Starting phenix.real_space_refine on Thu Jun 5 23:22:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wi0_32517/06_2025/7wi0_32517.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wi0_32517/06_2025/7wi0_32517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wi0_32517/06_2025/7wi0_32517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wi0_32517/06_2025/7wi0_32517.map" model { file = "/net/cci-nas-00/data/ceres_data/7wi0_32517/06_2025/7wi0_32517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wi0_32517/06_2025/7wi0_32517.cif" } resolution = 3.82 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= 0.000 sd= 0.012 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 4303 2.51 5 N 1148 2.21 5 O 1342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6823 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain: "B" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 940 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "C" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 929 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "E" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 830 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 935 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.50, per 1000 atoms: 0.81 Number of scatterers: 6823 At special positions: 0 Unit cell: (86.358, 94.916, 122.146, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1342 8.00 N 1148 7.00 C 4303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.01 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " 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 NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 938.0 milliseconds 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1606 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 22 sheets defined 2.7% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.848A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 removed outlier: 3.620A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 389' Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.563A pdb=" N ASP C 90 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 91 " --> pdb=" O VAL C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.807A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.726A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 454 removed outlier: 3.608A pdb=" N ARG A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.636A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 20 removed outlier: 3.689A pdb=" N LEU B 18 " --> pdb=" O MET B 83 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET B 83 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP B 73 " --> pdb=" O THR B 78 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B 80 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 6 through 7 removed outlier: 3.508A pdb=" N LEU C 18 " --> pdb=" O MET C 83 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR C 69 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12 removed outlier: 7.932A pdb=" N MET C 34 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N SER C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 7 removed outlier: 6.722A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AB3, first strand: chain 'D' and resid 53 through 54 removed outlier: 5.405A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE D 48 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN D 38 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR D 85 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.603A pdb=" N PHE E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.674A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.522A pdb=" N GLN E 37 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN E 89 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR E 85 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.909A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.054A pdb=" N GLU H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL H 119 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA H 92 " --> pdb=" O VAL H 119 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 18 through 19 removed outlier: 3.506A pdb=" N ASP H 82 " --> pdb=" O THR H 69 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 72 through 73 removed outlier: 3.561A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.646A pdb=" N TYR L 88 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL L 107 " --> pdb=" O ALA L 86 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA L 86 " --> pdb=" O VAL L 107 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.646A pdb=" N TYR L 88 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL L 107 " --> pdb=" O ALA L 86 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA L 86 " --> pdb=" O VAL L 107 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER L 92 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL L 100 " --> pdb=" O SER L 92 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 17 through 21 158 hydrogen bonds defined for protein. 384 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.77 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1101 1.26 - 1.40: 1858 1.40 - 1.54: 3952 1.54 - 1.68: 39 1.68 - 1.83: 40 Bond restraints: 6990 Sorted by residual: bond pdb=" C THR C 78 " pdb=" O THR C 78 " ideal model delta sigma weight residual 1.234 1.462 -0.228 1.22e-02 6.72e+03 3.49e+02 bond pdb=" C SER B 106 " pdb=" O SER B 106 " ideal model delta sigma weight residual 1.234 1.117 0.117 1.19e-02 7.06e+03 9.66e+01 bond pdb=" C VAL B 101 " pdb=" O VAL B 101 " ideal model delta sigma weight residual 1.235 1.150 0.084 1.45e-02 4.76e+03 3.38e+01 bond pdb=" CA SER B 106 " pdb=" C SER B 106 " ideal model delta sigma weight residual 1.521 1.452 0.069 1.22e-02 6.72e+03 3.22e+01 bond pdb=" C THR C 78 " pdb=" N LEU C 79 " ideal model delta sigma weight residual 1.331 1.401 -0.070 1.29e-02 6.01e+03 2.94e+01 ... (remaining 6985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 9380 3.67 - 7.34: 101 7.34 - 11.01: 15 11.01 - 14.68: 1 14.68 - 18.36: 2 Bond angle restraints: 9499 Sorted by residual: angle pdb=" N GLY B 105 " pdb=" CA GLY B 105 " pdb=" C GLY B 105 " ideal model delta sigma weight residual 112.49 130.85 -18.36 1.21e+00 6.83e-01 2.30e+02 angle pdb=" N VAL B 101 " pdb=" CA VAL B 101 " pdb=" C VAL B 101 " ideal model delta sigma weight residual 112.29 121.27 -8.98 9.40e-01 1.13e+00 9.12e+01 angle pdb=" N ASP B 112 " pdb=" CA ASP B 112 " pdb=" C ASP B 112 " ideal model delta sigma weight residual 111.36 120.42 -9.06 1.09e+00 8.42e-01 6.91e+01 angle pdb=" N ALA B 102 " pdb=" CA ALA B 102 " pdb=" C ALA B 102 " ideal model delta sigma weight residual 109.59 98.35 11.24 1.47e+00 4.63e-01 5.85e+01 angle pdb=" O SER B 106 " pdb=" C SER B 106 " pdb=" N SER B 107 " ideal model delta sigma weight residual 123.46 116.86 6.60 9.90e-01 1.02e+00 4.44e+01 ... (remaining 9494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3694 17.97 - 35.95: 350 35.95 - 53.92: 53 53.92 - 71.89: 9 71.89 - 89.87: 8 Dihedral angle restraints: 4114 sinusoidal: 1576 harmonic: 2538 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 149.43 -56.43 1 1.00e+01 1.00e-02 4.29e+01 dihedral pdb=" CA SER E 93 " pdb=" C SER E 93 " pdb=" N TYR E 94 " pdb=" CA TYR E 94 " ideal model delta harmonic sigma weight residual -180.00 -158.77 -21.23 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 88 " pdb=" CB CYS D 88 " ideal model delta sinusoidal sigma weight residual -86.00 -121.59 35.59 1 1.00e+01 1.00e-02 1.79e+01 ... (remaining 4111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 916 0.095 - 0.189: 97 0.189 - 0.284: 13 0.284 - 0.379: 1 0.379 - 0.474: 1 Chirality restraints: 1028 Sorted by residual: chirality pdb=" CA VAL B 101 " pdb=" N VAL B 101 " pdb=" C VAL B 101 " pdb=" CB VAL B 101 " both_signs ideal model delta sigma weight residual False 2.44 1.97 0.47 2.00e-01 2.50e+01 5.61e+00 chirality pdb=" CA SER B 107 " pdb=" N SER B 107 " pdb=" C SER B 107 " pdb=" CB SER B 107 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA TYR E 94 " pdb=" N TYR E 94 " pdb=" C TYR E 94 " pdb=" CB TYR