Starting phenix.real_space_refine on Sun Dec 29 15:04:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hip_34825/12_2024/8hip_34825.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hip_34825/12_2024/8hip_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_34825/12_2024/8hip_34825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hip_34825/12_2024/8hip_34825.map" model { file = "/net/cci-nas-00/data/ceres_data/8hip_34825/12_2024/8hip_34825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hip_34825/12_2024/8hip_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-5532/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: 6.63, per 1000 atoms: 0.64 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: 2.15 Conformation dependent library (CDL) restraints added in 1.3 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: 1.08 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: 3.14 Time building geometry restraints manager: 2.47 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: 1.420 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: 0.080 Set scattering table: 0.100 Process input model: 26.620 Find NCS groups from input model: 0.300 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:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.050 ------------------------------------------------------------------------------- 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 : 1.142 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: 1.1212 time to fit residues: 253.8611 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 : 1.079 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 1.001 Fit side-chains REVERT: B 45 LYS cc_start: 0.7943 (mmpt) cc_final: 0.6989 (tptp) REVERT: B 52 GLU cc_start: 0.7559 (mp0) cc_final: 0.7152 (mp0) REVERT: B 237 ILE cc_start: 0.7354 (mt) cc_final: 0.6357 (mt) REVERT: B 240 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.6187 (ttp-170) REVERT: B 449 PHE cc_start: 0.7495 (m-80) cc_final: 0.6981 (t80) REVERT: B 451 LYS cc_start: 0.8439 (tmmt) cc_final: 0.7994 (tmmt) REVERT: B 634 PHE cc_start: 0.7417 (m-80) cc_final: 0.6145 (p90) REVERT: B 729 LYS cc_start: 0.7816 (mtmm) cc_final: 0.7079 (mmmt) REVERT: A 45 LYS cc_start: 0.7948 (mmpt) cc_final: 0.6997 (tptp) REVERT: A 52 GLU cc_start: 0.7570 (mp0) cc_final: 0.7158 (mp0) REVERT: A 237 ILE cc_start: 0.7361 (mt) cc_final: 0.6381 (mt) REVERT: A 240 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.6267 (ttp-170) REVERT: A 449 PHE cc_start: 0.7519 (m-80) cc_final: 0.6990 (t80) REVERT: A 451 LYS cc_start: 0.8440 (tmmt) cc_final: 0.8001 (tmmt) REVERT: A 634 PHE cc_start: 0.7393 (m-80) cc_final: 0.6142 (p90) REVERT: A 675 MET cc_start: 0.8607 (mtm) cc_final: 0.8369 (mtp) REVERT: A 729 LYS cc_start: 0.7810 (mtmm) cc_final: 0.7063 (mmmt) outliers start: 31 outliers final: 12 residues processed: 166 average time/residue: 1.1036 time to fit residues: 199.2720 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 : 1.117 ------------------------------------------------------------------------------- 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 64 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 79 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 0.0370 chunk 125 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1826 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= 0.204 Angle : 0.563 6.890 14378 Z= 0.300 Chirality : 0.044 0.164 1714 Planarity : 0.004 0.062 1762 Dihedral : 8.407 77.375 1608 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.48 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: 0.46 (0.23), residues: 1278 helix: 1.05 (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 0.001 TRP B 567 HIS 0.004 0.001 HIS A 740 PHE 0.011 0.001 PHE B 528 TYR 0.018 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 162 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 1.210 Fit side-chains REVERT: B 45 LYS cc_start: 0.7919 (mmpt) cc_final: 0.6945 (tptp) REVERT: B 52 GLU cc_start: 0.7593 (mp0) cc_final: 0.7125 (mp0) REVERT: B 176 ASP cc_start: 0.6960 (OUTLIER) cc_final: 0.6748 (p0) REVERT: B 449 PHE cc_start: 0.7351 (m-80) cc_final: 0.6934 (t80) REVERT: B 634 PHE cc_start: 0.7327 (m-80) cc_final: 0.6085 (p90) REVERT: B 729 LYS cc_start: 0.7790 (mtmm) cc_final: 0.7029 (mmmt) REVERT: B 766 ILE cc_start: 0.7800 (tp) cc_final: 0.7585 (tp) REVERT: A 45 LYS cc_start: 0.7911 (mmpt) cc_final: 0.6986 (tptp) REVERT: A 52 GLU cc_start: 0.7596 (mp0) cc_final: 0.7120 (mp0) REVERT: A 449 PHE cc_start: 0.7406 (m-80) cc_final: 0.6944 (t80) REVERT: A 634 PHE cc_start: 0.7369 (m-80) cc_final: 0.6176 (p90) REVERT: A 675 MET cc_start: 0.8487 (mtm) cc_final: 0.8209 (mtp) REVERT: A 729 LYS cc_start: 0.7794 (mtmm) cc_final: 0.7031 (mmmt) outliers start: 29 outliers final: 16 residues processed: 150 average time/residue: 1.0014 time to fit residues: 165.0369 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 : 1.167 ------------------------------------------------------------------------------- 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 176 ASP 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 115 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 0.0070 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 overall best weight: 0.8602 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10622 Z= 0.256 Angle : 0.563 7.132 14378 Z= 0.297 Chirality : 0.045 0.160 1714 Planarity : 0.004 0.062 1762 Dihedral : 7.902 62.957 1608 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.57 % Allowed : 11.85 % 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: 0.94 (0.24), residues: 1278 helix: 1.72 (0.22), residues: 534 sheet: 1.28 (0.32), residues: 270 loop : -1.09 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 567 HIS 0.003 0.001 HIS A 450 PHE 0.013 0.001 PHE A 528 TYR 0.019 0.001 TYR A 650 ARG 0.002 0.000 ARG A 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 165 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 1.069 Fit side-chains REVERT: B 45 LYS cc_start: 0.7868 (mmpt) cc_final: 0.6931 (tptp) REVERT: B 52 GLU cc_start: 0.7593 (mp0) cc_final: 0.7068 (mp0) REVERT: B 287 CYS cc_start: 0.7069 (p) cc_final: 0.6607 (p) REVERT: B 449 PHE cc_start: 0.7396 (m-80) cc_final: 0.6970 (t80) REVERT: B 451 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7691 (tttm) REVERT: B 634 PHE cc_start: 0.7246 (m-80) cc_final: 0.6024 (p90) REVERT: B 659 ASN cc_start: 0.7295 (m110) cc_final: 0.7005 (OUTLIER) REVERT: B 729 LYS cc_start: 0.7809 (mtmm) cc_final: 0.7068 (mmmt) REVERT: A 45 LYS cc_start: 0.7856 (mmpt) cc_final: 0.6976 (tptp) REVERT: A 52 GLU cc_start: 0.7620 (mp0) cc_final: 0.7071 (mp0) REVERT: A 287 CYS cc_start: 0.7070 (p) cc_final: 0.6610 (p) REVERT: A 449 PHE cc_start: 0.7416 (m-80) cc_final: 0.6983 (t80) REVERT: A 451 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7688 (tttm) REVERT: A 634 PHE cc_start: 0.7240 (m-80) cc_final: 0.6024 (p90) REVERT: A 675 MET cc_start: 0.8516 (mtm) cc_final: 0.8220 (mtp) REVERT: A 729 LYS cc_start: 0.7796 (mtmm) cc_final: 0.7043 (mmmt) outliers start: 40 outliers final: 23 residues processed: 152 average time/residue: 1.0161 time to fit residues: 169.2562 Evaluate side-chains 141 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 105 optimal weight: 0.4980 chunk 85 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 31 optimal weight: 0.0980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10622 Z= 0.265 Angle : 0.561 6.811 14378 Z= 0.296 Chirality : 0.045 0.158 1714 Planarity : 0.004 0.062 1762 Dihedral : 7.695 58.624 1608 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.21 % Allowed : 12.30 % Favored : 84.49 % 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: 1.15 (0.24), residues: 1278 helix: 1.89 (0.22), residues: 538 sheet: 1.41 (0.32), residues: 266 loop : -0.98 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 567 HIS 0.003 0.001 HIS B 450 PHE 0.012 0.001 PHE B 528 TYR 0.018 0.002 TYR A 650 ARG 0.003 0.000 ARG A 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 159 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 1.081 Fit side-chains REVERT: B 45 LYS cc_start: 0.7897 (mmtt) cc_final: 0.6980 (tptp) REVERT: B 449 PHE cc_start: 