Starting phenix.real_space_refine on Tue Feb 3 21:07:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kvq_62599/02_2026/9kvq_62599.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kvq_62599/02_2026/9kvq_62599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kvq_62599/02_2026/9kvq_62599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kvq_62599/02_2026/9kvq_62599.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kvq_62599/02_2026/9kvq_62599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kvq_62599/02_2026/9kvq_62599.map" } resolution = 3.95 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= 0.010 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 40 5.16 5 C 4315 2.51 5 N 1140 2.21 5 O 1329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6824 Number of models: 1 Model: "" Number of chains: 8 Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 100} Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 918 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "B" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 836 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "A" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 921 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "G" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} 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': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "C" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 947 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.55, per 1000 atoms: 0.23 Number of scatterers: 6824 At special positions: 0 Unit cell: (87.914, 104.252, 107.364, 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 40 16.00 O 1329 8.00 N 1140 7.00 C 4315 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 98 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.02 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG E 1 " - " ASN G 343 " Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 249.6 milliseconds 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1588 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 16 sheets defined 4.0% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.155A pdb=" N THR H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'A' and resid 64 through 67 removed outlier: 3.872A pdb=" N LYS A 67 " --> pdb=" O GLU A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.773A pdb=" N ASP A 92 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR A 93 " --> pdb=" O ALA A 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 93' Processing helix chain 'G' and resid 383 through 387 removed outlier: 3.522A pdb=" N LYS G 386 " --> pdb=" O SER G 383 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU G 387 " --> pdb=" O PRO G 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 383 through 387' Processing helix chain 'G' and resid 404 through 408 removed outlier: 3.786A pdb=" N VAL G 407 " --> pdb=" O GLY G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 422 removed outlier: 3.735A pdb=" N TYR G 421 " --> pdb=" O ASN G 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.898A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.793A pdb=" N SER L 7 " --> pdb=" O THR L 22 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.513A pdb=" N THR L 99 " --> pdb=" O TYR L 85 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TRP L 34 " --> pdb=" O PHE L 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.505A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR H 80 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN H 82 " --> pdb=" O THR H 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.467A pdb=" N LEU H 45 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N THR H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.467A pdb=" N LEU H 45 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N THR H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 29 removed outlier: 7.183A pdb=" N THR B 69 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR B 72 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER B 65 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 48 removed outlier: 5.581A pdb=" N ALA B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLN B 37 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AB1, first strand: chain 'A' and resid 60 through 62 removed outlier: 3.656A pdb=" N TYR A 61 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 37 " --> pdb=" O TYR A 97 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 115 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 355 through 358 removed outlier: 3.512A pdb=" N VAL G 395 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN G 394 " --> pdb=" O GLU G 516 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS G 378 " --> pdb=" O VAL G 433 