E 94 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 1025 not shown) Planarity restraints: 1227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 77 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" C ASN C 77 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN C 77 " 0.018 2.00e-02 2.50e+03 pdb=" N THR C 78 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 372 " 0.043 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO A 373 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 45 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO L 46 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO L 46 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 46 " 0.035 5.00e-02 4.00e+02 ... (remaining 1224 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1858 2.79 - 3.32: 5543 3.32 - 3.85: 10966 3.85 - 4.37: 11967 4.37 - 4.90: 21668 Nonbonded interactions: 52002 Sorted by model distance: nonbonded pdb=" OE1 GLN H 6 " pdb=" OG1 THR H 117 " model vdw 2.265 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.272 3.040 nonbonded pdb=" OG SER D 63 " pdb=" O THR D 74 " model vdw 2.314 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.315 3.040 nonbonded pdb=" OD1 ASP B 90 " pdb=" OH TYR B 94 " model vdw 2.317 3.040 ... (remaining 51997 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 'D' and (resid 1 through 8 or resid 10 through 30 or resid 33 or resid 35 \ through 49 or resid 52 through 54 or resid 56 through 69 or resid 71 through 80 \ or resid 82 through 90 or resid 93 or resid 98 through 103 or resid 105 through \ 107)) selection = (chain 'E' and (resid 1 through 8 or resid 10 through 30 or resid 33 or resid 35 \ through 49 or resid 52 through 54 or resid 56 through 69 or resid 71 through 80 \ or resid 82 through 90 or resid 93 or resid 98 through 103 or resid 105 through \ 107)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.920 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 : 0.008 0.228 6998 Z= 0.490 Angle : 1.049 18.355 9516 Z= 0.635 Chirality : 0.064 0.474 1028 Planarity : 0.007 0.064 1226 Dihedral : 14.368 89.866 2487 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.60 % Favored : 91.28 % Rotamer: Outliers : 0.40 % Allowed : 10.08 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -4.32 (0.24), residues: 872 helix: -5.25 (0.15), residues: 30 sheet: -2.73 (0.25), residues: 349 loop : -2.85 (0.23), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 114 HIS 0.005 0.002 HIS L 36 PHE 0.019 0.002 PHE B 27 TYR 0.023 0.002 TYR C 95 ARG 0.005 0.000 ARG D 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 1) link_NAG-ASN : angle 1.84521 ( 3) hydrogen bonds : bond 0.30229 ( 155) hydrogen bonds : angle 10.94885 ( 384) SS BOND : bond 0.00810 ( 7) SS BOND : angle 1.30821 ( 14) covalent geometry : bond 0.00799 ( 6990) covalent geometry : angle 1.04817 ( 9499) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 226 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7452 (ttpt) REVERT: B 50 VAL cc_start: 0.9168 (p) cc_final: 0.8790 (p) REVERT: B 51 MET cc_start: 0.8872 (mmm) cc_final: 0.8489 (mmt) REVERT: B 116 GLN cc_start: 0.8414 (tp40) cc_final: 0.8191 (mm-40) REVERT: C 65 LYS cc_start: 0.7983 (ptpt) cc_final: 0.7657 (ttpt) REVERT: E 2 ILE cc_start: 0.7706 (mp) cc_final: 0.7208 (mp) REVERT: E 85 THR cc_start: 0.8060 (t) cc_final: 0.7840 (m) REVERT: E 90 GLN cc_start: 0.8712 (pp30) cc_final: 0.8374 (pp30) REVERT: H 62 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8251 (tm-30) REVERT: H 89 GLU cc_start: 0.7658 (mp0) cc_final: 0.7446 (mt-10) REVERT: L 63 ARG cc_start: 0.7981 (mtm-85) cc_final: 0.7772 (mtp-110) outliers start: 3 outliers final: 1 residues processed: 227 average time/residue: 0.2063 time to fit residues: 60.2878 Evaluate side-chains 167 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 512 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS D 31 ASN D 38 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN L 1 GLN L 36 HIS L 39 GLN L 40 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.128726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.105323 restraints weight = 11798.