0.7398 (m-80) cc_final: 0.6967 (t80) REVERT: B 451 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7643 (tttm) REVERT: B 634 PHE cc_start: 0.7354 (m-80) cc_final: 0.6073 (p90) REVERT: B 729 LYS cc_start: 0.7779 (mtmm) cc_final: 0.7024 (mmmt) REVERT: A 45 LYS cc_start: 0.7870 (mmtt) cc_final: 0.7012 (tptp) REVERT: A 52 GLU cc_start: 0.7606 (mp0) cc_final: 0.7039 (mp0) REVERT: A 240 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7488 (ttp-170) REVERT: A 449 PHE cc_start: 0.7418 (m-80) cc_final: 0.6982 (t80) REVERT: A 451 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7643 (tttm) REVERT: A 634 PHE cc_start: 0.7341 (m-80) cc_final: 0.6106 (p90) REVERT: A 675 MET cc_start: 0.8517 (mtm) cc_final: 0.8207 (mtp) REVERT: A 729 LYS cc_start: 0.7786 (mtmm) cc_final: 0.7029 (mmmt) outliers start: 36 outliers final: 23 residues processed: 145 average time/residue: 1.0245 time to fit residues: 163.2635 Evaluate side-chains 141 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 659 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 118 THR 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 240 ARG 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.1980 chunk 111 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 0.0170 chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 overall best weight: 0.7420 ------------------------------------------------------------------------------- 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 660 GLN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2133 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= 0.231 Angle : 0.541 6.745 14378 Z= 0.286 Chirality : 0.044 0.157 1714 Planarity : 0.004 0.060 1762 Dihedral : 7.491 59.400 1608 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.30 % Allowed : 12.83 % 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: 1.26 (0.24), residues: 1278 helix: 2.04 (0.22), residues: 548 sheet: 1.42 (0.33), residues: 262 loop : -1.02 (0.29), residues: 468 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 0.012 0.001 PHE A 528 TYR 0.018 0.001 TYR A 650 ARG 0.003 0.000 ARG B 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 153 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.7899 (mmtt) cc_final: 0.7001 (tptp) REVERT: B 449 PHE cc_start: 0.7348 (m-80) cc_final: 0.6947 (t80) REVERT: B 451 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7625 (tttm) REVERT: B 729 LYS cc_start: 0.7736 (mtmm) cc_final: 0.6979 (mmmt) REVERT: A 45 LYS cc_start: 0.7873 (mmtt) cc_final: 0.6992 (tptp) REVERT: A 449 PHE cc_start: 0.7411 (m-80) cc_final: 0.6981 (t80) REVERT: A 451 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7622 (tttm) REVERT: A 675 MET cc_start: 0.8501 (mtm) cc_final: 0.8191 (mtp) REVERT: A 729 LYS cc_start: 0.7743 (mtmm) cc_final: 0.6988 (mmmt) outliers start: 37 outliers final: 28 residues processed: 138 average time/residue: 0.9606 time to fit residues: 146.2821 Evaluate side-chains 143 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 634 PHE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 772 SER 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 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 772 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.0770 chunk 13 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- 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 660 GLN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10622 Z= 0.219 Angle : 0.534 6.655 14378 Z= 0.283 Chirality : 0.043 0.157 1714 Planarity : 0.004 0.060 1762 Dihedral : 7.387 59.646 1608 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.65 % Allowed : 12.39 % 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: 2.16 (0.22), residues: 546 sheet: 1.57 (0.33), residues: 256 loop : -1.03 (0.29), residues: 476 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 164 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 1.130 Fit side-chains REVERT: B 45 LYS cc_start: 0.7918 (mmtt) cc_final: 0.7022 (tptp) REVERT: B 287 CYS cc_start: 0.6767 (p) cc_final: 0.6208 (p) REVERT: B 429 GLN cc_start: 0.7395 (mm110) cc_final: 