Starting phenix.real_space_refine on Tue Feb 3 17:02:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nrj_49735/02_2026/9nrj_49735_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nrj_49735/02_2026/9nrj_49735.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9nrj_49735/02_2026/9nrj_49735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nrj_49735/02_2026/9nrj_49735.map" model { file = "/net/cci-nas-00/data/ceres_data/9nrj_49735/02_2026/9nrj_49735_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nrj_49735/02_2026/9nrj_49735_neut.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= 0.000 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: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 3378 2.51 5 N 918 2.21 5 O 1071 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5386 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1530 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 189} Chain: "B" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1945 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 226} Chain: "C" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "T" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 921 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 112} Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.27, per 1000 atoms: 0.24 Number of scatterers: 5386 At special positions: 0 Unit cell: (75.53, 86.32, 100.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 1071 8.00 N 918 7.00 C 3378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 89 " distance=2.16 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 183 " distance=2.19 Simple disulfide: pdb=" SG CYS A 158 " - pdb=" SG CYS B 171 " distance=2.13 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 93 " distance=2.26 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 210 " distance=2.12 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 95 " distance=2.16 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " BETA1-6 " NAG D 1 " - " FUC D 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG D 1 " - " ASN A 143 " " NAG E 1 " - " ASN A 18 " " NAG F 1 " - " ASN B 20 " Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 364.2 milliseconds 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1240 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 16 sheets defined 4.3% alpha, 49.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 Processing helix chain 'B' and resid 131 through 139 Processing helix chain 'B' and resid 198 through 202 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'T' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 removed outlier: 3.690A pdb=" N LEU A 61 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 14 removed outlier: 6.910A pdb=" N LEU A 11 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LYS A 109 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE A 13 " --> pdb=" O LYS A 109 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ARG A 36 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LEU A 45 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 14 removed outlier: 6.910A pdb=" N LEU A 11 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LYS A 109 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE A 13 " --> pdb=" O LYS A 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 122 removed outlier: 3.825A pdb=" N VAL A 132 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER A 176 " --> pdb=" O SER A 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 6 through 9 removed outlier: 3.539A pdb=" N SER B 9 " --> pdb=" O SER B 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.556A pdb=" N ALA B 33 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG B 38 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 16 Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 128 removed outlier: 3.541A pdb=" N VAL B 144 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N THR B 142 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL B 196 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL B 144 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU B 194 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU B 146 " --> pdb=" O SER B 192 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N SER B 192 