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.358A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU D 33 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LYS D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN D 37 " --> pdb=" O ARG D 45 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 18 through 20 removed outlier: 3.643A pdb=" N SER D 74 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER D 63 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.692A pdb=" N ILE C 20 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR C 78 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 58 through 60 removed outlier: 5.643A pdb=" N TRP C 47 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA C 92 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 115 " --> pdb=" O ALA C 92 " (cutoff:3.500A) 165 hydrogen bonds defined for protein. 423 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: 1.22 - 1.34: 2139 1.34 - 1.46: 1558 1.46 - 1.57: 3238 1.57 - 1.69: 0 1.69 - 1.81: 57 Bond restraints: 6992 Sorted by residual: bond pdb=" CA THR G 470 " pdb=" CB THR G 470 " ideal model delta sigma weight residual 1.526 1.556 -0.030 1.49e-02 4.50e+03 4.01e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.81e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.62e+00 bond pdb=" C ALA G 372 " pdb=" N PRO G 373 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.56e+00 bond pdb=" C GLN A 13 " pdb=" N PRO A 14 " ideal model delta sigma weight residual 1.332 1.353 -0.021 1.12e-02 7.97e+03 3.39e+00 ... (remaining 6987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 9049 1.89 - 3.77: 367 3.77 - 5.66: 51 5.66 - 7.55: 14 7.55 - 9.43: 3 Bond angle restraints: 9484 Sorted by residual: angle pdb=" C SER L 92 " pdb=" N TRP L 93 " pdb=" CA TRP L 93 " ideal model delta sigma weight residual 121.54 129.59 -8.05 1.91e+00 2.74e-01 1.78e+01 angle pdb=" C LEU G 518 " pdb=" N HIS G 519 " pdb=" CA HIS G 519 " ideal model delta sigma weight residual 122.46 127.70 -5.24 1.41e+00 5.03e-01 1.38e+01 angle pdb=" C SER D 30 " pdb=" N ASN D 31 " pdb=" CA ASN D 31 " ideal model delta sigma weight residual 121.54 128.49 -6.95 1.91e+00 2.74e-01 1.32e+01 angle pdb=" C SER L 49 " pdb=" N THR L 50 " pdb=" CA THR L 50 " ideal model delta sigma weight residual 121.54 128.05 -6.51 1.91e+00 2.74e-01 1.16e+01 angle pdb=" CA GLN L 89 " pdb=" CB GLN L 89 " pdb=" CG GLN L 89 " ideal model delta sigma weight residual 114.10 120.77 -6.67 2.00e+00 2.50e-01 1.11e+01 ... (remaining 9479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.45: 3841 21.45 - 42.89: 252 42.89 - 64.34: 27 64.34 - 85.78: 11 85.78 - 107.23: 7 Dihedral angle restraints: 4138 sinusoidal: 1638 harmonic: 2500 Sorted by residual: dihedral pdb=" CA CYS G 361 " pdb=" C CYS G 361 " pdb=" N VAL G 362 " pdb=" CA VAL G 362 " ideal model delta harmonic sigma weight residual 180.00 136.71 43.29 0 5.00e+00 4.00e-02 7.50e+01 dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 98 " pdb=" CB CYS A 98 " ideal model delta sinusoidal sigma weight residual 93.00 164.10 -71.10 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CA LEU G 518 " pdb=" C LEU G 518 " pdb=" N HIS G 519 " pdb=" CA HIS G 519 " ideal model delta harmonic sigma weight residual 180.00 148.65 31.35 0 5.00e+00 4.00e-02 3.93e+01 ... (remaining 4135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 727 0.053 - 0.107: 228 0.107 - 0.160: 59 0.160 - 0.213: 10 0.213 - 0.266: 4 Chirality restraints: 1028 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.29e+00 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 1.94e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 1025 not shown) Planarity restraints: 1209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 40 " 0.048 5.00e-02 4.00e+02 7.24e-02 8.39e+00 pdb=" N PRO H 41 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 94 " -0.048 5.00e-02 4.00e+02 7.20e-02 8.29e+00 pdb=" N PRO B 95 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " -0.040 5.00e-02 4.00e+02 6.15e-02 6.06e+00 pdb=" N PRO L 8 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.032 5.00e-02 4.00e+02 ... (remaining 1206 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1620 2.78 - 3.31: 5575 3.31 - 3.84: 10961 3.84 - 4.37: 11866 4.37 - 4.90: 21304 Nonbonded interactions: 51326 Sorted by model distance: nonbonded pdb=" OH TYR H 59 " pdb=" OH TYR H 103 " model vdw 2.256 3.040 nonbonded pdb=" OG SER G 443 " pdb=" O PHE G 497 " model vdw 2.284 3.040 nonbonded pdb=" OG SER G 349 " pdb=" O LEU G 452 " model vdw 2.286 3.040 nonbonded pdb=" OG SER L 92 " pdb=" O THR L 94 " model vdw 2.287 3.040 nonbonded pdb=" O SER D 7 " pdb=" OG SER D 22 " model vdw 2.290 3.040 ... (remaining 51321 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.83 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.210 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 