.7799 (m-80) cc_final: 0.7004 (t80) REVERT: A 451 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7705 (tttm) REVERT: A 634 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.5663 (p90) REVERT: A 675 MET cc_start: 0.9037 (mtm) cc_final: 0.8717 (mtp) REVERT: A 729 LYS cc_start: 0.7961 (mtmm) cc_final: 0.7054 (mmmt) outliers start: 34 outliers final: 28 residues processed: 138 average time/residue: 0.9937 time to fit residues: 150.8791 Evaluate side-chains 142 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 579 THR Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 634 PHE Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 634 PHE Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 728 ASN 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: 0.9980 chunk 72 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 HIS B 571 HIS B 590 ASN ** B 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS A 590 ASN ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.144329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.112052 restraints weight = 10489.544| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.88 r_work: 0.3170 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10622 Z= 0.250 Angle : 0.548 6.876 14378 Z= 0.289 Chirality : 0.044 0.156 1714 Planarity : 0.004 0.059 1762 Dihedral : 7.281 60.409 1608 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.67 % Allowed : 13.55 % Favored : 83.78 % 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: 1.47 (0.24), residues: 1278 helix: 2.16 (0.22), residues: 554 sheet: 1.53 (0.33), residues: 262 loop : -0.89 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 567 HIS 0.003 0.001 HIS B 571 PHE 0.011 0.001 PHE A 528 TYR 0.018 0.001 TYR A 650 ARG 0.004 0.000 ARG B 687 ********************** 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 142 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 1.173 Fit side-chains REVERT: B 45 LYS cc_start: 0.7921 (mmtt) cc_final: 0.6878 (tptp) REVERT: B 48 GLU cc_start: 0.8199 (tt0) cc_final: 0.7990 (tt0) REVERT: B 287 CYS cc_start: 0.7424 (p) cc_final: 0.6924 (p) REVERT: B 429 GLN cc_start: 0.7485 (mm110) cc_final: 0.7256 (mm110) REVERT: B 449 PHE cc_start: 0.7764 (m-80) cc_final: 0.6985 (t80) REVERT: B 451 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7701 (tttm) REVERT: B 659 ASN cc_start: 0.7921 (m110) cc_final: 0.7482 (OUTLIER) REVERT: B 729 LYS cc_start: 0.8017 (mtmm) cc_final: 0.7082 (mmmt) REVERT: A 45 LYS cc_start: 0.7927 (mmtt) cc_final: 0.6897 (tptp) REVERT: A 287 CYS cc_start: 0.7431 (p) cc_final: 0.6932 (p) REVERT: A 449 PHE cc_start: 0.7805 (m-80) cc_final: 0.6999 (t80) REVERT: A 451 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7713 (tttm) REVERT: A 634 PHE cc_start: 0.7138 (OUTLIER) cc_final: 0.5615 (p90) REVERT: A 675 MET cc_start: 0.9041 (mtm) cc_final: 0.8721 (mtp) REVERT: A 729 LYS cc_start: 0.8027 (mtmm) cc_final: 0.7084 (mmmt) outliers start: 30 outliers final: 27 residues processed: 131 average time/residue: 1.0291 time to fit residues: 148.2930 Evaluate side-chains 138 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 579 THR Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 634 PHE Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 634 PHE Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 727 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 HIS B 590 ASN B 728 ASN A 450 HIS A 590 ASN 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 = 0.143590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.111383 restraints weight = 10405.715| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.86 r_work: 0.3137 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10622 Z= 0.357 Angle : 0.602 6.954 14378 Z= 0.315 Chirality : 0.047 0.155 1714 Planarity : 0.004 0.061 1762 Dihedral : 7.477 64.052 1608 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.94 % Allowed : 13.55 % Favored : 83.51 % 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: 1.32 (0.24), residues: 1278 helix: 2.02 (0.22), residues: 554 sheet: 1.53 (0.33), residues: 262 loop : -0.99 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 717 HIS 0.004 0.001 HIS B 450 PHE 0.013 0.002 PHE B 528 TYR 0.019 0.002 TYR A 650 ARG 0.004 0.000 ARG A 687 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6464.28 seconds wall clock time: 115 minutes 10.62 seconds (6910.62 seconds total)