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.108380 restraints weight = 7195.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.110520 restraints weight = 5143.539| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6998 Z= 0.160 Angle : 0.649 7.444 9516 Z= 0.344 Chirality : 0.046 0.208 1028 Planarity : 0.005 0.049 1226 Dihedral : 5.549 39.177 1001 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 1.88 % Allowed : 19.76 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -3.53 (0.26), residues: 872 helix: -5.02 (0.20), residues: 18 sheet: -2.29 (0.26), residues: 347 loop : -2.29 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 47 HIS 0.003 0.001 HIS H 107 PHE 0.021 0.002 PHE B 29 TYR 0.027 0.002 TYR L 51 ARG 0.003 0.001 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00058 ( 1) link_NAG-ASN : angle 1.56039 ( 3) hydrogen bonds : bond 0.04533 ( 155) hydrogen bonds : angle 6.99307 ( 384) SS BOND : bond 0.00333 ( 7) SS BOND : angle 1.10461 ( 14) covalent geometry : bond 0.00358 ( 6990) covalent geometry : angle 0.64712 ( 9499) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: B 16 ARG cc_start: 0.8121 (ttm170) cc_final: 0.7897 (tpp80) REVERT: B 47 TRP cc_start: 0.8364 (t60) cc_final: 0.7774 (t60) REVERT: C 36 TRP cc_start: 0.7903 (m100) cc_final: 0.7488 (m100) REVERT: C 65 LYS cc_start: 0.8010 (ptpt) cc_final: 0.7656 (ttpt) REVERT: E 2 ILE cc_start: 0.7496 (mp) cc_final: 0.7253 (mp) REVERT: E 78 LEU cc_start: 0.8276 (mm) cc_final: 0.7896 (tt) REVERT: E 90 GLN cc_start: 0.8825 (pp30) cc_final: 0.8309 (pp30) REVERT: H 43 GLN cc_start: 0.8554 (mp10) cc_final: 0.7936 (mp10) REVERT: L 63 ARG cc_start: 0.8100 (mtm-85) cc_final: 0.7492 (ttp-110) outliers start: 14 outliers final: 3 residues processed: 201 average time/residue: 0.1832 time to fit residues: 48.9821 Evaluate side-chains 173 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain H residue 28 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 22 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 chunk 71 optimal weight: 5.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN D 6 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN H 62 GLN H 108 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.122738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.098804 restraints weight = 12326.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.101669 restraints weight = 7637.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.103684 restraints weight = 5566.881| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 6998 Z= 0.319 Angle : 0.758 8.489 9516 Z= 0.400 Chirality : 0.049 0.291 1028 Planarity : 0.006 0.056 1226 Dihedral : 5.713 41.959 996 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 4.84 % Allowed : 20.97 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -3.40 (0.27), residues: 872 helix: -5.12 (0.21), residues: 24 sheet: -2.28 (0.26), residues: 356 loop : -2.06 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 47 HIS 0.007 0.002 HIS L 36 PHE 0.025 0.002 PHE A 490 TYR 0.024 0.002 TYR E 94 ARG 0.004 0.001 ARG C 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 1) link_NAG-ASN : angle 2.19858 ( 3) hydrogen bonds : bond 0.04649 ( 155) hydrogen bonds : angle 6.69718 ( 384) SS BOND : bond 0.00515 ( 7) SS BOND : angle 1.34773 ( 14) covalent geometry : bond 0.00732 ( 6990) covalent geometry : angle 0.75618 ( 9499) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8467 (t60) cc_final: 0.7673 (t60) REVERT: C 36 TRP cc_start: 0.8038 (m100) cc_final: 0.7640 (m100) REVERT: C 86 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8168 (pp) REVERT: E 81 ASP cc_start: 0.7865 (t0) cc_final: 0.7638 (t0) REVERT: E 90 GLN cc_start: 0.8956 (pp30) cc_final: 0.8418 (pp30) REVERT: H 43 GLN cc_start: 0.8630 (mp10) cc_final: 0.8063 (mp10) REVERT: L 63 ARG cc_start: 0.8198 (mtm-85) cc_final: 0.7264 (mtp-110) REVERT: L 81 GLN cc_start: 0.7596 (mp-120) cc_final: 0.7376 (mp10) outliers start: 36 outliers final: 30 residues processed: 193 average time/residue: 0.1868 time to fit residues: 47.6804 Evaluate side-chains 191 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 83 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.126961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.103216 restraints weight = 12171.