7004 Z= 0.285 Angle : 0.912 9.630 9511 Z= 0.504 Chirality : 0.058 0.266 1028 Planarity : 0.007 0.072 1208 Dihedral : 14.904 107.229 2523 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.27 % Allowed : 7.94 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -4.21 (0.24), residues: 856 helix: -4.98 (0.32), residues: 14 sheet: -2.57 (0.27), residues: 317 loop : -2.99 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 61 TYR 0.021 0.002 TYR B 94 PHE 0.030 0.003 PHE L 46 TRP 0.030 0.002 TRP G 436 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00644 ( 6992) covalent geometry : angle 0.90102 ( 9484) SS BOND : bond 0.00553 ( 9) SS BOND : angle 1.38747 ( 18) hydrogen bonds : bond 0.28449 ( 155) hydrogen bonds : angle 11.15709 ( 423) link_BETA1-4 : bond 0.00921 ( 2) link_BETA1-4 : angle 2.52833 ( 6) link_NAG-ASN : bond 0.00167 ( 1) link_NAG-ASN : angle 6.88955 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 243 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 19 ILE cc_start: 0.8441 (tp) cc_final: 0.8228 (tp) REVERT: L 32 MET cc_start: 0.8151 (tpp) cc_final: 0.7711 (tpt) REVERT: L 48 TYR cc_start: 0.7859 (p90) cc_final: 0.7551 (p90) REVERT: L 60 ARG cc_start: 0.7382 (mtm-85) cc_final: 0.6695 (mtm180) REVERT: L 78 GLU cc_start: 0.7914 (tt0) cc_final: 0.7530 (pm20) REVERT: L 89 GLN cc_start: 0.8188 (tp40) cc_final: 0.7671 (tm-30) REVERT: H 34 MET cc_start: 0.7980 (mtp) cc_final: 0.7602 (mtt) REVERT: H 85 SER cc_start: 0.8350 (m) cc_final: 0.7536 (p) REVERT: H 89 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8059 (tm-30) REVERT: H 90 ASP cc_start: 0.8254 (m-30) cc_final: 0.7535 (m-30) REVERT: H 97 VAL cc_start: 0.8843 (t) cc_final: 0.8594 (p) REVERT: H 110 TYR cc_start: 0.7632 (m-80) cc_final: 0.7398 (m-10) REVERT: B 4 MET cc_start: 0.8037 (mmm) cc_final: 0.7564 (mmm) REVERT: B 8 GLN cc_start: 0.6880 (mt0) cc_final: 0.6563 (mt0) REVERT: B 42 GLN cc_start: 0.7980 (mp10) cc_final: 0.7709 (mp10) REVERT: B 45 LYS cc_start: 0.6985 (mtpp) cc_final: 0.6572 (mmtt) REVERT: B 77 ASN cc_start: 0.7411 (t0) cc_final: 0.6999 (t0) REVERT: B 83 LEU cc_start: 0.8339 (tp) cc_final: 0.7883 (pp) REVERT: A 36 TRP cc_start: 0.7799 (m100) cc_final: 0.7264 (m100) REVERT: A 58 HIS cc_start: 0.7836 (m170) cc_final: 0.7599 (m-70) REVERT: A 82 TYR cc_start: 0.7434 (m-80) cc_final: 0.7127 (m-80) REVERT: A 113 THR cc_start: 0.8603 (p) cc_final: 0.8377 (p) REVERT: G 334 ASN cc_start: 0.8026 (p0) cc_final: 0.7665 (p0) REVERT: G 376 THR cc_start: 0.7888 (t) cc_final: 0.7647 (p) REVERT: G 391 CYS cc_start: 0.8347 (m) cc_final: 0.8099 (p) REVERT: G 442 ASP cc_start: 0.7637 (t0) cc_final: 0.7335 (m-30) REVERT: G 478 LYS cc_start: 0.6883 (mmmm) cc_final: 0.5924 (ptmm) REVERT: D 49 LYS cc_start: 0.6980 (ptmt) cc_final: 0.6752 (ptpp) REVERT: C 23 LYS cc_start: 0.7630 (tttp) cc_final: 0.7426 (tttm) REVERT: C 104 TRP cc_start: 0.7895 (m-90) cc_final: 0.7560 (m100) outliers start: 2 outliers final: 0 residues processed: 245 average time/residue: 0.0742 time to fit residues: 23.9730 Evaluate side-chains 186 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 88 HIS ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 ASN A 84 GLN A 111 GLN G 394 ASN G 409 GLN G 437 ASN G 505 HIS ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN D 107 ASN C 1 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.101333 restraints weight = 11962.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.104129 restraints weight = 7287.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.106092 restraints weight = 5185.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.107423 restraints weight = 4064.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.108299 restraints weight = 3412.695| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7004 Z= 0.159 Angle : 0.679 8.613 9511 Z= 0.355 Chirality : 0.046 0.160 1028 Planarity : 0.006 0.072 1208 Dihedral : 8.881 88.660 1014 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.44 % Allowed : 16.42 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.47 (0.26), residues: 856 helix: -4.89 (0.38), residues: 14 sheet: -1.88 (0.27), residues: 332 loop : -2.60 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 52 TYR 0.013 0.001 TYR C 105 PHE 0.020 0.002 PHE B 71 TRP 0.022 0.001 TRP G 436 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6992) covalent geometry : angle 0.66905 ( 9484) SS BOND : bond 0.00540 ( 9) SS BOND : angle 1.00237 ( 18) hydrogen bonds : bond 0.04519 ( 155) hydrogen bonds : angle 7.71937 ( 423) link_BETA1-4 : bond 0.00707 ( 2) link_BETA1-4 : angle 2.70369 ( 6) link_NAG-ASN : bond 0.00570 ( 1) link_NAG-ASN : angle 5.13550 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 TYR cc_start: 0.9417 (m-80) cc_final: 0.9145 (m-80) REVERT: L 48 TYR cc_start: 0.8973 (p90) cc_final: 0.8761 (p90) REVERT: H 82 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: H 85 SER cc_start: 0.8821 (m) cc_final: 0.8454 (p) REVERT: H 90 ASP cc_start: 0.8537 (m-30) cc_final: 0.8038 (m-30) REVERT: B 10 PHE cc_start: 0.7489 (m-80) cc_final: 0.7203 (t80) REVERT: B 45 LYS cc_start: 0.8704 (mtpp) cc_final: 0.8328 (mmtt) REVERT: B 77 ASN cc_start: 0.8988 (t0) cc_final: 0.8398 (t0) REVERT: A 84 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6730 (tp40) REVERT: G 478 LYS cc_start: 0.7619 (mmmm) cc_final: 0.6878 (ttpt) REVERT: D 49 LYS cc_start: 0.8980 (ptmt) cc_final: 0.8692 (ptpp) REVERT: D 71 PHE cc_start: 0.8782 (m-80) cc_final: 0.8573 (m-80) outliers start: 33 outliers final: 20 residues processed: 220 average time/residue: 0.0769 time to fit residues: 22.2737 Evaluate side-chains 203 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 46 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 36 GLN L 37 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 474 GLN G 505 HIS D 6 GLN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.119537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.099901 restraints weight = 12143.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.102297 restraints weight = 7635.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.103981 restraints weight = 5574.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.105230 restraints weight = 4458.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.105982 restraints weight = 3781.027| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 7004 Z= 0.286 Angle : 0.746 9.302 9511 Z= 0.391 Chirality : 0.048 0.186 1028 Planarity : 0.006 0.061 1208 Dihedral : 7.774 86.256 1014 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 5.92 % Allowed : 17.63 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.25 (0.27), residues: 856 helix: -4.60 (0.73), residues: 8 sheet: -1.69 (0.27), residues: 337 loop : -2.52 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 89 TYR 0.021 0.002 TYR C 105 PHE 0.016 0.002 PHE B 62 TRP 0.018 0.002 TRP G 436 HIS 0.004 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00666 ( 6992) covalent geometry : angle 0.73553 ( 9484) SS BOND : bond 0.00395 ( 9) SS BOND : angle 1.37890 ( 18) hydrogen bonds : bond 0.04457 ( 155) hydrogen bonds : angle 7.01740 ( 423) link_BETA1-4 : bond 0.00513 ( 2) link_BETA1-4 : angle 2.67446 ( 6) link_NAG-ASN : bond 0.00208 ( 1) link_NAG-ASN : angle 5.37759 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 32 MET cc_start: 0.9290 (tpp) cc_final: 0.8484 (tpt) REVERT: H 82 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8320 (tm-30) REVERT: H 85 SER cc_start: 0.8935 (m) cc_final: 0.8612 (p) REVERT: B 45 LYS cc_start: 0.8814 (mtpp) cc_final: 0.8480 (mmtt) REVERT: B 77 ASN cc_start: 0.9124 (t0) cc_final: 0.8498 (t0) REVERT: A 6 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6588 (pt0) REVERT: G 436 TRP cc_start: 0.8816 (OUTLIER) cc_final: 0.7974 (m-90) REVERT: G 517 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8348 (tt) REVERT: D 71 PHE cc_start: 0.8896 (m-80) cc_final: 0.8640 (m-80) REVERT: C 45 LEU cc_start: 0.8491 (mt) cc_final: 0.8271 (mt) REVERT: C 80 TYR cc_start: 0.8668 (m-80) cc_final: 0.8414 (m-10) outliers start: 44 outliers final: 30 residues processed: 204 average time/residue: 0.0750 time to fit residues: 20.3360 Evaluate side-chains 205 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain G residue 401 VAL Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 436 TRP Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.0870 chunk 70 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 HIS G 474 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.121468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.101227 restraints weight = 12091.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.103769 restraints weight = 7722.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.105536 restraints weight = 5646.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.106735 restraints weight = 4522.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.107663 restraints weight = 3844.921| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7004 Z= 0.140 Angle : 0.646 7.302 9511 Z= 0.337 Chirality : 0.045 0.179 1028 Planarity : 0.005 0.058 1208 Dihedral : 6.702 83.462 1014 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 5.52 % Allowed : 19.65 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.90 (0.27), residues: 856 helix: -4.46 (0.79), residues: 8 sheet: -1.36 (0.28), residues: 333 loop : -2.35 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 89 TYR 0.027 0.001 TYR B 49 PHE 0.016 0.002 PHE B 71 TRP 0.016 0.001 TRP G 436 HIS 0.004 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6992) covalent geometry : angle 0.63753 ( 9484) SS BOND : bond 0.00222 ( 