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N THR B 148 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU B 190 " --> pdb=" O THR B 148 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 124 through 128 removed outlier: 3.541A pdb=" N VAL B 144 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N THR B 142 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL B 196 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL B 144 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU B 194 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU B 146 " --> pdb=" O SER B 192 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N SER B 192 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N THR B 148 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU B 190 " --> pdb=" O THR B 148 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 164 through 165 Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.556A pdb=" N THR C 109 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ARG C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.556A pdb=" N THR C 109 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 2 through 7 Processing sheet with id=AB6, first strand: chain 'T' and resid 10 through 12 removed outlier: 6.404A pdb=" N ARG T 38 " --> pdb=" O LYS T 47 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LYS T 47 " --> pdb=" O ARG T 38 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN T 56 " --> pdb=" O SER T 52 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'T' and resid 10 through 12 217 hydrogen bonds defined for protein. 516 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.25: 573 1.25 - 1.46: 2377 1.46 - 1.66: 2508 1.66 - 1.87: 47 1.87 - 2.08: 3 Bond restraints: 5508 Sorted by residual: bond pdb=" C VAL A 152 " pdb=" O VAL A 152 " ideal model delta sigma weight residual 1.236 1.637 -0.400 1.19e-02 7.06e+03 1.13e+03 bond pdb=" C TYR A 153 " pdb=" O TYR A 153 " ideal model delta sigma weight residual 1.235 1.573 -0.338 1.26e-02 6.30e+03 7.18e+02 bond pdb=" C TYR B 50 " pdb=" O TYR B 50 " ideal model delta sigma weight residual 1.234 1.578 -0.344 1.31e-02 5.83e+03 6.90e+02 bond pdb=" C ASP A 151 " pdb=" O ASP A 151 " ideal model delta sigma weight residual 1.235 1.552 -0.316 1.26e-02 6.30e+03 6.30e+02 bond pdb=" CA HIS B 207 " pdb=" CB HIS B 207 " ideal model delta sigma weight residual 1.528 1.867 -0.339 1.39e-02 5.18e+03 5.95e+02 ... (remaining 5503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.70: 5744 7.70 - 15.41: 1384 15.41 - 23.11: 274 23.11 - 30.81: 64 30.81 - 38.51: 11 Bond angle restraints: 7477 Sorted by residual: angle pdb=" CA GLY T 8 " pdb=" C GLY T 8 " pdb=" O GLY T 8 " ideal model delta sigma weight residual 122.45 105.61 16.84 7.20e-01 1.93e+00 5.47e+02 angle pdb=" O LEU B 92 " pdb=" C LEU B 92 " pdb=" N CYS B 93 " ideal model delta sigma weight residual 123.27 149.81 -26.54 1.22e+00 6.72e-01 4.73e+02 angle pdb=" CA TYR B 37 " pdb=" C TYR B 37 " pdb=" O TYR B 37 " ideal model delta sigma weight residual 120.40 97.87 22.53 1.05e+00 9.07e-01 4.60e+02 angle pdb=" CA LEU B 92 " pdb=" C LEU B 92 " pdb=" O LEU B 92 " ideal model delta sigma weight residual 120.66 96.01 24.65 1.15e+00 7.56e-01 4.60e+02 angle pdb=" C ALA T 97 " pdb=" CA ALA T 97 " pdb=" CB ALA T 97 " ideal model delta sigma weight residual 111.43 84.93 26.50 1.24e+00 6.50e-01 4.57e+02 ... (remaining 7472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 2403 17.97 - 35.94: 733 35.94 - 53.92: 172 53.92 - 71.89: 45 71.89 - 89.86: 27 Dihedral angle restraints: 3380 sinusoidal: 1439 harmonic: 1941 Sorted by residual: dihedral pdb=" C PRO B 77 " pdb=" N PRO B 77 " pdb=" CA PRO B 77 " pdb=" CB PRO B 77 " ideal model delta harmonic sigma weight residual -120.70 -74.76 -45.94 0 2.50e+00 1.60e-01 3.38e+02 dihedral pdb=" C VAL A 152 " pdb=" N VAL A 152 " pdb=" CA VAL A 152 " pdb=" CB VAL A 152 " ideal model delta harmonic sigma weight residual -122.00 -167.01 45.01 0 2.50e+00 1.60e-01 3.24e+02 dihedral pdb=" N THR B 88 " pdb=" C THR B 88 " pdb=" CA THR B 88 " pdb=" CB THR B 88 " ideal model delta harmonic sigma weight residual 123.40 81.51 41.89 0 2.50e+00 1.60e-01 2.81e+02 ... (remaining 3377 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.911: 792 0.911 - 1.821: 31 1.821 - 2.731: 3 2.731 - 3.641: 2 3.641 - 