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.106280 restraints weight = 7340.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108409 restraints weight = 5235.973| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6998 Z= 0.145 Angle : 0.647 8.249 9516 Z= 0.334 Chirality : 0.044 0.214 1028 Planarity : 0.005 0.050 1226 Dihedral : 5.178 36.707 996 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 2.96 % Allowed : 23.79 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -3.08 (0.27), residues: 872 helix: -4.77 (0.29), residues: 18 sheet: -2.05 (0.26), residues: 373 loop : -1.87 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 47 HIS 0.003 0.001 HIS H 107 PHE 0.015 0.001 PHE A 490 TYR 0.027 0.001 TYR E 94 ARG 0.004 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00024 ( 1) link_NAG-ASN : angle 1.38381 ( 3) hydrogen bonds : bond 0.03392 ( 155) hydrogen bonds : angle 6.15570 ( 384) SS BOND : bond 0.00470 ( 7) SS BOND : angle 0.97043 ( 14) covalent geometry : bond 0.00329 ( 6990) covalent geometry : angle 0.64620 ( 9499) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: B 16 ARG cc_start: 0.8077 (ttm170) cc_final: 0.7805 (tpp80) REVERT: B 47 TRP cc_start: 0.8291 (t60) cc_final: 0.7744 (t60) REVERT: B 109 ASP cc_start: 0.8296 (t70) cc_final: 0.8038 (t70) REVERT: C 36 TRP cc_start: 0.7877 (m100) cc_final: 0.7611 (m100) REVERT: C 86 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8047 (pp) REVERT: E 90 GLN cc_start: 0.8823 (pp30) cc_final: 0.8356 (pp30) REVERT: H 43 GLN cc_start: 0.8598 (mp10) cc_final: 0.8113 (mp10) REVERT: L 63 ARG cc_start: 0.8197 (mtm-85) cc_final: 0.7580 (ttp-110) outliers start: 22 outliers final: 15 residues processed: 184 average time/residue: 0.1955 time to fit residues: 47.6079 Evaluate side-chains 174 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN L 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.126502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.102712 restraints weight = 11975.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.105742 restraints weight = 7303.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.107838 restraints weight = 5241.198| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6998 Z= 0.163 Angle : 0.650 9.405 9516 Z= 0.334 Chirality : 0.044 0.220 1028 Planarity : 0.005 0.053 1226 Dihedral : 5.045 34.664 996 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 3.90 % Allowed : 24.60 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -2.93 (0.27), residues: 872 helix: -4.69 (0.32), residues: 18 sheet: -1.95 (0.26), residues: 369 loop : -1.78 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 47 HIS 0.003 0.001 HIS L 36 PHE 0.015 0.001 PHE A 490 TYR 0.022 0.001 TYR E 94 ARG 0.004 0.000 ARG C 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00039 ( 1) link_NAG-ASN : angle 1.45921 ( 3) hydrogen bonds : bond 0.03372 ( 155) hydrogen bonds : angle 6.02925 ( 384) SS BOND : bond 0.00351 ( 7) SS BOND : angle 0.80527 ( 14) covalent geometry : bond 0.00376 ( 6990) covalent geometry : angle 0.64948 ( 9499) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: B 28 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.8075 (t) REVERT: B 47 TRP cc_start: 0.8219 (t60) cc_final: 0.7797 (t60) REVERT: B 109 ASP cc_start: 0.8382 (t70) cc_final: 0.8119 (t70) REVERT: C 36 TRP cc_start: 0.7925 (m100) cc_final: 0.7684 (m100) REVERT: C 86 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8087 (pp) REVERT: E 90 GLN cc_start: 0.8786 (pp30) cc_final: 0.8118 (pp30) REVERT: H 43 GLN cc_start: 0.8610 (mp10) cc_final: 0.8149 (mp10) REVERT: L 63 ARG cc_start: 0.8218 (mtm-85) cc_final: 0.7716 (mtm-85) outliers start: 29 outliers final: 18 residues processed: 183 average time/residue: 0.2165 time to fit residues: 52.2532 Evaluate side-chains 176 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 18 optimal weight: 3.9990 chunk 39 optimal weight: 0.0670 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 0.0980 chunk 65 optimal weight: 4.