9) SS BOND : angle 0.90630 ( 18) hydrogen bonds : bond 0.03426 ( 155) hydrogen bonds : angle 6.52348 ( 423) link_BETA1-4 : bond 0.00755 ( 2) link_BETA1-4 : angle 2.65544 ( 6) link_NAG-ASN : bond 0.00394 ( 1) link_NAG-ASN : angle 4.17720 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 TYR cc_start: 0.9245 (m-80) cc_final: 0.9030 (m-10) REVERT: L 60 ARG cc_start: 0.7375 (mpp80) cc_final: 0.7030 (mpp80) REVERT: H 82 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8171 (tm-30) REVERT: H 85 SER cc_start: 0.8938 (m) cc_final: 0.8647 (p) REVERT: H 91 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8770 (t) REVERT: H 97 VAL cc_start: 0.9513 (t) cc_final: 0.9292 (m) REVERT: B 45 LYS cc_start: 0.8799 (mtpp) cc_final: 0.8473 (mmtt) REVERT: B 77 ASN cc_start: 0.9129 (t0) cc_final: 0.8565 (t0) REVERT: A 39 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8306 (tm-30) REVERT: G 436 TRP cc_start: 0.8718 (OUTLIER) cc_final: 0.7876 (m-90) REVERT: G 517 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8413 (tt) REVERT: D 103 LYS cc_start: 0.7343 (ptmt) cc_final: 0.6803 (tttp) REVERT: C 65 ARG cc_start: 0.6926 (mtp85) cc_final: 0.6724 (mtm-85) REVERT: C 104 TRP cc_start: 0.8769 (m100) cc_final: 0.8566 (m100) outliers start: 41 outliers final: 29 residues processed: 198 average time/residue: 0.0663 time to fit residues: 17.5806 Evaluate side-chains 200 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 436 TRP Chi-restraints excluded: chain G residue 483 VAL Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 30 optimal weight: 1.9990 chunk 78 optimal weight: 0.0670 chunk 58 optimal weight: 0.9980 chunk 47 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.122863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.102972 restraints weight = 12005.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.105542 restraints weight = 7509.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.107336 restraints weight = 5417.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.108473 restraints weight = 4284.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.109444 restraints weight = 3646.931| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7004 Z= 0.139 Angle : 0.629 6.591 9511 Z= 0.327 Chirality : 0.045 0.162 1028 Planarity : 0.005 0.057 1208 Dihedral : 6.388 81.093 1014 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 6.06 % Allowed : 19.25 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.64 (0.28), residues: 856 helix: -4.51 (0.77), residues: 8 sheet: -1.14 (0.29), residues: 330 loop : -2.20 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 89 TYR 0.022 0.001 TYR B 49 PHE 0.014 0.001 PHE B 71 TRP 0.016 0.001 TRP G 436 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6992) covalent geometry : angle 0.62156 ( 9484) SS BOND : bond 0.00263 ( 9) SS BOND : angle 0.98450 ( 18) hydrogen bonds : bond 0.03322 ( 155) hydrogen bonds : angle 6.40101 ( 423) link_BETA1-4 : bond 0.00424 ( 2) link_BETA1-4 : angle 2.21436 ( 6) link_NAG-ASN : bond 0.00404 ( 1) link_NAG-ASN : angle 4.23538 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 TYR cc_start: 0.9264 (m-80) cc_final: 0.9027 (m-10) REVERT: H 85 SER cc_start: 0.8949 (m) cc_final: 0.8681 (p) REVERT: H 91 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8782 (t) REVERT: H 97 VAL cc_start: 0.9506 (t) cc_final: 0.9303 (m) REVERT: H 108 MET cc_start: 0.8548 (mtm) cc_final: 0.8321 (mtm) REVERT: B 45 LYS cc_start: 0.8804 (mtpp) cc_final: 0.8481 (mmtt) REVERT: B 77 ASN cc_start: 0.9137 (t0) cc_final: 0.8593 (t0) REVERT: A 76 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7239 (t0) REVERT: G 436 TRP cc_start: 0.8674 (OUTLIER) cc_final: 0.7907 (m-90) REVERT: D 103 LYS cc_start: 0.7338 (ptmt) cc_final: 0.6819 (tttp) outliers start: 45 outliers final: 32 residues processed: 206 average time/residue: 0.0752 time to fit residues: 20.6379 Evaluate side-chains 208 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 436 TRP Chi-restraints excluded: chain G residue 483 VAL Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 48 optimal weight: 0.0870 chunk 70 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 437 ASN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.102984 restraints weight = 12106.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.105524 restraints weight = 7580.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.107297 restraints weight = 5491.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.108458 restraints weight = 4357.