0.7165 (mm110) REVERT: B 449 PHE cc_start: 0.7348 (m-80) cc_final: 0.6949 (t80) REVERT: B 451 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7580 (tttm) REVERT: B 592 LEU cc_start: 0.8360 (tp) cc_final: 0.8099 (mt) REVERT: B 729 LYS cc_start: 0.7720 (mtmm) cc_final: 0.6965 (mmmt) REVERT: A 45 LYS cc_start: 0.7891 (mmtt) cc_final: 0.7000 (tptp) REVERT: A 287 CYS cc_start: 0.6789 (p) cc_final: 0.6228 (p) REVERT: A 449 PHE cc_start: 0.7409 (m-80) cc_final: 0.6983 (t80) REVERT: A 451 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7579 (tttm) REVERT: A 592 LEU cc_start: 0.8345 (tp) cc_final: 0.8091 (mt) REVERT: A 675 MET cc_start: 0.8543 (mtm) cc_final: 0.8237 (mtp) REVERT: A 729 LYS cc_start: 0.7724 (mtmm) cc_final: 0.6974 (mmmt) outliers start: 41 outliers final: 31 residues processed: 147 average time/residue: 0.9783 time to fit residues: 158.4106 Evaluate side-chains 149 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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 634 PHE Chi-restraints excluded: chain B residue 659 ASN Chi-restraints excluded: chain B residue 663 THR 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 6.9990 chunk 73 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 HIS B 571 HIS B 590 ASN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS A 590 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10622 Z= 0.223 Angle : 0.534 6.960 14378 Z= 0.283 Chirality : 0.043 0.157 1714 Planarity : 0.004 0.059 1762 Dihedral : 7.329 59.591 1608 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.21 % Allowed : 12.39 % Favored : 84.40 % 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: 1.43 (0.24), residues: 1278 helix: 2.22 (0.22), residues: 546 sheet: 1.60 (0.33), residues: 256 loop : -1.00 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 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 B 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 152 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 1.141 Fit side-chains REVERT: B 45 LYS cc_start: 0.7837 (mmtt) cc_final: 0.6999 (tptp) REVERT: B 429 GLN cc_start: 0.7408 (mm110) cc_final: 0.7185 (mm110) REVERT: B 449 PHE cc_start: 0.7346 (m-80) cc_final: 0.6947 (t80) REVERT: B 451 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7567 (tttm) REVERT: A 45 LYS cc_start: 0.7916 (mmtt) cc_final: 0.7016 (tptp) REVERT: A 449 PHE cc_start: 0.7407 (m-80) cc_final: 0.6981 (t80) REVERT: A 451 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7568 (tttm) REVERT: A 675 MET cc_start: 0.8541 (mtm) cc_final: 0.8236 (mtp) REVERT: A 729 LYS cc_start: 0.7824 (mtmm) cc_final: 0.7004 (mmmt) outliers start: 36 outliers final: 26 residues processed: 139 average time/residue: 0.9910 time to fit residues: 151.3931 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 : 1.157 ------------------------------------------------------------------------------- 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 659 ASN Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 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 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 118 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 571 HIS A 590 ASN A 728 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10622 Z= 0.299 Angle : 0.570 7.294 14378 Z= 0.300 Chirality : 0.045 0.172 1714 Planarity : 0.004 0.061 1762 Dihedral : 7.428 58.900 1608 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.03 % Allowed : 12.92 % 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: 1.36 (0.24), residues: 1278 helix: 2.12 (0.22), residues: 550 sheet: 1.49 (0.33), residues: 262 loop : -1.00 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 567 HIS 0.003 0.001 HIS A 450 PHE 0.012 0.002 PHE A 528 TYR 0.018 0.002 TYR A 650 ARG 0.004 0.000 ARG B 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 152 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.7845 (mmtt) cc_final: 0.6985 (tptp) REVERT: B 429 GLN cc_start: 0.7430 (mm110) cc_final: 0.7190 (mm110) REVERT: B 449 PHE cc_start: 0.7404 (m-80) cc_final: 0.6989 (t80) REVERT: B 451 