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.127060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.103213 restraints weight = 12094.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.106243 restraints weight = 7391.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.108345 restraints weight = 5316.651| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6998 Z= 0.161 Angle : 0.653 8.662 9516 Z= 0.336 Chirality : 0.044 0.218 1028 Planarity : 0.004 0.047 1226 Dihedral : 4.982 33.231 996 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.76 % Allowed : 24.60 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -2.74 (0.28), residues: 872 helix: -4.50 (0.42), residues: 12 sheet: -1.86 (0.26), residues: 370 loop : -1.66 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 47 HIS 0.004 0.001 HIS C 35 PHE 0.015 0.001 PHE A 490 TYR 0.024 0.001 TYR E 94 ARG 0.004 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00015 ( 1) link_NAG-ASN : angle 1.42538 ( 3) hydrogen bonds : bond 0.03287 ( 155) hydrogen bonds : angle 5.83380 ( 384) SS BOND : bond 0.00308 ( 7) SS BOND : angle 0.75074 ( 14) covalent geometry : bond 0.00372 ( 6990) covalent geometry : angle 0.65266 ( 9499) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: B 28 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8118 (t) REVERT: B 47 TRP cc_start: 0.8168 (t60) cc_final: 0.7821 (t60) REVERT: B 109 ASP cc_start: 0.8368 (t70) cc_final: 0.8154 (t70) REVERT: B 118 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8372 (p) REVERT: C 36 TRP cc_start: 0.7885 (m100) cc_final: 0.7684 (m100) REVERT: C 86 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8097 (pp) REVERT: E 90 GLN cc_start: 0.8731 (pp30) cc_final: 0.8254 (pp30) REVERT: H 43 GLN cc_start: 0.8615 (mp10) cc_final: 0.8186 (mp10) REVERT: L 63 ARG cc_start: 0.8165 (mtm-85) cc_final: 0.7451 (ttp-110) outliers start: 28 outliers final: 19 residues processed: 181 average time/residue: 0.1915 time to fit residues: 45.7342 Evaluate side-chains 176 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 65 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 0.0000 chunk 9 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN C 77 ASN D 27 GLN D 90 GLN L 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.128690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.105107 restraints weight = 11827.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108172 restraints weight = 7182.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.110346 restraints weight = 5135.001| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3445 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6998 Z= 0.127 Angle : 0.636 8.202 9516 Z= 0.324 Chirality : 0.043 0.188 1028 Planarity : 0.004 0.051 1226 Dihedral : 4.775 29.995 996 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.90 % Allowed : 25.13 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -2.52 (0.28), residues: 872 helix: -4.55 (0.39), residues: 12 sheet: -1.64 (0.26), residues: 373 loop : -1.57 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 47 HIS 0.003 0.001 HIS C 35 PHE 0.012 0.001 PHE A 490 TYR 0.023 0.001 TYR E 94 ARG 0.004 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00081 ( 1) link_NAG-ASN : angle 1.19728 ( 3) hydrogen bonds : bond 0.02979 ( 155) hydrogen bonds : angle 5.64141 ( 384) SS BOND : bond 0.00354 ( 7) SS BOND : angle 0.69016 ( 14) covalent geometry : bond 0.00295 ( 6990) covalent geometry : angle 0.63562 ( 9499) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: B 28 THR cc_start: 0.8244 (OUTLIER) cc_final: 0.8032 (t) REVERT: B 47 TRP cc_start: 0.8066 (t60) cc_final: 0.7800 (t60) REVERT: B 118 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8247 (p) REVERT: C 18 LEU cc_start: 0.7080 (mp) cc_final: 0.6820 (tp) REVERT: C 34 MET cc_start: 