4.551: 1 Chirality restraints: 829 Sorted by residual: chirality pdb=" CB ILE A 192 " pdb=" CA ILE A 192 " pdb=" CG1 ILE A 192 " pdb=" CG2 ILE A 192 " both_signs ideal model delta sigma weight residual False 2.64 -1.91 4.55 2.00e-01 2.50e+01 5.18e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-02 2.50e+03 4.97e+02 chirality pdb=" CB ILE T 53 " pdb=" CA ILE T 53 " pdb=" CG1 ILE T 53 " pdb=" CG2 ILE T 53 " both_signs ideal model delta sigma weight residual False 2.64 -0.85 3.49 2.00e-01 2.50e+01 3.05e+02 ... (remaining 826 not shown) Planarity restraints: 970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 240 " -0.283 2.00e-02 2.50e+03 2.02e-01 1.02e+03 pdb=" CG TRP B 240 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP B 240 " 0.079 2.00e-02 2.50e+03 pdb=" CD2 TRP B 240 " 0.275 2.00e-02 2.50e+03 pdb=" NE1 TRP B 240 " 0.125 2.00e-02 2.50e+03 pdb=" CE2 TRP B 240 " -0.056 2.00e-02 2.50e+03 pdb=" CE3 TRP B 240 " 0.089 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 240 " -0.445 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 240 " 0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP B 240 " 0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 91 " 0.203 2.00e-02 2.50e+03 1.86e-01 6.89e+02 pdb=" CG TYR B 91 " -0.107 2.00e-02 2.50e+03 pdb=" CD1 TYR B 91 " -0.069 2.00e-02 2.50e+03 pdb=" CD2 TYR B 91 " -0.244 2.00e-02 2.50e+03 pdb=" CE1 TYR B 91 " -0.100 2.00e-02 2.50e+03 pdb=" CE2 TYR B 91 " 0.025 2.00e-02 2.50e+03 pdb=" CZ TYR B 91 " 0.376 2.00e-02 2.50e+03 pdb=" OH TYR B 91 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.244 2.00e-02 2.50e+03 2.05e-01 5.27e+02 pdb=" C7 NAG E 2 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.171 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.345 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.013 2.00e-02 2.50e+03 ... (remaining 967 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.03: 17 2.03 - 2.75: 1361 2.75 - 3.47: 6487 3.47 - 4.18: 14582 4.18 - 4.90: 22079 Nonbonded interactions: 44526 Sorted by model distance: nonbonded pdb=" O ASP A 151 " pdb=" OG SER A 176 " model vdw 1.317 3.040 nonbonded pdb=" O VAL A 152 " pdb=" O TRP A 175 " model vdw 1.640 3.040 nonbonded pdb=" OD1 ASP A 151 " pdb=" OG SER A 176 " model vdw 1.710 3.040 nonbonded pdb=" C ASP A 151 " pdb=" OG SER A 176 " model vdw 1.738 3.270 nonbonded pdb=" O LYS A 178 " pdb=" CA SER A 179 " model vdw 1.826 2.776 ... (remaining 44521 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and resid 1 through 2) selection = (chain 'E' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.620 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 : 0.050 0.400 5522 Z= 3.382 Angle : 7.270 38.515 7513 Z= 4.673 Chirality : 0.497 4.551 829 Planarity : 0.054 0.247 967 Dihedral : 22.764 89.856 2122 Min Nonbonded Distance : 1.317 Molprobity Statistics. All-atom Clashscore : 42.86 Ramachandran Plot: Outliers : 5.42 % Allowed : 11.14 % Favored : 83.43 % Rotamer: Outliers : 16.75 % Allowed : 15.72 % Favored : 67.53 % Cbeta Deviations : 61.94 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.16 % Twisted Proline : 17.24 % Twisted General : 8.61 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.68 (0.27), residues: 664 helix: -4.21 (0.56), residues: 14 sheet: -2.59 (0.28), residues: 266 loop : -3.57 (0.24), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.197 0.024 ARG T 100 TYR 0.376 0.064 TYR B 91 PHE 0.221 0.053 PHE B 200 TRP 0.445 0.070 TRP B 240 HIS 0.122 0.038 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.05024 ( 5508) covalent geometry : angle 7.26078 ( 7477) SS BOND : bond 0.14461 ( 6) SS BOND : angle 9.54525 ( 12) hydrogen bonds : bond 0.27584 ( 186) hydrogen bonds : angle 11.07588 ( 516) link_BETA1-4 : bond 0.01689 ( 4) link_BETA1-4 : angle 7.40617 ( 12) link_BETA1-6 : bond 0.08235 ( 1) link_BETA1-6 : angle 8.02373 ( 3) link_NAG-ASN : bond 0.03495 ( 3) link_NAG-ASN : angle 10.33450 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 185 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.6790 (OUTLIER) cc_final: 0.6381 (tp-100) REVERT: A 32 LEU cc_start: 0.7906 (mt) cc_final: 0.7190 (mp) REVERT: A 34 TRP cc_start: 0.8416 (m100) cc_final: 0.8125 (m100) REVERT: A 64 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8257 (pp30) REVERT: A 97 