Starting phenix.real_space_refine on Thu Aug 6 04:43:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hxz_35083/08_2026/8hxz_35083.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hxz_35083/08_2026/8hxz_35083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8hxz_35083/08_2026/8hxz_35083.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hxz_35083/08_2026/8hxz_35083.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hxz_35083/08_2026/8hxz_35083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hxz_35083/08_2026/8hxz_35083.map" model { file = "/net/cci-nas-00/data/ceres_data/8hxz_35083/08_2026/8hxz_35083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hxz_35083/08_2026/8hxz_35083.cif" } resolution = 3.4 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 328 5.49 5 S 16 5.16 5 C 7628 2.51 5 N 2563 2.21 5 O 3205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13740 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 837 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3345 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "J" Number of atoms: 3379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3379 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "M" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 915 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain breaks: 1 Time building chain proxies: 2.39, per 1000 atoms: 0.17 Number of scatterers: 13740 At special positions: 0 Unit cell: (75.6, 119.7, 142.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 328 15.00 O 3205 8.00 N 2563 7.00 C 7628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 263.6 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: 1644 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 8 sheets defined 66.3% alpha, 6.5% beta 164 base pairs and 294 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.630A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.571A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.907A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.775A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.090A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.538A pdb=" N GLY B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.292A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.740A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.784A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.959A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 4.272A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.260A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.892A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.884A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.224A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.797A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.065A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.562A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 80 Processing helix chain 'H' and resid 87 through 98 removed outlier: 3.978A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.944A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 89 Processing helix chain 'M' and resid 101 through 131 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.521A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.525A pdb=" N ILE C 78 " --> pdb=" O GLY D 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.999A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'M' and resid 58 through 59 removed outlier: 6.564A pdb=" N PHE M 78 " --> pdb=" O LEU M 28 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 58 through 59 445 hydrogen bonds defined for protein. 1299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 416 hydrogen bonds 832 hydrogen bond angles 0 basepair planarities 164 basepair parallelities 294 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2322 1.33 - 1.45: 5135 1.45 - 1.58: 6519 1.58 - 1.70: 654 1.70 - 1.82: 30 Bond restraints: 14660 Sorted by residual: bond pdb=" C3' DG I 128 " pdb=" O3' DG I 128 " ideal model delta sigma weight residual 1.435 1.489 -0.054 1.30e-02 5.92e+03 1.75e+01 bond pdb=" C3' DT I 0 " pdb=" O3' DT I 0 " ideal model delta sigma weight residual 1.435 1.487 -0.052 1.30e-02 5.92e+03 1.60e+01 bond pdb=" C3' DT I 108 " pdb=" C2' DT I 108 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.34e+01 bond pdb=" C3' DC I 95 " pdb=" C2' DC I 95 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" CA ASN G 73 " pdb=" C ASN G 73 " ideal model delta sigma weight residual 1.523 1.571 -0.048 1.41e-02 5.03e+03 1.16e+01 ... (remaining 14655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 20763 2.94 - 5.89: 367 5.89 - 8.83: 55 8.83 - 11.78: 7 11.78 - 14.72: 4 Bond angle restraints: 21196 Sorted by residual: angle pdb=" N HIS M 18 " pdb=" CA HIS M 18 " pdb=" C HIS M 18 " ideal model delta sigma weight residual 110.80 96.08 14.72 2.13e+00 2.20e-01 4.78e+01 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 112.64 120.58 -7.94 1.21e+00 6.83e-01 4.30e+01 angle pdb=" N GLU F 63 " pdb=" CA GLU F 63 " pdb=" CB GLU F 63 " ideal model delta sigma weight residual 110.28 119.35 -9.07 1.55e+00 4.16e-01 3.43e+01 angle pdb=" N VAL D 95 " pdb=" CA