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.109337 restraints weight = 3692.387| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7004 Z= 0.149 Angle : 0.635 7.358 9511 Z= 0.330 Chirality : 0.045 0.159 1028 Planarity : 0.005 0.058 1208 Dihedral : 6.241 78.752 1014 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 5.52 % Allowed : 21.00 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.55 (0.28), residues: 856 helix: -4.78 (0.45), residues: 14 sheet: -0.99 (0.30), residues: 315 loop : -2.14 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 89 TYR 0.020 0.001 TYR B 49 PHE 0.012 0.001 PHE B 71 TRP 0.017 0.001 TRP G 436 HIS 0.002 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6992) covalent geometry : angle 0.62735 ( 9484) SS BOND : bond 0.00295 ( 9) SS BOND : angle 1.07266 ( 18) hydrogen bonds : bond 0.03310 ( 155) hydrogen bonds : angle 6.25805 ( 423) link_BETA1-4 : bond 0.00500 ( 2) link_BETA1-4 : angle 2.06730 ( 6) link_NAG-ASN : bond 0.00304 ( 1) link_NAG-ASN : angle 4.25726 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 TYR cc_start: 0.9292 (m-80) cc_final: 0.9045 (m-10) REVERT: L 60 ARG cc_start: 0.7587 (mpp80) cc_final: 0.7319 (mpp80) REVERT: H 85 SER cc_start: 0.8972 (m) cc_final: 0.8647 (p) REVERT: H 91 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8779 (t) REVERT: H 97 VAL cc_start: 0.9509 (t) cc_final: 0.9307 (m) REVERT: H 108 MET cc_start: 0.8544 (mtm) cc_final: 0.8313 (mtm) REVERT: B 45 LYS cc_start: 0.8798 (mtpp) cc_final: 0.8505 (mmtt) REVERT: B 77 ASN cc_start: 0.9153 (t0) cc_final: 0.8623 (t0) REVERT: A 33 TRP cc_start: 0.8528 (p90) cc_final: 0.8067 (p90) REVERT: A 39 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8392 (tm-30) REVERT: G 436 TRP cc_start: 0.8675 (OUTLIER) cc_final: 0.7892 (m-90) REVERT: G 442 ASP cc_start: 0.7845 (m-30) cc_final: 0.7636 (m-30) REVERT: D 71 PHE cc_start: 0.8874 (m-80) cc_final: 0.8564 (m-10) REVERT: D 103 LYS cc_start: 0.7372 (ptmt) cc_final: 0.6855 (tttp) outliers start: 41 outliers final: 34 residues processed: 203 average time/residue: 0.0672 time to fit residues: 18.2905 Evaluate side-chains 210 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 436 TRP Chi-restraints excluded: chain G residue 483 VAL Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 75 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 51 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 0.2980 chunk 43 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.120254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.098804 restraints weight = 12078.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.101567 restraints weight = 7446.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.103474 restraints weight = 5364.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.104726 restraints weight = 4262.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.105740 restraints weight = 3612.364| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7004 Z= 0.160 Angle : 0.650 9.440 9511 Z= 0.337 Chirality : 0.045 0.157 1028 Planarity : 0.005 0.057 1208 Dihedral : 6.203 76.173 1014 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 6.19 % Allowed : 20.73 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.39 (0.28), residues: 856 helix: -4.76 (0.47), residues: 14 sheet: -0.86 (0.30), residues: 315 loop : -2.04 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 509 TYR 0.019 0.001 TYR B 49 PHE 0.013 0.001 PHE D 83 TRP 0.018 0.001 TRP G 436 HIS 0.003 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 6992) covalent geometry : angle 0.64308 ( 9484) SS BOND : bond 0.00308 ( 9) SS BOND : angle 1.09622 ( 18) hydrogen bonds : bond 0.03329 ( 155) hydrogen bonds : angle 6.22109 ( 423) link_BETA1-4 : bond 0.00534 ( 2) link_BETA1-4 : angle 1.99840 ( 6) link_NAG-ASN : bond 0.00299 ( 1) link_NAG-ASN : angle 4.32402 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 TYR cc_start: 0.9286 (m-80) cc_final: 0.9046 (m-10) REVERT: H 85 SER cc_start: 0.8885 (m) cc_final: 0.8586 (p) REVERT: H 91 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8805 (t) REVERT: H 108 MET cc_start: 0.8529 (mtm) cc_final: 0.8236 (mtm) REVERT: B 45 LYS cc_start: 0.8817 (mtpp) cc_final: 0.8517 (mmtt) REVERT: B 77 ASN cc_start: 0.9186 (t0) cc_final: 0.8669 (t0) REVERT: A 33 TRP cc_start: 0.8573 (p90) cc_final: 0.8076 (p90) REVERT: A 39 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8409 (tm-30) REVERT: A 50 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7727 (tt0) REVERT: G 436 TRP cc_start: 0.8626 (OUTLIER) cc_final: 0.7839 (m-90) REVERT: G 471 GLU cc_start: 0.7110 (tp30) cc_final: 0.6760 (tp30) REVERT: D 71 PHE cc_start: 0.8886 (m-80) cc_final: 0.8573 (m-10) REVERT: D 103 LYS cc_start: 0.7361 (ptmt) cc_final: 0.6906 (tttp) outliers start: 46 outliers final: 39 residues processed: 203 average time/residue: 0.0694 time to fit residues: 19.0339 Evaluate side-chains 211 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 436 TRP Chi-restraints excluded: chain G residue 483 VAL Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 75 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 69 optimal weight: 3.9990 chunk 37 optimal weight: 0.0030 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.120580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.098919 restraints weight = 12196.