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7589 (tttm) REVERT: B 729 LYS cc_start: 0.7826 (mtmm) cc_final: 0.7025 (mmmt) REVERT: A 45 LYS cc_start: 0.7839 (mmtt) cc_final: 0.6973 (tptp) REVERT: A 449 PHE cc_start: 0.7426 (m-80) cc_final: 0.6995 (t80) REVERT: A 451 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7583 (tttm) REVERT: A 675 MET cc_start: 0.8516 (mtm) cc_final: 0.8210 (mtp) REVERT: A 729 LYS cc_start: 0.7829 (mtmm) cc_final: 0.7031 (mmmt) outliers start: 34 outliers final: 29 residues processed: 139 average time/residue: 1.0268 time to fit residues: 156.9058 Evaluate side-chains 146 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 659 ASN 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 579 THR Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 634 PHE Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 728 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 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 571 HIS B 590 ASN B 728 ASN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS A 571 HIS A 590 ASN A 728 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2258 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= 0.241 Angle : 0.550 7.283 14378 Z= 0.291 Chirality : 0.044 0.155 1714 Planarity : 0.004 0.060 1762 Dihedral : 7.367 60.026 1608 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.76 % Allowed : 13.37 % 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: 1.40 (0.24), residues: 1278 helix: 2.20 (0.22), residues: 546 sheet: 1.50 (0.33), residues: 262 loop : -1.00 (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 B 571 PHE 0.011 0.001 PHE B 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 147 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.7841 (mmtt) cc_final: 0.6961 (tptp) REVERT: B 429 GLN cc_start: 0.7420 (mm110) cc_final: 0.7200 (mm110) REVERT: B 449 PHE cc_start: 0.7349 (m-80) cc_final: 0.6956 (t80) REVERT: B 451 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7578 (tttm) REVERT: B 729 LYS cc_start: 0.7780 (mtmm) cc_final: 0.6971 (mmmt) REVERT: A 45 LYS cc_start: 0.7832 (mmtt) cc_final: 0.7006 (tptp) REVERT: A 449 PHE cc_start: 0.7419 (m-80) cc_final: 0.6991 (t80) REVERT: A 451 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7575 (tttm) REVERT: A 675 MET cc_start: 0.8551 (mtm) cc_final: 0.8239 (mtp) REVERT: A 729 LYS cc_start: 0.7894 (mtmm) cc_final: 0.7068 (mmmt) outliers start: 31 outliers final: 30 residues processed: 137 average time/residue: 1.0413 time to fit residues: 156.2601 Evaluate side-chains 143 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 659 ASN Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 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 579 THR Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 634 PHE Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 728 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 0.0000 chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 overall best weight: 0.6986 ------------------------------------------------------------------------------- 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 728 ASN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.145067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.112841 restraints weight = 10373.293| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.87 r_work: 0.3165 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.251 10622 Z= 0.403 Angle : 1.020 59.200 14378 Z= 0.635 Chirality : 0.054 1.170 1714 Planarity : 0.008 0.154 1762 Dihedral : 7.443 60.030 1608 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.85 % Allowed : 13.28 % Favored : 83.87 % Cbeta Deviations : 0.32 % 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: 1.41 (0.24), residues: 1278 helix: 2.17 (0.22), residues: 550 sheet: 1.50 (0.33), residues: 262 loop : -0.98 (0.30), residues: 466 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 0.021 0.001 PHE B 634 TYR 0.018 0.001 TYR A 650 ARG 0.003 0.000 ARG B 687 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3403.21 seconds wall clock time: 62 minutes 14.71 seconds (3734.71 seconds total)