VAL D 95 " pdb=" C VAL D 95 " ideal model delta sigma weight residual 110.62 104.73 5.89 1.02e+00 9.61e-01 3.34e+01 angle pdb=" O4' DG I 100 " pdb=" C4' DG I 100 " pdb=" C3' DG I 100 " ideal model delta sigma weight residual 106.00 102.65 3.35 6.00e-01 2.78e+00 3.12e+01 ... (remaining 21191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 6308 35.86 - 71.73: 1647 71.73 - 107.59: 32 107.59 - 143.45: 1 143.45 - 179.32: 4 Dihedral angle restraints: 7992 sinusoidal: 5444 harmonic: 2548 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 150.91 29.09 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LYS F 79 " pdb=" C LYS F 79 " pdb=" N THR F 80 " pdb=" CA THR F 80 " ideal model delta harmonic sigma weight residual 180.00 151.03 28.97 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA LYS H 31 " pdb=" C LYS H 31 " pdb=" N GLU H 32 " pdb=" CA GLU H 32 " ideal model delta harmonic sigma weight residual -180.00 -155.05 -24.95 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 7989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1957 0.067 - 0.134: 379 0.134 - 0.200: 46 0.200 - 0.267: 7 0.267 - 0.334: 2 Chirality restraints: 2391 Sorted by residual: chirality pdb=" CG LEU E 70 " pdb=" CB LEU E 70 " pdb=" CD1 LEU E 70 " pdb=" CD2 LEU E 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CB THR D 112 " pdb=" CA THR D 112 " pdb=" OG1 THR D 112 " pdb=" CG2 THR D 112 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 2388 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.055 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO G 80 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.050 5.00e-02 4.00e+02 7.55e-02 9.13e+00 pdb=" N PRO C 80 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 88 " -0.011 2.00e-02 2.50e+03 2.02e-02 8.16e+00 pdb=" CG TYR B 88 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR B 88 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B 88 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR B 88 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR B 88 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR B 88 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 88 " -0.006 2.00e-02 2.50e+03 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3364 2.82 - 3.34: 13003 3.34 - 3.86: 29103 3.86 - 4.38: 32268 4.38 - 4.90: 44145 Nonbonded interactions: 121883 Sorted by model distance: nonbonded pdb=" NZ LYS F 79 " pdb=" OP1 DG I 101 " model vdw 2.303 3.120 nonbonded pdb=" N THR H 87 " pdb=" OE2 GLU H 90 " model vdw 2.318 3.120 nonbonded pdb=" O ILE F 50 " pdb=" OG1 THR F 54 " model vdw 2.325 3.040 nonbonded pdb=" NH2 ARG A 42 " pdb=" OP1 DA I 69 " model vdw 2.329 3.120 nonbonded pdb=" NZ LYS G 15 " pdb=" OG SER G 19 " model vdw 2.337 3.120 ... (remaining 121878 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 37 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 121) selection = (chain 'H' and resid 28 through 121) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.720 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 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 : 0.007 0.063 14660 Z= 0.554 Angle : 1.101 14.720 21196 Z= 0.826 Chirality : 0.055 0.334 2391 Planarity : 0.007 0.084 1543 Dihedral : 29.122 179.316 6348 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.26), residues: 856 helix: -0.86 (0.20), residues: 541 sheet: -0.52 (0.90), residues: 30 loop : -1.15 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 89 TYR 0.042 0.004 TYR B 88 PHE 0.016 0.003 PHE G 25 TRP 0.010 0.002 TRP M 84 HIS 0.014 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.55 (14660) covalent geometry : angle 1.10140 / 0.83 (21196) hydrogen bonds : bond 0.09779 / 6.77 ( 855) hydrogen bonds : angle 4.87077 / 3.48 ( 2131) *********************** 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 262 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.352 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: symmetry clash 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: A 97 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8506 (mt-10) REVERT: B 35 ARG cc_start: 0.9274 (mtp-110) cc_final: 0.8910 (mtp-110) REVERT: B 59 LYS cc_start: 0.9445 (tmmt) cc_final: 0.9059 (ttpp) REVERT: B 63 GLU cc_start: 0.8892 (pp20) cc_final: 0.8633 (pp20) REVERT: B 91 LYS cc_start: 0.9645 (tppp) cc_final: 0.9255 (tppp) REVERT: C 36 LYS cc_start: 0.9435 (mmpt) cc_final: 0.9075 (mmmt) REVERT: C 104 GLN cc_start: 0.9082 (mp10) cc_final: 0.8818 (mp10) REVERT: C 111 ILE cc_start: 0.8570 (mm) cc_final: 0.8357 (mm) REVERT: C 112 GLN cc_start: 0.8562 (mp10) cc_final: 0.7283 (mp10) REVERT: D 80 TYR cc_start: 0.8714 (m-80) cc_final: 0.8443 (m-80) REVERT: D 102 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8953 (tp30) REVERT: E 108 ASN cc_start: 0.9228 (t0) cc_final: 0.8489 (t0) REVERT: E 109 LEU cc_start: 0.9619 (mm) cc_final: 0.9137 (mm) REVERT: F 25 ASN cc_start: 0.9415 (m-40) cc_final: 0.9196 (m110) REVERT: F 27 GLN cc_start: 0.9122 (mp10) cc_final: 0.8764 (mp10) REVERT: F 59 LYS cc_start: 0.9375 (ptmm) cc_final: 0.9167 (ptmm) REVERT: F 63 GLU cc_start: 0.9305 (pm20) cc_final: 0.9067 (pm20) REVERT: F 88 TYR cc_start: 0.8691 (m-10) cc_final: 0.7946 (m-10) REVERT: F 93 GLN cc_start: 0.8448 (tm-30) cc_final: 0.7908 (tm-30) REVERT: G 56 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8275 (mm-30) REVERT: G 92 GLU cc_start: 0.8361 (tt0) cc_final: 0.8067 (tt0) REVERT: G 112 GLN cc_start: 0.9080 (mp10) cc_final: 0.8683 (mp10) REVERT: H 65 ASP cc_start: 0.9351 (t0) cc_final: 0.9051 (t0) REVERT: H 92 GLN cc_start: 0.9210 (tm-30) cc_final: 0.8622 (tm-30) REVERT: H 97 LEU cc_start: 0.9181 (tt) cc_final: 0.8895 (tt) REVERT: H 103 LEU cc_start: 0.9449 (mt) cc_final: 0.8816 (mt) REVERT: M 89 ASP cc_start: 0.7245 (m-30) cc_final: 0.7023 (m-30) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.1285 time to fit residues: 45.4788 Evaluate side-chains 188 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN M 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.045964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.031010 restraints weight = 103676.548| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 4.17 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14660 Z= 0.249 Angle : 0.840 9.112 21196 Z= 0.471 Chirality : 0.050 0.326 2391 Planarity : 0.006 0.074 1543 Dihedral : 32.755 176.946 4579 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.64 % Allowed : 13.25 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.27), residues: 856 helix: -0.01 (0.21), residues: 550 sheet: -0.85 (0.95), residues: 29 loop : -0.95 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 35 TYR 0.041 0.003 TYR B 88 PHE 0.021 0.002 PHE A 84 TRP 0.006 0.001 TRP M 31 HIS 0.011 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.25 (14660) covalent geometry : angle 0.84008 / 0.47 (21196) hydrogen bonds : bond 0.06744 / 4.51 ( 855) hydrogen bonds : angle 4.04447 / 2.93 ( 2131) *********************** 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 217 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 205 time to evaluate : 0.377 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9568 (t0) cc_final: 0.8929 (t0) REVERT: B 59 LYS cc_start: 0.9487 (tmmt) cc_final: 0.9088 (ttpp) REVERT: B 63 GLU cc_start: 0.9068 (pp20) cc_final: 0.8826 (pp20) REVERT: B 93 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8768 (pp30) REVERT: C 25 PHE cc_start: 0.8925 (m-10) cc_final: 0.8668 (m-80) REVERT: C 36 LYS cc_start: 0.9643 (mmpt) cc_final: 0.9305 (mtmm) REVERT: C 89 ASN cc_start: 0.9810 (m-40) cc_final: 0.9500 (m110) REVERT: C 104 GLN cc_start: 0.9230 (mp10) cc_final: 0.8878 (mp10) REVERT: C 112 GLN cc_start: 0.7999 (mp10) cc_final: 0.7648 (mp10) REVERT: D 80 TYR cc_start: 0.8879 (m-80) cc_final: 0.8480 (m-80) REVERT: D 102 GLU cc_start: 0.9536 (mm-30) cc_final: 0.8905 (tp30) REVERT: E 108 ASN cc_start: 0.9276 (t0) cc_final: 0.8705 (t0) REVERT: F 27 GLN cc_start: 0.9192 (mp10) cc_final: 0.8834 (mp10) REVERT: F 74 GLU cc_start: 0.9015 (pm20) cc_final: 0.8791 (pm20) REVERT: G 56 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8479 (mm-30) REVERT: G 61 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8707 (mm-30) REVERT: G 94 ASN cc_start: 0.9071 (m-40) cc_final: 0.8381 (m-40) REVERT: G 112 GLN cc_start: 0.9047 (mp10) cc_final: 0.8302 (mp10) REVERT: H 65 ASP cc_start: 0.9622 (t0) cc_final: 0.9372 (t0) REVERT: H 92 GLN cc_start: 0.9301 (tm130) cc_final: 0.8957 (tm-30) outliers start: 12 outliers final: 7 residues processed: 209 average time/residue: 0.1493 time to fit residues: 42.5920 Evaluate side-chains 180 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain E residue 41 TYR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain M residue 28 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 30.0000 chunk 84 optimal weight: 30.0000 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.046284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.031569 restraints weight = 102479.014| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 4.29 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14660 Z= 0.192 Angle : 0.776 10.751 21196 Z= 0.439 Chirality : 0.048 0.360 2391 Planarity : 0.005 0.062 1543 Dihedral : 32.753 179.145 4579 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.19 % Allowed : 16.67 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.27), residues: 856 helix: 0.17 (0.21), residues: 555 sheet: -0.67 (1.02), residues: 29 loop : -0.84 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 99 TYR 0.043 0.002 TYR F 88 PHE 0.024 0.002 PHE A 67 TRP 0.006 0.001 TRP M 31 HIS 0.009 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.19 (14660) covalent geometry : angle 0.77609 / 0.44 (21196) hydrogen bonds : bond 0.05368 / 3.61 ( 855) hydrogen bonds : angle 3.85105 / 2.80 ( 2131) *********************** 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 221 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.372 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9583 (t0) cc_final: 0.9031 (t0) REVERT: B 59 LYS cc_start: 0.9487 (tmmt) cc_final: 0.9075 (ttpp) REVERT: B 63 GLU cc_start: 0.8986 (pp20) cc_final: 0.8760 (pp20) REVERT: C 25 PHE cc_start: 0.8776 (m-10) cc_final: 0.8478 (m-10) REVERT: C 36 LYS cc_start: 0.9576 (mmpt) cc_final: 0.9327 (mtmm) REVERT: C 104 GLN