Starting phenix.real_space_refine on Tue Mar 3 16:02:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wi0_32517/03_2026/7wi0_32517.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wi0_32517/03_2026/7wi0_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_32517/03_2026/7wi0_32517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wi0_32517/03_2026/7wi0_32517.map" model { file = "/net/cci-nas-00/data/ceres_data/7wi0_32517/03_2026/7wi0_32517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wi0_32517/03_2026/7wi0_32517.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.45, per 1000 atoms: 0.21 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: 0.52 Conformation dependent library (CDL) restraints added in 283.6 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: 0.29 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: 0.90 Time building geometry restraints manager: 0.73 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.500 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.480 ------------------------------------------------------------------------------- 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 : 6.73 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.000 ARG D 61 TYR 0.023 0.002 TYR C 95 PHE 0.019 0.002 PHE B 27 TRP 0.017 0.002 TRP B 114 HIS 0.005 0.002 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00799 ( 6990) covalent geometry : angle 1.04817 ( 9499) SS BOND : bond 0.00810 ( 7) SS BOND : angle 1.30821 ( 14) hydrogen bonds : bond 0.30229 ( 155) hydrogen bonds : angle 10.94885 ( 384) link_NAG-ASN : bond 0.00220 ( 1) link_NAG-ASN : angle 1.84521 ( 3) *********************** 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 : 0.270 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: 0.7453 (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: 0.8487 (mmt) REVERT: B 116 GLN cc_start: 0.8414 (tp40) cc_final: 0.8188 (mm-40) REVERT: C 65 LYS cc_start: 0.7983 (ptpt) cc_final: 0.7655 (ttpt) REVERT: C 76 LYS cc_start: 0.8675 (mtpp) cc_final: 0.8424 (mtpp) REVERT: E 2 ILE cc_start: 0.7706 (mp) cc_final: 0.7210 (mp) REVERT: E 85 THR cc_start: 0.8060 (t) cc_final: 0.7838 (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: 0.8252 (tm-30) REVERT: H 89 GLU cc_start: 0.7658 (mp0) cc_final: 0.7446 (mt-10) REVERT: L 53 ASN cc_start: 0.7528 (m-40) cc_final: 0.7328 (t0) REVERT: L 63 ARG cc_start: 0.7981 (mtm-85) cc_final: 0.7774 (mtp-110) outliers start: 3 outliers final: 1 residues processed: 227 average time/residue: 0.0951 time to fit residues: 28.0495 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 : 0.258 ------------------------------------------------------------------------------- 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 49 optimal weight: 8.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 0.0270 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS D 31 ASN E 37 GLN L 1 GLN L 36 HIS L 39 GLN L 40 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.131040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.107654 restraints weight = 11756.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.110850 restraints weight = 7023.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.113050 restraints weight = 4949.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.114457 restraints weight = 3884.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.115565 restraints weight = 3289.501| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6998 Z= 0.129 Angle : 0.637 8.019 9516 Z= 0.338 Chirality : 0.045 0.181 1028 Planarity : 0.005 0.050 1226 Dihedral : 5.417 37.474 1001 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 1.75 % Allowed : 19.35 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.26), residues: 872 helix: -5.02 (0.17), residues: 24 sheet: -2.28 (0.26), residues: 354 loop : -2.27 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 24 TYR 0.026 0.001 TYR L 51 PHE 0.021 0.001 PHE B 29 TRP 0.030 0.001 TRP B 47 HIS 0.004 0.001 HIS H 107 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6990) covalent geometry : angle 0.63591 ( 9499) SS BOND : bond 0.00409 ( 7) SS BOND : angle 1.12953 ( 14) hydrogen bonds : bond 0.04705 ( 155) hydrogen bonds : angle 7.03942 ( 384) link_NAG-ASN : bond 0.00017 ( 1) link_NAG-ASN : angle 1.35003 ( 3) *********************** 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 212 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8258 (t60) cc_final: 0.7734 (t60) REVERT: B 51 MET cc_start: 0.8796 (mmm) cc_final: 0.8449 (mmt) REVERT: C 34 MET cc_start: 0.7593 (mtt) cc_final: 0.7371 (mmm) REVERT: C 36 TRP