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.101830 restraints weight = 7387.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.103871 restraints weight = 5246.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.105180 restraints weight = 4109.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.106177 restraints weight = 3462.688| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7004 Z= 0.165 Angle : 0.662 7.761 9511 Z= 0.344 Chirality : 0.045 0.206 1028 Planarity : 0.005 0.058 1208 Dihedral : 6.183 72.991 1014 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 5.65 % Allowed : 21.67 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.33 (0.28), residues: 856 helix: -4.78 (0.46), residues: 14 sheet: -0.76 (0.30), residues: 315 loop : -2.04 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 509 TYR 0.019 0.001 TYR H 32 PHE 0.022 0.002 PHE A 70 TRP 0.018 0.001 TRP G 436 HIS 0.003 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 6992) covalent geometry : angle 0.65531 ( 9484) SS BOND : bond 0.00405 ( 9) SS BOND : angle 1.10176 ( 18) hydrogen bonds : bond 0.03430 ( 155) hydrogen bonds : angle 6.29191 ( 423) link_BETA1-4 : bond 0.00541 ( 2) link_BETA1-4 : angle 1.97805 ( 6) link_NAG-ASN : bond 0.00321 ( 1) link_NAG-ASN : angle 4.30842 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 TYR cc_start: 0.9309 (m-80) cc_final: 0.9095 (m-10) REVERT: H 108 MET cc_start: 0.8578 (mtm) cc_final: 0.8284 (mtm) REVERT: B 45 LYS cc_start: 0.8823 (mtpp) cc_final: 0.8496 (mmtt) REVERT: B 77 ASN cc_start: 0.9217 (t0) cc_final: 0.8684 (t0) REVERT: A 18 MET cc_start: 0.8478 (tmm) cc_final: 0.8192 (tmm) REVERT: A 33 TRP cc_start: 0.8598 (p90) cc_final: 0.8112 (p90) REVERT: A 39 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8422 (tm-30) REVERT: A 50 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: G 436 TRP cc_start: 0.8634 (OUTLIER) cc_final: 0.7838 (m-90) REVERT: D 71 PHE cc_start: 0.8906 (m-80) cc_final: 0.8600 (m-80) REVERT: D 103 LYS cc_start: 0.7328 (ptmt) cc_final: 0.6881 (tttp) outliers start: 42 outliers final: 34 residues processed: 196 average time/residue: 0.0683 time to fit residues: 18.2222 Evaluate side-chains 206 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 436 TRP Chi-restraints excluded: chain G residue 483 VAL Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 75 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 27 optimal weight: 0.0370 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 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 = 0.3353 r_free = 0.3353 target = 0.120850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.099694 restraints weight = 12229.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.102505 restraints weight = 7480.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.104508 restraints weight = 5336.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.105855 restraints weight = 4177.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.106564 restraints weight = 3499.100| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7004 Z= 0.162 Angle : 0.675 9.593 9511 Z= 0.345 Chirality : 0.045 0.180 1028 Planarity : 0.005 0.057 1208 Dihedral : 6.100 68.514 1014 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 5.79 % Allowed : 20.86 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.28 (0.28), residues: 856 helix: -4.46 (0.65), residues: 14 sheet: -0.72 (0.30), residues: 315 loop : -2.03 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 92 TYR 0.019 0.001 TYR H 32 PHE 0.018 0.002 PHE A 70 TRP 0.020 0.001 TRP A 36 HIS 0.003 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 6992) covalent geometry : angle 0.66835 ( 9484) SS BOND : bond 0.00263 ( 9) SS BOND : angle 0.95153 ( 18) hydrogen bonds : bond 0.03417 ( 155) hydrogen bonds : angle 6.39596 ( 423) link_BETA1-4 : bond 0.00545 ( 2) link_BETA1-4 : angle 1.95708 ( 6) link_NAG-ASN : bond 0.00290 ( 1) link_NAG-ASN : angle 4.27155 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 108 MET cc_start: 0.8508 (mtm) cc_final: 0.8209 (mtm) REVERT: B 45 LYS cc_start: 0.8803 (mtpp) cc_final: 0.8525 (mmtt) REVERT: B 77 ASN cc_start: 0.9231 (t0) cc_final: 0.8711 (t0) REVERT: A 33 TRP cc_start: 0.8570 (p90) cc_final: 0.8074 (p90) REVERT: A 50 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: G 436 TRP cc_start: 0.8627 (OUTLIER) cc_final: 0.7840 (m-90) REVERT: D 71 PHE cc_start: 0.8909 (m-80) cc_final: 0.8595 (m-80) REVERT: D 103 LYS cc_start: 0.7380 (ptmt) cc_final: 0.6953 (tttp) REVERT: C 45 LEU cc_start: 0.8589 (mt) cc_final: 0.8338 (mt) outliers start: 43 outliers final: 38 residues processed: 201 average time/residue: 0.0705 time to fit residues: 18.9958 Evaluate side-chains 207 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 436 TRP Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 75 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 43 optimal weight: 0.0170 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 0.0050 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.3832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.123723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.102215 restraints weight = 11962.