cc_start: 0.9027 (mp10) cc_final: 0.8674 (mp10) REVERT: C 112 GLN cc_start: 0.8208 (mp10) cc_final: 0.7912 (mp10) REVERT: D 56 MET cc_start: 0.9294 (tpp) cc_final: 0.9068 (tpp) REVERT: D 80 TYR cc_start: 0.8557 (m-80) cc_final: 0.8172 (m-80) REVERT: D 102 GLU cc_start: 0.9358 (mm-30) cc_final: 0.9068 (mp0) REVERT: E 90 MET cc_start: 0.9210 (mmm) cc_final: 0.8951 (mmp) REVERT: E 97 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7816 (mt-10) REVERT: E 108 ASN cc_start: 0.9402 (t0) cc_final: 0.8758 (t0) REVERT: G 56 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8352 (mm-30) REVERT: G 61 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8623 (mm-30) REVERT: G 72 ASP cc_start: 0.9109 (m-30) cc_final: 0.8847 (p0) REVERT: G 92 GLU cc_start: 0.8420 (tt0) cc_final: 0.8176 (tt0) REVERT: G 94 ASN cc_start: 0.8996 (m-40) cc_final: 0.8244 (m110) REVERT: G 112 GLN cc_start: 0.9066 (mp10) cc_final: 0.8484 (mp10) REVERT: H 65 ASP cc_start: 0.9460 (t0) cc_final: 0.9198 (t0) REVERT: H 92 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.8956 (tm-30) REVERT: H 98 LEU cc_start: 0.9225 (tp) cc_final: 0.9023 (tt) outliers start: 16 outliers final: 5 residues processed: 210 average time/residue: 0.1461 time to fit residues: 41.9149 Evaluate side-chains 183 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 177 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 92 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 40.0000 chunk 84 optimal weight: 30.0000 chunk 1 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 95 optimal weight: 30.0000 chunk 29 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 85 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.044614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.029769 restraints weight = 103242.442| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 4.08 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14660 Z= 0.255 Angle : 0.817 10.289 21196 Z= 0.456 Chirality : 0.049 0.331 2391 Planarity : 0.006 0.062 1543 Dihedral : 32.740 179.033 4579 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.28 % Allowed : 18.31 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.27), residues: 856 helix: 0.24 (0.21), residues: 557 sheet: -1.71 (1.32), residues: 15 loop : -0.76 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 76 TYR 0.063 0.003 TYR F 88 PHE 0.023 0.002 PHE A 67 TRP 0.005 0.001 TRP M 84 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.26 (14660) covalent geometry : angle 0.81709 / 0.46 (21196) hydrogen bonds : bond 0.07553 / 5.08 ( 855) hydrogen bonds : angle 3.88646 / 2.81 ( 2131) *********************** 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 217 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.405 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9613 (tt0) cc_final: 0.9170 (tp-100) REVERT: A 108 ASN cc_start: 0.9593 (t0) cc_final: 0.9134 (t0) REVERT: B 59 LYS cc_start: 0.9516 (tmmt) cc_final: 0.9110 (ttpp) REVERT: B 63 GLU cc_start: 0.9122 (pp20) cc_final: 0.8916 (pp20) REVERT: C 104 GLN cc_start: 0.9258 (mp10) cc_final: 0.8898 (mp10) REVERT: D 80 TYR cc_start: 0.8772 (m-80) cc_final: 0.8313 (m-80) REVERT: D 102 GLU cc_start: 0.9587 (mm-30) cc_final: 0.9114 (tp30) REVERT: F 27 GLN cc_start: 0.9107 (mp10) cc_final: 0.8860 (mp10) REVERT: F 63 GLU cc_start: 0.9554 (OUTLIER) cc_final: 0.9257 (pm20) REVERT: F 79 LYS cc_start: 0.9152 (pttm) cc_final: 0.8924 (pttm) REVERT: G 61 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8871 (mm-30) REVERT: G 72 ASP cc_start: 0.9280 (m-30) cc_final: 0.8984 (p0) REVERT: G 94 ASN cc_start: 0.8993 (m-40) cc_final: 0.8313 (m110) REVERT: G 100 VAL cc_start: 0.8937 (t) cc_final: 0.8659 (p) REVERT: G 112 GLN cc_start: 0.8922 (mp10) cc_final: 0.8352 (mp10) REVERT: H 65 ASP cc_start: 0.9667 (t0) cc_final: 0.9404 (t0) REVERT: H 92 GLN cc_start: 0.9415 (OUTLIER) cc_final: 0.9056 (tm-30) REVERT: H 96 ARG cc_start: 0.9064 (ptm-80) cc_final: 0.8372 (ttp80) outliers start: 24 outliers final: 15 residues processed: 202 average time/residue: 0.1464 time to fit residues: 40.6282 Evaluate side-chains 195 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain M residue 123 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 66 optimal weight: 8.9990 chunk 80 optimal weight: 30.0000 chunk 70 optimal weight: 1.9990 chunk 103 optimal weight: 40.0000 chunk 59 optimal weight: 9.9990 chunk 100 optimal weight: 30.0000 chunk 111 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.045819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.030726 restraints weight = 100319.838| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 4.05 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14660 Z= 0.186 Angle : 0.778 10.381 21196 Z= 0.435 Chirality : 0.048 0.337 2391 Planarity : 0.005 0.054 1543 Dihedral : 32.691 178.996 4579 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.55 % Allowed : 20.90 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.27), residues: 856 helix: 0.36 (0.21), residues: 558 sheet: -1.05 (0.99), residues: 30 loop : -0.71 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 76 TYR 0.055 0.002 TYR F 88 PHE 0.038 0.002 PHE A 67 TRP 