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.8020 (p0) REVERT: A 153 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.5533 (p90) REVERT: A 165 MET cc_start: 0.7123 (mmt) cc_final: 0.6923 (mmm) REVERT: B 34 MET cc_start: 0.7564 (mmt) cc_final: 0.7312 (mmt) REVERT: B 49 TYR cc_start: 0.6667 (OUTLIER) cc_final: 0.5821 (m-80) REVERT: B 59 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6939 (mtpt) REVERT: B 77 PRO cc_start: 0.7687 (OUTLIER) cc_final: 0.7180 (Cg_exo) REVERT: B 90 PHE cc_start: 0.8447 (t80) cc_final: 0.7877 (t80) REVERT: B 150 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7554 (p90) REVERT: B 205 ARG cc_start: 0.8659 (mtm180) cc_final: 0.8456 (ttt90) REVERT: B 209 ARG cc_start: 0.8714 (mtm110) cc_final: 0.8302 (ttp80) REVERT: B 218 SER cc_start: 0.6452 (OUTLIER) cc_final: 0.6126 (m) REVERT: B 225 GLN cc_start: 0.8458 (mm110) cc_final: 0.8091 (tp40) REVERT: C 34 VAL cc_start: 0.8941 (t) cc_final: 0.8160 (m) REVERT: C 51 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7930 (mt) REVERT: C 79 TYR cc_start: 0.8416 (m-80) cc_final: 0.8110 (m-80) REVERT: C 97 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7995 (t80) REVERT: C 109 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7813 (p) REVERT: T 72 ASP cc_start: 0.8055 (m-30) cc_final: 0.7785 (t70) REVERT: T 93 TYR cc_start: 0.8638 (m-80) cc_final: 0.8393 (m-80) REVERT: T 100 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7630 (mtp180) outliers start: 97 outliers final: 23 residues processed: 253 average time/residue: 0.0783 time to fit residues: 24.6283 Evaluate side-chains 153 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLN Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 TYR Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 77 PRO Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 150 PHE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 97 PHE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain T residue 22 CYS Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 53 ILE Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 71 ARG Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain T residue 100 ARG Chi-restraints excluded: chain T residue 104 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN A 95 GLN A 97 ASN A 170 ASN A 185 ASN B 8 GLN ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN B 58 GLN B 103 GLN B 206 ASN B 211 GLN C 13 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 HIS ** T 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.180141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.151415 restraints weight = 6167.550| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.17 r_work: 0.3647 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 5522 Z= 0.294 Angle : 1.136 14.175 7513 Z= 0.592 Chirality : 0.058 0.282 829 Planarity : 0.008 0.079 967 Dihedral : 11.702 66.773 976 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 1.05 % Allowed : 6.02 % Favored : 92.92 % Rotamer: Outliers : 5.18 % Allowed : 20.38 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.27), residues: 664 helix: -2.30 (1.12), residues: 15 sheet: -1.77 (0.27), residues: 282 loop : -2.85 (0.25), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 60 TYR 0.037 0.003 TYR T 59 PHE 0.019 0.003 PHE C 67 TRP 0.035 0.003 TRP T 36 HIS 0.011 0.002 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 5508) covalent geometry : angle 1.11852 ( 7477) SS BOND : bond 0.00566 ( 6) SS BOND : angle 1.67718 ( 12) hydrogen bonds : bond 0.04958 ( 186) hydrogen bonds : angle 8.07564 ( 516) link_BETA1-4 : bond 0.00660 ( 4) link_BETA1-4 : angle 4.35727 ( 12) link_BETA1-6 : bond 0.01688 ( 1) link_BETA1-6 : angle 2.93411 ( 3) link_NAG-ASN : bond 0.00505 ( 3) link_NAG-ASN : angle 2.49838 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7457 (m-30) cc_final: 0.7097 (m-30) REVERT: A 88 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8211 (mp) REVERT: A 107 SER cc_start: 0.8481 (m) cc_final: 0.8226 (t) REVERT: A 175 TRP cc_start: 0.4721 (OUTLIER) cc_final: 0.3719 (p-90) REVERT: A 181 PHE cc_start: 0.4424 (OUTLIER) cc_final: 0.3285 (p90) REVERT: B 74 GLU cc_start: 0.6773 (tt0) cc_final: 0.6533 (tt0) REVERT: B 132 GLU cc_start: 0.8094 (tp30) cc_final: 0.7852 (mm-30) REVERT: T 52 SER cc_start: 0.9311 (m) cc_final: 