cc_start: 0.7891 (m100) cc_final: 0.7554 (m100) REVERT: C 65 LYS cc_start: 0.7931 (ptpt) cc_final: 0.7571 (ttpt) REVERT: E 78 LEU cc_start: 0.8078 (mm) cc_final: 0.7858 (mm) REVERT: E 90 GLN cc_start: 0.8774 (pp30) cc_final: 0.8301 (pp30) REVERT: H 43 GLN cc_start: 0.8521 (mp10) cc_final: 0.7930 (mp10) REVERT: H 87 ARG cc_start: 0.6938 (mtm110) cc_final: 0.6583 (mtm110) REVERT: L 63 ARG cc_start: 0.8049 (mtm-85) cc_final: 0.7618 (ttp-110) outliers start: 13 outliers final: 3 residues processed: 205 average time/residue: 0.0910 time to fit residues: 24.5354 Evaluate side-chains 174 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 171 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain E residue 39 LYS 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 61 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.0070 chunk 32 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 17 optimal weight: 0.0370 chunk 85 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN H 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.130059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.106895 restraints weight = 11809.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.110034 restraints weight = 7061.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.112267 restraints weight = 4987.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.113737 restraints weight = 3893.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.114717 restraints weight = 3284.291| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2687 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= 0.127 Angle : 0.616 9.026 9516 Z= 0.322 Chirality : 0.044 0.180 1028 Planarity : 0.005 0.053 1226 Dihedral : 4.902 32.577 996 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.02 % Allowed : 21.10 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.28), residues: 872 helix: -5.08 (0.18), residues: 24 sheet: -1.96 (0.27), residues: 354 loop : -1.94 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 87 TYR 0.027 0.001 TYR L 51 PHE 0.014 0.001 PHE A 490 TRP 0.018 0.001 TRP B 47 HIS 0.003 0.001 HIS H 107 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6990) covalent geometry : angle 0.61452 ( 9499) SS BOND : bond 0.00304 ( 7) SS BOND : angle 1.21156 ( 14) hydrogen bonds : bond 0.03495 ( 155) hydrogen bonds : angle 6.29823 ( 384) link_NAG-ASN : bond 0.00066 ( 1) link_NAG-ASN : angle 1.15311 ( 3) *********************** 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 197 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8207 (t60) cc_final: 0.7583 (t60) REVERT: C 36 TRP cc_start: 0.7837 (m100) cc_final: 0.7598 (m100) REVERT: C 46 GLU cc_start: 0.7789 (tt0) cc_final: 0.7530 (pt0) REVERT: C 65 LYS cc_start: 0.7912 (ptpt) cc_final: 0.7561 (ttpt) REVERT: C 86 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7908 (pp) REVERT: E 90 GLN cc_start: 0.8800 (pp30) cc_final: 0.8247 (pp30) REVERT: H 43 GLN cc_start: 0.8532 (mp10) cc_final: 0.7933 (mp10) REVERT: H 48 MET cc_start: 0.8157 (mtt) cc_final: 0.7875 (mtp) REVERT: H 81 MET cc_start: 0.8098 (tmm) cc_final: 0.7755 (tmm) REVERT: L 63 ARG cc_start: 0.8057 (mtm-85) cc_final: 0.7624 (mtp-110) outliers start: 15 outliers final: 6 residues processed: 190 average time/residue: 0.0893 time to fit residues: 22.4914 Evaluate side-chains 177 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 170 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain H residue 28 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 55 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN E 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.130942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.107310 restraints weight = 12039.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110378 restraints weight = 7261.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.112523 restraints weight = 5192.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.113954 restraints weight = 4109.