0.006 0.001 TRP M 88 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.19 (14660) covalent geometry : angle 0.77843 / 0.43 (21196) hydrogen bonds : bond 0.05160 / 3.48 ( 855) hydrogen bonds : angle 3.77719 / 2.74 ( 2131) *********************** 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 231 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.369 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9591 (tt0) cc_final: 0.9096 (tp40) REVERT: A 108 ASN cc_start: 0.9588 (t0) cc_final: 0.9129 (t0) REVERT: A 120 MET cc_start: 0.8928 (mmm) cc_final: 0.8487 (mmm) REVERT: B 59 LYS cc_start: 0.9514 (tmmt) cc_final: 0.9095 (ttpp) REVERT: B 63 GLU cc_start: 0.9075 (pp20) cc_final: 0.8846 (pp20) REVERT: C 36 LYS cc_start: 0.9654 (mmpt) cc_final: 0.9387 (mtmm) REVERT: C 104 GLN cc_start: 0.9177 (mp10) cc_final: 0.8787 (mp10) REVERT: C 112 GLN cc_start: 0.8008 (mp10) cc_final: 0.7692 (mp10) REVERT: D 56 MET cc_start: 0.9514 (tpp) cc_final: 0.9227 (tpp) REVERT: D 102 GLU cc_start: 0.9502 (mm-30) cc_final: 0.9037 (tp30) REVERT: E 68 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.8918 (tm-30) REVERT: E 105 GLU cc_start: 0.9359 (tp30) cc_final: 0.9122 (mm-30) REVERT: E 108 ASN cc_start: 0.9529 (t0) cc_final: 0.9205 (t0) REVERT: F 63 GLU cc_start: 0.9470 (pm20) cc_final: 0.9172 (pm20) REVERT: F 74 GLU cc_start: 0.9020 (pp20) cc_final: 0.8784 (pp20) REVERT: G 61 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8755 (mm-30) REVERT: G 94 ASN cc_start: 0.9018 (m-40) cc_final: 0.8310 (m110) REVERT: G 112 GLN cc_start: 0.8881 (mp10) cc_final: 0.8307 (mp10) REVERT: H 65 ASP cc_start: 0.9651 (t0) cc_final: 0.9384 (t0) REVERT: H 76 ARG cc_start: 0.9381 (mtm-85) cc_final: 0.9116 (mtm-85) REVERT: H 82 LYS cc_start: 0.9548 (mmmt) cc_final: 0.9227 (mmmt) REVERT: H 92 GLN cc_start: 0.9419 (OUTLIER) cc_final: 0.9191 (tm-30) REVERT: H 96 ARG cc_start: 0.9052 (ptm-80) cc_final: 0.8437 (ttp80) outliers start: 26 outliers final: 13 residues processed: 215 average time/residue: 0.1302 time to fit residues: 38.6421 Evaluate side-chains 199 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain M residue 123 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 42 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 82 optimal weight: 30.0000 chunk 9 optimal weight: 4.9990 chunk 81 optimal weight: 30.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 ASN M 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.050545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.036774 restraints weight = 127178.259| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 4.07 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14660 Z= 0.172 Angle : 0.775 9.452 21196 Z= 0.432 Chirality : 0.047 0.338 2391 Planarity : 0.005 0.054 1543 Dihedral : 32.589 178.722 4579 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.14 % Allowed : 23.36 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.27), residues: 856 helix: 0.35 (0.21), residues: 558 sheet: -0.87 (1.04), residues: 29 loop : -0.75 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 76 TYR 0.065 0.003 TYR F 88 PHE 0.028 0.002 PHE A 67 TRP 0.015 0.002 TRP M 84 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (14660) covalent geometry : angle 0.77487 / 0.43 (21196) hydrogen bonds : bond 0.04784 / 3.20 ( 855) hydrogen bonds : angle 3.74809 / 2.71 ( 2131) *********************** 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 225 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.355 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9528 (tt0) cc_final: 0.9046 (tp40) REVERT: A 108 ASN cc_start: 0.9565 (t0) cc_final: 0.9067 (t0) REVERT: B 59 LYS cc_start: 0.9534 (tmmt) cc_final: 0.9116 (ttpp) REVERT: B 63 GLU cc_start: 0.9076 (pp20) cc_final: 0.8830 (pp20) REVERT: C 25 PHE cc_start: 0.9045 (m-10) cc_final: 0.8618 (m-10) REVERT: C 36 LYS cc_start: 0.9656 (mmpt) cc_final: 0.9384 (mtmm) REVERT: C 104 GLN cc_start: 0.9161 (mp10) cc_final: 0.8778 (mp10) REVERT: C 112 GLN cc_start: 0.7919 (mp10) cc_final: 0.7314 (mp10) REVERT: D 31 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8762 (mmtt) REVERT: D 56 MET cc_start: 0.9474 (tpp) cc_final: 0.9198 (tpp) REVERT: D 102 GLU cc_start: 0.9433 (mm-30) cc_final: 0.9004 (tp30) REVERT: E 108 ASN cc_start: 0.9544 (t0) cc_final: 0.9155 (t0) REVERT: F 27 GLN cc_start: 0.9030 (mp10) cc_final: 0.8723 (mp10) REVERT: F 31 LYS cc_start: 0.9644 (tmtt) cc_final: 0.9262 (tptp) REVERT: F 74 GLU cc_start: 0.8877 (pp20) cc_final: 0.8623 (pp20) REVERT: F 88 TYR cc_start: 0.8947 (m-10) cc_final: 0.8742 (m-80) REVERT: F 91 LYS cc_start: 0.9735 (tppt) cc_final: 0.9432 (mtpt) REVERT: G 56 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8559 (mm-30) REVERT: G 61 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8681 (mm-30) REVERT: G 72 ASP cc_start: 0.9127 (m-30) cc_final: 0.8786 (p0) REVERT: G 94 ASN cc_start: 0.8998 (m-40) cc_final: 0.8253 (m110) REVERT: G 112 GLN cc_start: 0.8876 (mp10) cc_final: 0.8307 (mp10) REVERT: H 42 LEU cc_start: 0.9815 (tt) cc_final: 0.9588 (pp) REVERT: H 65 ASP cc_start: 0.9526 (t0) cc_final: 0.9256 (t0) REVERT: H 80 TYR cc_start: 0.8436 (m-80) cc_final: 0.8068 (m-80) REVERT: H 82 LYS cc_start: 0.9576 (mmmt) cc_final: 0.9351 (mmmt) REVERT: H 92 GLN cc_start: 0.9404 (OUTLIER) cc_final: 0.9167 (tm-30) REVERT: H 96 ARG cc_start: 0.8994 (ptm-80) cc_final: 0.8425 (ttp80) outliers start: 23 outliers final: 14 residues processed: 212 average time/residue: 0.1435 time to fit residues: 41.7173 Evaluate side-chains 199 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain M residue 123 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 103 optimal weight: 40.0000 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 83 optimal weight: 30.0000 chunk 75 optimal weight: 30.0000 chunk 98 optimal weight: 30.0000 chunk 29 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 overall best weight: 4.