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.105153 restraints weight = 7222.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.107217 restraints weight = 5107.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.108684 restraints weight = 3984.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.109553 restraints weight = 3314.116| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7004 Z= 0.124 Angle : 0.670 9.458 9511 Z= 0.341 Chirality : 0.045 0.194 1028 Planarity : 0.005 0.059 1208 Dihedral : 5.814 63.212 1014 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 5.11 % Allowed : 22.48 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.11 (0.28), residues: 856 helix: -4.18 (0.96), residues: 14 sheet: -0.60 (0.30), residues: 315 loop : -1.90 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 60 TYR 0.020 0.001 TYR H 32 PHE 0.014 0.001 PHE D 83 TRP 0.022 0.001 TRP A 36 HIS 0.002 0.000 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6992) covalent geometry : angle 0.66486 ( 9484) SS BOND : bond 0.00215 ( 9) SS BOND : angle 0.82954 ( 18) hydrogen bonds : bond 0.03260 ( 155) hydrogen bonds : angle 6.23298 ( 423) link_BETA1-4 : bond 0.00414 ( 2) link_BETA1-4 : angle 1.88861 ( 6) link_NAG-ASN : bond 0.00342 ( 1) link_NAG-ASN : angle 3.79786 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 108 MET cc_start: 0.8312 (mtm) cc_final: 0.8094 (mtm) REVERT: H 115 THR cc_start: 0.7430 (OUTLIER) cc_final: 0.6690 (p) REVERT: B 45 LYS cc_start: 0.8800 (mtpp) cc_final: 0.8474 (mmtt) REVERT: B 77 ASN cc_start: 0.9234 (t0) cc_final: 0.8756 (t0) REVERT: A 18 MET cc_start: 0.8500 (tmm) cc_final: 0.7564 (tmm) REVERT: A 33 TRP cc_start: 0.8547 (p90) cc_final: 0.8041 (p90) REVERT: A 39 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8419 (tm-30) REVERT: A 43 LYS cc_start: 0.8353 (mmtt) cc_final: 0.7941 (mmtp) REVERT: A 50 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7614 (tt0) REVERT: A 85 MET cc_start: 0.7304 (mmp) cc_final: 0.6003 (mmp) REVERT: G 436 TRP cc_start: 0.8594 (OUTLIER) cc_final: 0.7842 (m-90) REVERT: D 71 PHE cc_start: 0.8896 (m-80) cc_final: 0.8564 (m-80) REVERT: D 103 LYS cc_start: 0.7333 (ptmt) cc_final: 0.6951 (tttp) outliers start: 38 outliers final: 30 residues processed: 202 average time/residue: 0.0648 time to fit residues: 17.8446 Evaluate side-chains 205 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 436 TRP Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 16 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 24 optimal weight: 0.0370 chunk 40 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 73 optimal weight: 0.0000 chunk 60 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 overall best weight: 0.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.123536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.102115 restraints weight = 12016.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.105010 restraints weight = 7339.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.106979 restraints weight = 5232.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.108386 restraints weight = 4111.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.109275 restraints weight = 3462.611| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7004 Z= 0.127 Angle : 0.684 9.574 9511 Z= 0.346 Chirality : 0.045 0.199 1028 Planarity : 0.005 0.058 1208 Dihedral : 5.769 59.406 1014 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.58 % Allowed : 22.75 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.03 (0.28), residues: 856 helix: -4.06 (1.04), residues: 14 sheet: -0.55 (0.29), residues: 320 loop : -1.86 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 60 TYR 0.019 0.001 TYR H 32 PHE 0.015 0.001 PHE A 70 TRP 0.022 0.001 TRP A 36 HIS 0.002 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6992) covalent geometry : angle 0.67943 ( 9484) SS BOND : bond 0.00204 ( 9) SS BOND : angle 0.80333 ( 18) hydrogen bonds : bond 0.03329 ( 155) hydrogen bonds : angle 6.07639 ( 423) link_BETA1-4 : bond 0.00555 ( 2) link_BETA1-4 : angle 1.77487 ( 6) link_NAG-ASN : bond 0.00319 ( 1) link_NAG-ASN : angle 3.79717 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1489.53 seconds wall clock time: 26 minutes 25.32 seconds (1585.32 seconds total)