0.9077 (t) outliers start: 30 outliers final: 8 residues processed: 138 average time/residue: 0.0796 time to fit residues: 14.2880 Evaluate side-chains 102 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 175 TRP Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 69 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 0.0980 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 0.3980 chunk 14 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN B 39 GLN B 58 GLN B 175 GLN ** T 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.178960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.147483 restraints weight = 6140.862| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.18 r_work: 0.3695 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5522 Z= 0.192 Angle : 0.841 11.187 7513 Z= 0.428 Chirality : 0.049 0.198 829 Planarity : 0.006 0.057 967 Dihedral : 8.172 42.044 906 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.90 % Allowed : 6.33 % Favored : 92.77 % Rotamer: Outliers : 4.49 % Allowed : 20.21 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.28), residues: 664 helix: -1.49 (1.38), residues: 15 sheet: -1.32 (0.28), residues: 273 loop : -2.24 (0.27), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 43 TYR 0.021 0.002 TYR B 35 PHE 0.024 0.002 PHE C 67 TRP 0.025 0.002 TRP B 201 HIS 0.006 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 5508) covalent geometry : angle 0.82846 ( 7477) SS BOND : bond 0.00801 ( 6) SS BOND : angle 1.60567 ( 12) hydrogen bonds : bond 0.03952 ( 186) hydrogen bonds : angle 7.26422 ( 516) link_BETA1-4 : bond 0.00532 ( 4) link_BETA1-4 : angle 2.78260 ( 12) link_BETA1-6 : bond 0.00613 ( 1) link_BETA1-6 : angle 2.14565 ( 3) link_NAG-ASN : bond 0.00116 ( 3) link_NAG-ASN : angle 2.06836 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7589 (mp) REVERT: A 167 PHE cc_start: 0.6776 (t80) cc_final: 0.6518 (t80) REVERT: A 175 TRP cc_start: 0.4693 (OUTLIER) cc_final: 0.3761 (p-90) REVERT: A 181 PHE cc_start: 0.4305 (OUTLIER) cc_final: 0.3326 (p90) REVERT: B 132 GLU cc_start: 0.7990 (tp30) cc_final: 0.7780 (mm-30) REVERT: C 67 PHE cc_start: 0.7653 (m-10) cc_final: 0.7105 (m-80) REVERT: T 59 TYR cc_start: 0.7473 (m-80) cc_final: 0.7154 (m-80) outliers start: 26 outliers final: 11 residues processed: 114 average time/residue: 0.0672 time to fit residues: 10.1564 Evaluate side-chains 96 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 175 TRP Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 85 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 189 ASN B 207 HIS ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.182405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.150247 restraints weight = 6147.884| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.22 r_work: 0.3629 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5522 Z= 0.185 Angle : 0.758 10.543 7513 Z= 0.385 Chirality : 0.046 0.182 829 Planarity : 0.005 0.058 967 Dihedral : 6.956 41.437 906 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.75 % Allowed : 4.97 % Favored : 94.28 % Rotamer: Outliers : 4.84 % Allowed : 18.48 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.29), residues: 664 helix: -1.12 (1.46), residues: 15 sheet: -1.14 (0.28), residues: 266 loop : -1.96 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 60 TYR 0.019 0.002 TYR A 35 PHE 0.017 0.002 PHE B 57 TRP 0.028 0.002 TRP B 201 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 5508) covalent geometry : angle 0.74719 ( 7477) SS BOND : bond 0.00554 ( 6) SS BOND : angle 1.24646 ( 12) hydrogen bonds : bond 0.03702 ( 186) hydrogen bonds : angle 6.79933 ( 516) link_BETA1-4 : bond 0.00537 ( 4) link_BETA1-4 : angle 2.75845 ( 12) link_BETA1-6 : bond 0.00466 ( 1) link_BETA1-6 : angle 1.80263 ( 3) link_NAG-ASN : bond 0.00147 ( 3) link_NAG-ASN : angle 1.64670 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7610 (mp) REVERT: A 107 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.8130 (t) REVERT: A 181 PHE cc_start: 0.4343 (OUTLIER) cc_final: 0.3262 (p90) REVERT: B 132 GLU cc_start: 0.8016 (tp30) cc_final: 0.7779 (mm-30) REVERT: B 140 LYS cc_start: 0.7860 (mptt) cc_final: 0.7638 (mttp) REVERT: C 34 VAL cc_start: 0.8324 (t) cc_final: 0.8062 (m) REVERT: C 59 TYR cc_start: 0.8698 (m-80) cc_final: 0.8316 (m-80) REVERT: C 67 PHE cc_start: 0.7287 (m-10) cc_final: 0.7013 (m-80) outliers start: 28 outliers final: 12 residues processed: 117 average time/residue: 0.0657 time to fit residues: 10.0493 Evaluate side-chains 98 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 85 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 53 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 27 GLN ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.177321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.144951 restraints weight = 6266.424| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.26 r_work: 0.3648 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.6248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5522 Z= 0.156 Angle : 0.719 10.362 7513 Z= 0.360 Chirality : 0.044 0.178 829 Planarity : 0.005 0.046 967 Dihedral : 6.175 41.995 906 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.48 % Favored : 92.92 % Rotamer: Outliers : 4.32 % Allowed : 20.21 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.29), residues: 664 helix: -1.00 (1.50), residues: 15 sheet: -1.06 (0.28), residues: 275 loop : -1.83 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 86 TYR 0.015 0.002 TYR A 35 PHE 0.014 0.002 PHE B 150 TRP 0.029 0.002 TRP B 201 HIS 0.003 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 5508) covalent geometry : angle 0.70966 ( 7477) SS BOND : bond 0.00366 ( 6) SS BOND : angle 1.17599 ( 12) hydrogen bonds : bond 0.03381 ( 186) hydrogen bonds : angle 6.38564 ( 516) link_BETA1-4 : bond 0.00530 ( 4) link_BETA1-4 : angle 2.50402 ( 12) link_BETA1-6 : bond 0.00415 ( 1) link_BETA1-6 : angle 1.66316 ( 3) link_NAG-ASN : bond 0.00160 ( 3) link_NAG-ASN : angle 1.42106 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8555 (tp) REVERT: A 88 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7628 (mp) REVERT: A 107 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.8122 (t) REVERT: A 175 TRP cc_start: 0.5088 (OUTLIER) cc_final: 0.4076 (p-90) REVERT: A 181 PHE cc_start: 0.4445 (OUTLIER) cc_final: 0.3583 (p90) REVERT: B 132 GLU cc_start: 0.7876 (tp30) cc_final: 0.7617 (mm-30) REVERT: C 34 VAL cc_start: 0.8309 (t) cc_final: 0.8046 (m) REVERT: C 59 TYR cc_start: 0.8641 (m-80) cc_final: 0.8290 (m-80) REVERT: T 59 TYR cc_start: 0.7515 (m-80) cc_final: 0.7169 (m-80) outliers start: 25 outliers final: 13 residues processed: 115 average time/residue: 0.0614 time to fit residues: 9.1356 Evaluate side-chains 104 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 175 TRP Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 99 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 ASN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.162831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.129445 restraints weight = 6517.246| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.31 r_work: 0.3422 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.6371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.121 5522 Z= 0.432 Angle : 0.972 13.200 7513 Z= 0.491 Chirality : 0.053 0.219 829 Planarity : 0.006 0.054 967 Dihedral : 6.916 50.132 906 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.08 % Favored : 92.47 % Rotamer: Outliers : 5.18 % Allowed : 20.03 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.29), residues: 664 helix: -1.01 (1.49), residues: 15 sheet: -1.28 (0.28), residues: 273 loop : -1.99 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 110 TYR 0.027 0.003 TYR A 35 PHE 0.027 0.004 PHE A 198 TRP 0.040 0.004 TRP B 201 HIS 0.006 0.002 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00991 ( 5508) covalent geometry : angle 0.96258 ( 7477) SS BOND : bond 0.00916 ( 6) SS BOND : angle 1.73412 ( 12) hydrogen bonds : bond 0.04934 ( 186) hydrogen bonds : angle 6.97272 ( 516) link_BETA1-4 : bond 0.00632 ( 4) link_BETA1-4 : angle 2.69420 ( 12) link_BETA1-6 : bond 0.00511 ( 1) link_BETA1-6 : angle 2.19854 ( 3) link_NAG-ASN : bond 0.00276 ( 3) link_NAG-ASN : angle 1.92760 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8835 (tp) REVERT: A 88 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7886 (mp) REVERT: A 107 SER cc_start: 0.8617 (OUTLIER) cc_final: 0.8177 (t) REVERT: B 132 GLU cc_start: 0.8131 (tp30) cc_final: 0.7893 (mm-30) REVERT: B 209 ARG cc_start: 0.8406 (mtm110) cc_final: 