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.049499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.035857 restraints weight = 128084.460| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.96 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 14660 Z= 0.238 Angle : 0.810 9.073 21196 Z= 0.450 Chirality : 0.048 0.328 2391 Planarity : 0.005 0.053 1543 Dihedral : 32.582 179.852 4579 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.42 % Allowed : 23.63 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.27), residues: 856 helix: 0.39 (0.21), residues: 559 sheet: -1.59 (1.43), residues: 15 loop : -0.73 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 76 TYR 0.051 0.003 TYR F 88 PHE 0.032 0.002 PHE A 67 TRP 0.010 0.002 TRP M 84 HIS 0.006 0.002 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.24 (14660) covalent geometry : angle 0.81049 / 0.45 (21196) hydrogen bonds : bond 0.06636 / 4.44 ( 855) hydrogen bonds : angle 3.87663 / 2.81 ( 2131) *********************** 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 218 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.271 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9457 (tt0) cc_final: 0.9028 (tp40) REVERT: A 93 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8773 (mm110) REVERT: A 108 ASN cc_start: 0.9589 (t0) cc_final: 0.9081 (t0) REVERT: A 120 MET cc_start: 0.8899 (mmm) cc_final: 0.8465 (mmm) REVERT: B 59 LYS cc_start: 0.9536 (tmmt) cc_final: 0.9137 (ttpp) REVERT: C 36 LYS cc_start: 0.9641 (mmpt) cc_final: 0.9427 (mtmm) REVERT: C 104 GLN cc_start: 0.9132 (mp10) cc_final: 0.8777 (mp10) REVERT: C 112 GLN cc_start: 0.8028 (mp10) cc_final: 0.7584 (mp10) REVERT: D 56 MET cc_start: 0.9395 (tpp) cc_final: 0.9115 (tpp) REVERT: D 102 GLU cc_start: 0.9329 (mm-30) cc_final: 0.8927 (tp30) REVERT: D 105 LYS cc_start: 0.9273 (mmtt) cc_final: 0.8974 (ptpp) REVERT: E 97 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8167 (mt-10) REVERT: E 108 ASN cc_start: 0.9555 (t0) cc_final: 0.9071 (t0) REVERT: F 74 GLU cc_start: 0.8791 (pp20) cc_final: 0.8534 (pp20) REVERT: F 88 TYR cc_start: 0.8998 (m-10) cc_final: 0.8693 (m-80) REVERT: G 61 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8718 (mm-30) REVERT: G 72 ASP cc_start: 0.9110 (m-30) cc_final: 0.8747 (p0) REVERT: G 94 ASN cc_start: 0.8933 (m-40) cc_final: 0.8155 (m110) REVERT: G 112 GLN cc_start: 0.8917 (mp10) cc_final: 0.8377 (mp10) REVERT: H 65 ASP cc_start: 0.9511 (t0) cc_final: 0.9153 (t0) REVERT: H 76 ARG cc_start: 0.9336 (ttm110) cc_final: 0.9112 (ttp-110) REVERT: H 92 GLN cc_start: 0.9374 (OUTLIER) cc_final: 0.9055 (tm-30) REVERT: H 96 ARG cc_start: 0.9069 (ptm-80) cc_final: 0.8560 (ttp80) outliers start: 25 outliers final: 20 residues processed: 203 average time/residue: 0.1330 time to fit residues: 37.2351 Evaluate side-chains 204 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain M residue 123 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 30.0000 chunk 68 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 89 optimal weight: 50.0000 chunk 96 optimal weight: 30.0000 chunk 70 optimal weight: 3.9990 chunk 88 optimal weight: 50.0000 chunk 112 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 104 optimal weight: 50.0000 chunk 92 optimal weight: 30.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.049448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.035823 restraints weight = 126582.071| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 3.88 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14660 Z= 0.225 Angle : 0.821 9.780 21196 Z= 0.454 Chirality : 0.048 0.323 2391 Planarity : 0.005 0.051 1543 Dihedral : 32.602 179.736 4579 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.42 % Allowed : 24.04 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.27), residues: 856 helix: 0.29 (0.21), residues: 560 sheet: -1.60 (1.43), residues: 15 loop : -0.72 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 76 TYR 0.056 0.003 TYR F 88 PHE 0.063 0.003 PHE A 67 TRP 0.011 0.002 TRP M 88 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.23 (14660) covalent geometry : angle 0.82126 / 0.45 (21196) hydrogen bonds : bond 0.05964 / 3.99 ( 855) hydrogen bonds : angle 3.92672 / 2.84 ( 2131) *********************** 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 215 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.304 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9449 (tt0) cc_final: 0.9024 (tp-100) REVERT: A 108 ASN cc_start: 0.9575 (t0) cc_final: 0.9064 (t0) REVERT: A 120 MET cc_start: 0.8891 (mmm) cc_final: 0.8471 (mmm) REVERT: B 59 LYS cc_start: 0.9518 (tmmt) cc_final: 0.9235 (ttpp) REVERT: C 104 GLN cc_start: 0.9120 (mp10) cc_final: 0.8764 (mp10) REVERT: C 112 GLN cc_start: 0.8097 (mp10) cc_final: 0.7593 (mp10) REVERT: D 56 MET cc_start: 0.9347 (tpp) cc_final: 0.9084 (tpp) REVERT: D 73 GLU cc_start: 0.8885 (tp30) cc_final: 0.8576 (tp30) REVERT: D 76 ARG cc_start: 0.9361 (ttm110) cc_final: 0.8868 (ttm110) REVERT: D 102 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8836 (tp30) REVERT: E 97 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8235 (mt-10) REVERT: E 108 ASN cc_start: 0.9495 (t0) cc_final: 0.9105 (t0) REVERT: F 74 GLU cc_start: 0.8752 (pp20) cc_final: 0.8508 (pp20) REVERT: G 56 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8615 (mm-30) REVERT: G 61 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8706 (mm-30) REVERT: G 64 GLU cc_start: 0.9085 (pp20) cc_final: 0.8864 (pp20) REVERT: G 72 ASP cc_start: 0.9069 (m-30) cc_final: 0.8692 (p0) REVERT: G 94 ASN cc_start: 0.8932 (m-40) cc_final: 0.8146 (m110) REVERT: G 112 GLN cc_start: 0.8915 (mp10) cc_final: 0.8361 (mp10) REVERT: H 42 LEU cc_start: 0.9787 (tt) cc_final: 0.9578 (pp) REVERT: H 65 ASP cc_start: 0.9494 (t0) cc_final: 0.9156 (t0) REVERT: H 76 ARG cc_start: 0.9384 (ttm110) cc_final: 0.9108 (ttp-110) REVERT: H 80 TYR cc_start: 0.8495 (m-80) cc_final: 0.7994 (m-80) REVERT: H 92 GLN cc_start: 0.9359 (OUTLIER) cc_final: 0.9111 (tm-30) REVERT: H 96 ARG cc_start: 0.9094 (ptm-80) cc_final: 0.8573 (ttp80) REVERT: M 89 ASP cc_start: 0.8666 (m-30) cc_final: 0.8242 (t70) outliers start: 25 outliers final: 18 residues processed: 201 average time/residue: 0.1364 time to fit residues: 37.7439 Evaluate side-chains 199 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain H residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 23 optimal weight: 7.9990 chunk 103 optimal weight: 40.0000 chunk 87 optimal weight: 30.0000 chunk 29 optimal weight: 2.9990 chunk 85 optimal weight: 30.0000 chunk 73 optimal weight: 50.0000 chunk 65 optimal weight: 6.9990 chunk 84 optimal weight: 30.0000 chunk 97 optimal weight: 30.0000 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 50.0000 overall best weight: 11.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.041121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.026774 restraints weight = 108982.706| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.51 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 14660 Z= 0.461 Angle : 1.049 10.240 21196 Z= 0.564 Chirality : 0.057 0.289 2391 Planarity : 0.007 0.062 1543 Dihedral : 33.006 178.122 4579 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 32.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.83 % Allowed : 24.45 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.27), residues: 856 helix: -0.21 (0.21), residues: 563 sheet: -1.81 (1.42), residues: 15 loop : -1.08 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 131 TYR 0.050 0.004 TYR B 88 PHE 0.026 0.003 PHE D 62 TRP 0.020 0.003 TRP M 84 HIS 0.010 0.003 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00876 / 0.46 (14660) covalent geometry : angle 1.04874 / 0.56 (21196) hydrogen bonds : bond 0.14213 / 9.54 ( 855) hydrogen bonds : angle 4.60593 / 3.30 ( 2131) *********************** 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 205 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.347 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: A 68 GLN cc_start: 0.9418 (tt0) cc_final: 0.8949 (tp40) REVERT: A 94 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8322 (tt0) REVERT: A 108 ASN cc_start: 0.9631 (t0) cc_final: 0.9151 (t0) REVERT: A 120 MET cc_start: 0.8867 (mmm) cc_final: 0.8094 (mmm) REVERT: A 125 GLN cc_start: 0.9245 (mt0) cc_final: 0.9000 (mt0) REVERT: B 59 LYS cc_start: 0.9552 (tmmt) cc_final: 0.9294 (ttpp) REVERT: C 104 GLN cc_start: 0.9003 (mp10) cc_final: 0.8747 (mp10) REVERT: D 56 MET cc_start: 0.9356 (tpp) cc_final: 0.9129 (tpp) REVERT: D 73 GLU cc_start: 0.9085 (tp30) cc_final: 0.8644 (tp30) REVERT: D 76 ARG cc_start: 0.9490 (ttm110) cc_final: 0.9155 (ttm110) REVERT: D 77 LEU cc_start: 0.9682 (OUTLIER) cc_final: 0.9416 (pt) REVERT: D 102 GLU cc_start: 0.9399 (mm-30) cc_final: 0.9041 (mm-30) REVERT: D 105 LYS cc_start: 0.9416 (mmtt) cc_final: 0.9108 (ptpp) REVERT: E 84 PHE cc_start: 0.9220 (m-80) cc_final: 0.8892 (m-80) REVERT: E 97 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8238 (mt-10) REVERT: G 61 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8850 (mm-30) REVERT: G 64 GLU cc_start: 0.9213 (pp20) cc_final: 0.8962 (pp20) REVERT: G 72 ASP cc_start: 0.9114 (m-30) cc_final: 0.8713 (p0) REVERT: G 112 GLN cc_start: 0.9001 (mp10) cc_final: 0.8462 (mp10) REVERT: H 65 ASP cc_start: 0.9563 (t0) cc_final: 0.9239 (t0) REVERT: H 76 ARG cc_start: 0.9439 (ttm110) cc_final: 0.9233 (ttp-110) REVERT: H 92 GLN cc_start: 0.9431 (OUTLIER) cc_final: 0.8944 (tm-30) REVERT: H 96 ARG cc_start: 0.9343 (ptm-80) cc_final: 0.8656 (ttp80) outliers start: 28 outliers