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.115040 restraints weight = 3486.679| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6998 Z= 0.125 Angle : 0.619 10.444 9516 Z= 0.315 Chirality : 0.044 0.188 1028 Planarity : 0.005 0.069 1226 Dihedral : 4.714 28.928 996 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.55 % Allowed : 23.66 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.28), residues: 872 helix: -5.03 (0.17), residues: 30 sheet: -1.72 (0.27), residues: 368 loop : -1.84 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 346 TYR 0.025 0.001 TYR L 51 PHE 0.012 0.001 PHE A 490 TRP 0.016 0.001 TRP C 106 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6990) covalent geometry : angle 0.61689 ( 9499) SS BOND : bond 0.00343 ( 7) SS BOND : angle 1.25841 ( 14) hydrogen bonds : bond 0.03193 ( 155) hydrogen bonds : angle 5.96917 ( 384) link_NAG-ASN : bond 0.00065 ( 1) link_NAG-ASN : angle 1.17559 ( 3) *********************** 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 196 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.205 Fit side-chains REVERT: A 346 ARG cc_start: 0.7538 (mmm160) cc_final: 0.7281 (mmm-85) REVERT: B 47 TRP cc_start: 0.8172 (t60) cc_final: 0.7709 (t60) REVERT: C 36 TRP cc_start: 0.7759 (m100) cc_final: 0.7516 (m100) REVERT: C 65 LYS cc_start: 0.7922 (ptpt) cc_final: 0.7562 (ttpt) REVERT: C 86 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7957 (pp) REVERT: E 90 GLN cc_start: 0.8785 (pp30) cc_final: 0.8328 (pp30) REVERT: H 43 GLN cc_start: 0.8582 (mp10) cc_final: 0.8014 (mp10) REVERT: H 63 LYS cc_start: 0.8767 (tttp) cc_final: 0.8461 (ttpp) REVERT: L 63 ARG cc_start: 0.8034 (mtm-85) cc_final: 0.7682 (mtp-110) outliers start: 19 outliers final: 13 residues processed: 186 average time/residue: 0.0852 time to fit residues: 21.0862 Evaluate side-chains 174 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 97 VAL 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 H residue 28 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 1 optimal weight: 0.2980 chunk 74 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN D 6 GLN E 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.130536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.106995 restraints weight = 11996.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.110054 restraints weight = 7215.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.112190 restraints weight = 5145.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.113649 restraints weight = 4078.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.114679 restraints weight = 3456.923| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6998 Z= 0.128 Angle : 0.622 10.288 9516 Z= 0.313 Chirality : 0.043 0.185 1028 Planarity : 0.004 0.054 1226 Dihedral : 4.615 26.471 996 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.23 % Allowed : 23.92 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.27), residues: 872 helix: -5.07 (0.18), residues: 24 sheet: -1.68 (0.26), residues: 371 loop : -1.74 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 346 TYR 0.019 0.001 TYR E 94 PHE 0.020 0.001 PHE A 342 TRP 0.014 0.001 TRP B 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6990) covalent geometry : angle 0.62136 ( 9499) SS BOND : bond 0.00567 ( 7) SS BOND : angle 0.78716 ( 14) hydrogen bonds : bond 0.03066 ( 155) hydrogen bonds : angle 5.74159 ( 384) link_NAG-ASN : bond 0.00079 ( 1) link_NAG-ASN : angle 1.16873 ( 3) *********************** 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 192 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8169 (t60) cc_final: 0.7728 (t60) REVERT: C 65 LYS cc_start: 0.7991 (ptpt) cc_final: 0.7663 (ttpt) REVERT: C 86 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7961 (pp) REVERT: E 90 GLN cc_start: 0.8718 (pp30) cc_final: 0.8189 (pp30) REVERT: H 43 GLN cc_start: 0.8588 (mp10) cc_final: 0.8072 (mp10) REVERT: H 48 MET cc_start: 0.8094 (mtt) cc_final: 0.7811 (mtp) REVERT: L 63 ARG cc_start: 0.8030 (mtm-85) cc_final: 0.7277 (ttp-110) outliers start: 24 outliers final: 17 residues processed: 182 average time/residue: 0.0858 time to fit residues: 20.9339 Evaluate side-chains 180 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 69 THR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 101 VAL 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 72 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 53 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 85 optimal weight: 0.6980 chunk 40 optimal weight: 0.0970 chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** 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 = 0.3653 r_free = 0.3653 target = 0.126470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.104024 restraints weight = 12015.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.107072 restraints weight = 7096.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109189 restraints weight = 4953.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.110597 restraints weight = 3862.