0.8993 (mmt) cc_final: 0.8773 (mmt) REVERT: C 86 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8016 (pp) REVERT: D 90 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7392 (pp30) REVERT: E 4 MET cc_start: 0.6376 (mmm) cc_final: 0.5952 (mmt) REVERT: H 43 GLN cc_start: 0.8597 (mp10) cc_final: 0.8166 (mp10) REVERT: L 63 ARG cc_start: 0.8161 (mtm-85) cc_final: 0.7561 (ttp-110) outliers start: 29 outliers final: 18 residues processed: 178 average time/residue: 0.2134 time to fit residues: 50.5992 Evaluate side-chains 176 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 75 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.128412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.104703 restraints weight = 11988.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.107809 restraints weight = 7267.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.109873 restraints weight = 5180.396| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6998 Z= 0.137 Angle : 0.654 8.706 9516 Z= 0.333 Chirality : 0.044 0.190 1028 Planarity : 0.004 0.048 1226 Dihedral : 4.759 28.527 996 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.63 % Allowed : 25.94 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -2.48 (0.28), residues: 872 helix: -4.57 (0.37), residues: 12 sheet: -1.62 (0.26), residues: 373 loop : -1.53 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 36 HIS 0.003 0.001 HIS C 35 PHE 0.012 0.001 PHE A 490 TYR 0.021 0.001 TYR E 94 ARG 0.006 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00043 ( 1) link_NAG-ASN : angle 1.23743 ( 3) hydrogen bonds : bond 0.03027 ( 155) hydrogen bonds : angle 5.56472 ( 384) SS BOND : bond 0.00442 ( 7) SS BOND : angle 0.74328 ( 14) covalent geometry : bond 0.00317 ( 6990) covalent geometry : angle 0.65406 ( 9499) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: B 28 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.8024 (t) REVERT: B 47 TRP cc_start: 0.8056 (t60) cc_final: 0.7790 (t60) REVERT: B 118 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8213 (p) REVERT: C 34 MET cc_start: 0.9009 (mmt) cc_final: 0.8801 (mmt) REVERT: C 86 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8078 (pp) REVERT: E 4 MET cc_start: 0.6401 (mmm) cc_final: 0.5939 (mmt) REVERT: E 90 GLN cc_start: 0.8734 (pp30) cc_final: 0.8383 (pp30) REVERT: H 43 GLN cc_start: 0.8590 (mp10) cc_final: 0.8203 (mp10) REVERT: L 63 ARG cc_start: 0.8200 (mtm-85) cc_final: 0.7576 (ttp-110) outliers start: 27 outliers final: 19 residues processed: 172 average time/residue: 0.2275 time to fit residues: 51.1695 Evaluate side-chains 169 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 66 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 27 optimal weight: 0.0970 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN L 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.124223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.101876 restraints weight = 12043.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.104909 restraints weight = 6941.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.107052 restraints weight = 4790.112| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6998 Z= 0.133 Angle : 0.649 8.743 9516 Z= 0.331 Chirality : 0.044 0.184 1028 Planarity : 0.004 0.051 1226 Dihedral : 4.734 26.459 996 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 3.09 % Allowed : 26.34 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -2.49 (0.28), residues: 872 helix: -4.61 (0.34), residues: 19 sheet: -1.59 (0.26), residues: 370 loop : -1.51 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 36 HIS 0.003 0.001 HIS C 35 PHE 0.011 0.001 PHE A 490 TYR 0.021 0.001 TYR E 94 ARG 0.012 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00041 ( 1) link_NAG-ASN : angle 1.20248 ( 3) hydrogen bonds : bond 0.02983 ( 155) hydrogen bonds : angle 5.53712 ( 384) SS BOND : bond 0.00394 ( 7) SS BOND : angle 0.66447 ( 14) covalent geometry : bond 0.00308 ( 6990) covalent geometry : angle 0.64851 ( 9499) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8013 (t60) cc_final: 0.7774 (t60) REVERT: B 118 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8196 (p) REVERT: C 86 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8072 (pp) REVERT: E 4 MET cc_start: 0.6375 (mmm) cc_final: 0.5927 (mmt) REVERT: E 90 GLN cc_start: 0.8759 (pp30) cc_final: 0.8380 (pp30) REVERT: H 43 GLN cc_start: 0.8593 (mp10) cc_final: 0.8159 (mp10) REVERT: L 63 ARG cc_start: 0.8270 (mtm-85) cc_final: 0.7612 (ttp-110) outliers start: 23 outliers final: 18 residues processed: 174 average time/residue: 0.2230 time to fit residues: 51.3708 Evaluate side-chains 170 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 0.0570 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 67 optimal weight: 0.1980 chunk 15 optimal weight: 0.0970 chunk 7 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.124347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.102099 restraints weight = 12052.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.105127 restraints weight = 6875.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.107291 restraints weight = 4728.027| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6998 Z= 0.135 Angle : 0.675 9.141 9516 Z= 0.343 Chirality : 0.044 0.203 1028 Planarity : 0.004 0.049 1226 Dihedral : 4.726 25.151 996 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.23 % Allowed : 26.34 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -2.43 (0.28), residues: 872 helix: -4.59 (0.37), residues: 18 sheet: -1.50 (0.26), residues: 370 loop : -1.53 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 36 HIS 0.003 0.001 HIS C 35 PHE 0.014 0.001 PHE H 64 TYR 0.024 0.001 TYR E 94 ARG 0.013 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00058 ( 1) link_NAG-ASN : angle 1.16100 ( 3) hydrogen bonds : bond 0.02949 ( 155) hydrogen bonds : angle 5.47068 ( 384) SS BOND : bond 0.00378 ( 7) SS BOND : angle 0.61381 ( 14) covalent geometry : bond 0.00313 ( 6990) covalent geometry : angle 0.67495 ( 9499) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8000 (t60) cc_final: 0.7795 (t60) REVERT: B 118 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8133 (p) REVERT: C 86 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8031 (pp) REVERT: E 90 GLN cc_start: 0.8749 (pp30) cc_final: 0.8013 (pp30) REVERT: H 23 LYS cc_start: 0.8573 (ttpp) cc_final: 0.8354 (ttpp) REVERT: H 43 GLN cc_start: 0.8588 (mp10) cc_final: 0.8149 (mp10) REVERT: L 63 ARG cc_start: 0.8264 (mtm-85) cc_final: 0.7590 (ttp-110) outliers start: 24 outliers final: 21 residues processed: 171 average time/residue: 0.1717 time to fit residues: 39.6214 Evaluate side-chains 176 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 0.0070 chunk 59 optimal weight: 9.9990 chunk 36 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.124088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.101464 restraints weight = 12033.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.104536 restraints weight = 6964.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.106690 restraints weight = 4812.986| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6998 Z= 0.140 Angle : 0.681 10.364 9516 Z= 0.344 Chirality : 0.044 0.202 1028 Planarity : 0.004 0.048 1226 Dihedral : 4.695 24.535 996 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 3.23 % Allowed : 26.75 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -2.39 (0.28), residues: 872 helix: -4.58 (0.37), residues: 18 sheet: -1.51 (0.26), residues: 377 loop : -1.46 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 36 HIS 0.003 0.001 HIS C 35 PHE 0.012 0.001 PHE A 490 TYR 0.029 0.001 TYR E 94 ARG 0.012 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00048 ( 1) link_NAG-ASN : angle 1.21896 ( 3) hydrogen bonds : bond 0.02973 ( 155) hydrogen bonds : angle 5.42316 ( 384) SS BOND : bond 0.00418 ( 7) SS BOND : angle 0.68893 ( 14) covalent geometry : bond 0.00325 ( 6990) covalent geometry : angle 0.68111 ( 9499) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3016.79 seconds wall clock time: 54 minutes 19.46 seconds (3259.46 seconds total)