final: 19 residues processed: 188 average time/residue: 0.1453 time to fit residues: 37.5383 Evaluate side-chains 187 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 106 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain M residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 41 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 96 optimal weight: 30.0000 chunk 57 optimal weight: 6.9990 chunk 75 optimal weight: 40.0000 chunk 58 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN H 46 HIS ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.043057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.028603 restraints weight = 102031.553| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.46 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14660 Z= 0.228 Angle : 0.908 14.681 21196 Z= 0.497 Chirality : 0.051 0.317 2391 Planarity : 0.006 0.049 1543 Dihedral : 33.056 178.724 4579 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.60 % Allowed : 26.91 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.27), residues: 856 helix: -0.04 (0.21), residues: 560 sheet: -1.99 (1.44), residues: 15 loop : -0.93 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 32 TYR 0.044 0.003 TYR D 80 PHE 0.015 0.002 PHE A 67 TRP 0.018 0.003 TRP M 88 HIS 0.012 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.23 (14660) covalent geometry : angle 0.90802 / 0.50 (21196) hydrogen bonds : bond 0.06458 / 4.31 ( 855) hydrogen bonds : angle 4.19997 / 3.01 ( 2131) ********************** 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 209 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.310 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: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9550 (tt0) cc_final: 0.9018 (tp-100) REVERT: A 108 ASN cc_start: 0.9592 (t0) cc_final: 0.9105 (t0) REVERT: A 120 MET cc_start: 0.8773 (mmm) cc_final: 0.8175 (mmm) REVERT: B 59 LYS cc_start: 0.9531 (tmmt) cc_final: 0.9280 (ttpp) REVERT: B 88 TYR cc_start: 0.8677 (m-80) cc_final: 0.8463 (m-80) REVERT: C 104 GLN cc_start: 0.9108 (mp10) cc_final: 0.8756 (mp10) REVERT: D 56 MET cc_start: 0.9372 (tpp) cc_final: 0.9169 (tpp) REVERT: D 73 GLU cc_start: 0.8941 (tp30) cc_final: 0.8257 (tp30) REVERT: D 76 ARG cc_start: 0.9427 (ttm110) cc_final: 0.8853 (ttm110) REVERT: D 102 GLU cc_start: 0.9340 (mm-30) cc_final: 0.8854 (tp30) REVERT: E 84 PHE cc_start: 0.9210 (m-80) cc_final: 0.8869 (m-80) REVERT: E 97 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8228 (mt-10) REVERT: E 108 ASN cc_start: 0.9588 (t0) cc_final: 0.9261 (t0) REVERT: F 27 GLN cc_start: 0.9053 (mp10) cc_final: 0.8692 (mp10) REVERT: F 31 LYS cc_start: 0.9585 (tmtt) cc_final: 0.9217 (tptp) REVERT: F 84 MET cc_start: 0.9160 (tpp) cc_final: 0.8895 (tpp) REVERT: F 91 LYS cc_start: 0.9730 (tppt) cc_final: 0.9432 (mtpt) REVERT: G 56 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8665 (mm-30) REVERT: G 61 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8814 (mm-30) REVERT: G 64 GLU cc_start: 0.9212 (pp20) cc_final: 0.8948 (pp20) REVERT: G 72 ASP cc_start: 0.9158 (m-30) cc_final: 0.8716 (p0) REVERT: G 112 GLN cc_start: 0.8965 (mp10) cc_final: 0.8382 (mp10) REVERT: H 42 LEU cc_start: 0.9791 (tt) cc_final: 0.9568 (pp) REVERT: H 65 ASP cc_start: 0.9513 (t0) cc_final: 0.9288 (t0) REVERT: H 76 ARG cc_start: 0.9477 (ttm110) cc_final: 0.9201 (ttp-110) REVERT: H 92 GLN cc_start: 0.9396 (OUTLIER) cc_final: 0.8788 (tm-30) REVERT: H 96 ARG cc_start: 0.9261 (ptm-80) cc_final: 0.8499 (ttp80) outliers start: 19 outliers final: 14 residues processed: 198 average time/residue: 0.1366 time to fit residues: 37.4254 Evaluate side-chains 194 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain E residue 41 TYR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain H residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 23 optimal weight: 2.9990 chunk 80 optimal weight: 30.0000 chunk 77 optimal weight: 30.0000 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 96 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 84 optimal weight: 30.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.043386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.028680 restraints weight = 102689.035| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.43 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14660 Z= 0.230 Angle : 0.885 10.926 21196 Z= 0.485 Chirality : 0.050 0.304 2391 Planarity : 0.005 0.050 1543 Dihedral : 32.848 178.877 4579 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.60 % Allowed : 26.78 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.27), residues: 856 helix: 0.07 (0.21), residues: 560 sheet: -1.92 (1.47), residues: 15 loop : -0.93 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 76 TYR 0.069 0.003 TYR D 80 PHE 0.012 0.002 PHE D 62 TRP 0.014 0.002 TRP M 88 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.23 (14660) covalent geometry : angle 0.88463 / 0.48 (21196) hydrogen bonds : bond 0.06515 / 4.36 ( 855) hydrogen bonds : angle 4.12088 / 2.94 ( 2131) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2582.14 seconds wall clock time: 45 minutes 13.60 seconds (2713.60 seconds total)