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.111634 restraints weight = 3253.477| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3449 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6998 Z= 0.128 Angle : 0.629 9.561 9516 Z= 0.317 Chirality : 0.043 0.179 1028 Planarity : 0.004 0.051 1226 Dihedral : 4.587 24.938 996 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.90 % Allowed : 24.06 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.28), residues: 872 helix: -4.97 (0.21), residues: 18 sheet: -1.51 (0.27), residues: 374 loop : -1.64 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 87 TYR 0.020 0.001 TYR C 80 PHE 0.016 0.001 PHE A 342 TRP 0.015 0.001 TRP C 36 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6990) covalent geometry : angle 0.62857 ( 9499) SS BOND : bond 0.00355 ( 7) SS BOND : angle 0.70054 ( 14) hydrogen bonds : bond 0.03021 ( 155) hydrogen bonds : angle 5.74888 ( 384) link_NAG-ASN : bond 0.00135 ( 1) link_NAG-ASN : angle 1.20809 ( 3) *********************** 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 193 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8125 (t60) cc_final: 0.7673 (t60) REVERT: C 65 LYS cc_start: 0.7968 (ptpt) cc_final: 0.7662 (ttpt) REVERT: C 86 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7978 (pp) REVERT: E 90 GLN cc_start: 0.8767 (pp30) cc_final: 0.8067 (pp30) REVERT: H 43 GLN cc_start: 0.8587 (mp10) cc_final: 0.8053 (mp10) REVERT: L 63 ARG cc_start: 0.7900 (mtm-85) cc_final: 0.7501 (ttp-110) outliers start: 29 outliers final: 18 residues processed: 182 average time/residue: 0.0821 time to fit residues: 20.2446 Evaluate side-chains 178 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 69 THR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 30 SER 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 72 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 53 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 0.0770 chunk 79 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 chunk 51 optimal weight: 0.0770 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.128066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.105095 restraints weight = 11965.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.108180 restraints weight = 7157.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.110311 restraints weight = 5034.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.111803 restraints weight = 3945.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.112809 restraints weight = 3312.689| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3535 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= 0.111 Angle : 0.641 10.488 9516 Z= 0.319 Chirality : 0.043 0.158 1028 Planarity : 0.004 0.051 1226 Dihedral : 4.496 21.974 996 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 2.55 % Allowed : 25.00 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.28), residues: 872 helix: -4.96 (0.22), residues: 18 sheet: -1.32 (0.27), residues: 374 loop : -1.56 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 87 TYR 0.018 0.001 TYR E 94 PHE 0.014 0.001 PHE A 342 TRP 0.019 0.001 TRP C 36 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6990) covalent geometry : angle 0.64072 ( 9499) SS BOND : bond 0.00321 ( 7) SS BOND : angle 0.67451 ( 14) hydrogen bonds : bond 0.02908 ( 155) hydrogen bonds : angle 5.58481 ( 384) link_NAG-ASN : bond 0.00122 ( 1) link_NAG-ASN : angle 1.03739 ( 3) *********************** 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 186 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8021 (t60) cc_final: 0.7685 (t60) REVERT: B 82 GLU cc_start: 0.7691 (tp30) cc_final: 0.7370 (mm-30) REVERT: C 65 LYS cc_start: 0.7997 (ptpt) cc_final: 0.7659 (ttpt) REVERT: C 86 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7963 (pp) REVERT: E 90 GLN cc_start: 0.8752 (pp30) cc_final: 0.8279 (pp30) REVERT: H 43 GLN cc_start: 0.8578 (mp10) cc_final: 0.8037 (mp10) REVERT: H 55 TYR cc_start: 0.8001 (m-10) cc_final: 0.7782 (m-80) REVERT: L 63 ARG cc_start: 0.7985 (mtm-85) cc_final: 0.7690 (ttp-110) REVERT: L 81 GLN cc_start: 0.7982 (mp10) cc_final: 0.7742 (mp10) outliers start: 19 outliers final: 14 residues processed: 178 average time/residue: 0.0812 time to fit residues: 19.5296 Evaluate side-chains 170 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 119 THR 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 72 THR Chi-restraints excluded: chain H residue 28 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 14 optimal weight: 6.9990 chunk 30 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 38 GLN E 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.122138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.099364 restraints weight = 12065.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.102430 restraints weight = 6876.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.104567 restraints weight = 4728.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.105904 restraints weight = 3654.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.106939 restraints weight = 3078.313| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6998 Z= 0.163 Angle : 0.664 9.215 9516 Z= 0.334 Chirality : 0.044 0.204 1028 Planarity : 0.004 0.053 1226 Dihedral : 4.684 24.370 996 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 2.96 % Allowed : 24.73 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.28), residues: 872 helix: -4.93 (0.22), residues: 18 sheet: -1.28 (0.28), residues: 365 loop : -1.54 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 87 TYR 0.016 0.002 TYR E 94 PHE 0.015 0.001 PHE A 490 TRP 0.021 0.002 TRP C 36 HIS 0.004 0.002 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 6990) covalent geometry : angle 0.66330 ( 9499) SS BOND : bond 0.00325 ( 7) SS BOND : angle 0.74519 ( 14) hydrogen bonds : bond 0.03229 ( 155) hydrogen bonds : angle 5.62122 ( 384) link_NAG-ASN : bond 0.00023 ( 1) link_NAG-ASN : angle 1.44393 ( 3) *********************** 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 184 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8168 (t60) cc_final: 0.7753 (t60) REVERT: B 82 GLU cc_start: 0.7742 (tp30) cc_final: 0.7352 (mm-30) REVERT: C 65 LYS cc_start: 0.7995 (ptpt) cc_final: 0.7700 (ttpt) REVERT: C 86 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8019 (pp) REVERT: C 103 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.7820 (mp10) REVERT: E 90 GLN cc_start: 0.8844 (pp30) cc_final: 0.8191 (pp30) REVERT: H 43 GLN cc_start: 0.8561 (mp10) cc_final: 0.7980 (mp10) REVERT: H 73 ASP cc_start: 0.7849 (t0) cc_final: 0.7460 (t0) REVERT: H 87 ARG cc_start: 0.7204 (mtm110) cc_final: 0.6810 (mtm110) REVERT: H 89 GLU cc_start: 0.8427 (pt0) cc_final: 0.8182 (pt0) REVERT: L 63 ARG cc_start: 0.8093 (mtm-85) cc_final: 0.7674 (ttp-110) outliers start: 22 outliers final: 16 residues processed: 176 average time/residue: 0.0738 time to fit residues: 17.7268 Evaluate side-chains 174 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 96 CYS 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 103 GLN 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 72 THR Chi-restraints excluded: chain H residue 28 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 62 optimal weight: 0.0980 chunk 10 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 2 optimal weight: 0.3980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN H 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.125717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.103145 restraints weight = 12014.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.106242 restraints weight = 6895.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108348 restraints weight = 4741.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.109815 restraints weight = 3669.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.110805 restraints weight = 3067.858| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3680 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= 0.133 Angle : 0.669 9.439 9516 Z= 0.335 Chirality : 0.044 0.180 1028 Planarity : 0.004 0.050 1226 Dihedral : 4.658 23.378 996 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.55 % Allowed : 26.21 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.29), residues: 872 helix: -4.91 (0.21), residues: 19 sheet: -1.16 (0.28), residues: 369 loop : -1.53 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 61 TYR 0.017 0.001 TYR E 94 PHE 0.018 0.001 PHE H 64 TRP 0.023 0.001 TRP C 36 HIS 0.004 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6990) covalent geometry : angle 0.66808 ( 9499) SS BOND : bond 0.00436 ( 7) SS BOND : angle 0.84877 ( 14) hydrogen bonds : bond 0.02990 ( 155) hydrogen bonds : angle 5.45740 ( 384) link_NAG-ASN : bond 0.00059 ( 1) link_NAG-ASN : angle 1.21382 ( 3) *********************** 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 178 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8107 (t60) cc_final: 0.7752 (t60) REVERT: B 82 GLU cc_start: 0.7748 (tp30) cc_final: 0.7389 (mm-30) REVERT: C 65 LYS cc_start: 0.7995 (ptpt) cc_final: 0.7696 (ttpt) REVERT: E 90 GLN cc_start: 0.8808 (pp30) cc_final: 0.8153 (pp30) REVERT: H 43 GLN cc_start: 0.8567 (mp10) cc_final: 0.8013 (mp10) REVERT: H 73 ASP cc_start: 0.7800 (t0) cc_final: 0.7415 (t0) REVERT: L 63 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7689 (ttp-110) outliers start: 19 outliers final: 17 residues processed: 169 average time/residue: 0.0816 time to fit residues: 18.7869 Evaluate side-chains 169 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 96 CYS 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 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 72 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 53 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 30 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 83 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN H 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.124769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.102042 restraints weight = 11949.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.105164 restraints weight = 6848.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.107311 restraints weight = 4715.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.108784 restraints weight = 3650.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.109734 restraints weight = 3048.467| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3773 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= 0.139 Angle : 0.670 9.997 9516 Z= 0.335 Chirality : 0.044 0.183 1028 Planarity : 0.004 0.053 1226 Dihedral : 4.665 23.263 996 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.15 % Allowed : 26.61 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.28), residues: 872 helix: -4.90 (0.21), residues: 19 sheet: -1.14 (0.28), residues: 369 loop : -1.48 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 61 TYR 0.024 0.001 TYR C 80 PHE 0.014 0.001 PHE A 342 TRP 0.023 0.002 TRP C 36 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 6990) covalent geometry : angle 0.66942 ( 9499) SS BOND : bond 0.00447 ( 7) SS BOND : angle 0.74814 ( 14) hydrogen bonds : bond 0.02967 ( 155) hydrogen bonds : angle 5.48804 ( 384) link_NAG-ASN : bond 0.00065 ( 1) link_NAG-ASN : angle 1.25053 ( 3) ********************** 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 174 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.246 Fit side-chains REVERT: B 47 TRP cc_start: 0.8111 (t60) cc_final: 0.7759 (t60) REVERT: B 82 GLU cc_start: 0.7865 (tp30) cc_final: 0.7474 (mm-30) REVERT: C 65 LYS cc_start: 0.8026 (ptpt) cc_final: 0.7708 (ttpt) REVERT: C 103 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7851 (mp10) REVERT: E 4 MET cc_start: 0.6328 (mmm) cc_final: 0.5935 (mmt) REVERT: E 90 GLN cc_start: 0.8805 (pp30) cc_final: 0.8384 (pp30) REVERT: H 43 GLN cc_start: 0.8570 (mp10) cc_final: 0.8048 (mp10) REVERT: H 73 ASP cc_start: 0.7797 (t0) cc_final: 0.7385 (t0) REVERT: L 63 ARG cc_start: 0.8066 (mtm-85) cc_final: 0.7295 (mtp-110) outliers start: 16 outliers final: 15 residues processed: 167 average time/residue: 0.0832 time to fit residues: 18.5659 Evaluate side-chains 170 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 96 CYS 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 103 GLN 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 72 THR Chi-restraints excluded: chain H residue 28 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** 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 = 0.3582 r_free = 0.3582 target = 0.122005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.098875 restraints weight = 12004.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.101884 restraints weight = 6990.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.103959 restraints weight = 4860.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.105410 restraints weight = 3797.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.106322 restraints weight = 3193.837| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6998 Z= 0.198 Angle : 0.705 9.157 9516 Z= 0.358 Chirality : 0.046 0.227 1028 Planarity : 0.004 0.052 1226 Dihedral : 4.951 27.446 996 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 2.55 % Allowed : 26.21 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.28), residues: 872 helix: -4.87 (0.22), residues: 18 sheet: -1.10 (0.27), residues: 365 loop : -1.54 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 17 TYR 0.017 0.002 TYR L 51 PHE 0.018 0.002 PHE A 490 TRP 0.022 0.002 TRP C 36 HIS 0.004 0.002 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 6990) covalent geometry : angle 0.70395 ( 9499) SS BOND : bond 0.00461 ( 7) SS BOND : angle 0.79413 ( 14) hydrogen bonds : bond 0.03280 ( 155) hydrogen bonds : angle 5.59780 ( 384) link_NAG-ASN : bond 0.00061 ( 1) link_NAG-ASN : angle 1.64752 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1510.33 seconds wall clock time: 26 minutes 44.18 seconds (1604.18 seconds total)