0.8205 (mtm110) REVERT: C 60 ARG cc_start: 0.7393 (ttt-90) cc_final: 0.7144 (ttt-90) REVERT: C 67 PHE cc_start: 0.7679 (m-10) cc_final: 0.7225 (m-80) outliers start: 30 outliers final: 22 residues processed: 118 average time/residue: 0.0590 time to fit residues: 8.8288 Evaluate side-chains 116 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 51 ILE Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 99 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 63 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.169993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.137182 restraints weight = 6357.467| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.29 r_work: 0.3544 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.6640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5522 Z= 0.159 Angle : 0.729 10.984 7513 Z= 0.367 Chirality : 0.044 0.190 829 Planarity : 0.004 0.045 967 Dihedral : 6.055 50.567 906 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.82 % Favored : 94.73 % Rotamer: Outliers : 3.80 % Allowed : 22.63 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.29), residues: 664 helix: -1.49 (1.17), residues: 21 sheet: -1.17 (0.28), residues: 276 loop : -1.94 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 43 TYR 0.016 0.002 TYR C 37 PHE 0.013 0.002 PHE C 97 TRP 0.023 0.002 TRP B 201 HIS 0.003 0.001 HIS T 50 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 5508) covalent geometry : angle 0.72239 ( 7477) SS BOND : bond 0.00395 ( 6) SS BOND : angle 0.90288 ( 12) hydrogen bonds : bond 0.03365 ( 186) hydrogen bonds : angle 6.37146 ( 516) link_BETA1-4 : bond 0.00527 ( 4) link_BETA1-4 : angle 2.25915 ( 12) link_BETA1-6 : bond 0.00402 ( 1) link_BETA1-6 : angle 1.67960 ( 3) link_NAG-ASN : bond 0.00133 ( 3) link_NAG-ASN : angle 1.35630 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8591 (tp) REVERT: A 88 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7801 (mp) REVERT: A 107 SER cc_start: 0.8545 (OUTLIER) cc_final: 0.8150 (t) REVERT: A 181 PHE cc_start: 0.4994 (OUTLIER) cc_final: 0.4171 (p90) REVERT: B 132 GLU cc_start: 0.7967 (tp30) cc_final: 0.7721 (mm-30) REVERT: C 60 ARG cc_start: 0.7241 (ttt-90) cc_final: 0.7007 (ttt-90) REVERT: C 67 PHE cc_start: 0.7379 (m-10) cc_final: 0.6917 (m-80) outliers start: 22 outliers final: 12 residues processed: 112 average time/residue: 0.0721 time to fit residues: 10.4039 Evaluate side-chains 108 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 99 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 5 optimal weight: 0.0770 chunk 25 optimal weight: 9.9990 chunk 45 optimal weight: 30.0000 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 ASN A 189 ASN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 50 HIS ** 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 = 0.3945 r_free = 0.3945 target = 0.167514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.133298 restraints weight = 6332.720| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.31 r_work: 0.3498 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.6723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 5522 Z= 0.264 Angle : 0.817 10.711 7513 Z= 0.414 Chirality : 0.047 0.216 829 Planarity : 0.005 0.042 967 Dihedral : 6.158 53.246 906 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.48 % Favored : 93.07 % Rotamer: Outliers : 4.32 % Allowed : 22.63 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.29), residues: 664 helix: -1.40 (1.18), residues: 21 sheet: -1.34 (0.28), residues: 284 loop : -1.91 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 43 TYR 0.019 0.002 TYR A 35 PHE 0.018 0.002 PHE A 181 TRP 0.043 0.003 TRP B 201 HIS 0.004 0.001 HIS B 154 Details of bonding type rmsd covalent geometry : bond 0.00603 ( 5508) covalent geometry : angle 0.80425 ( 7477) SS BOND : bond 0.01292 ( 6) SS BOND : angle 2.75446 ( 12) hydrogen bonds : bond 0.03839 ( 186) hydrogen bonds : angle 6.47171 ( 516) link_BETA1-4 : bond 0.00517 ( 4) link_BETA1-4 : angle 2.26799 ( 12) link_BETA1-6 : bond 0.00405 ( 1) link_BETA1-6 : angle 1.80480 ( 3) link_NAG-ASN : bond 0.00157 ( 3) link_NAG-ASN : angle 1.42677 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8618 (tp) REVERT: A 88 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7638 (mp) REVERT: A 107 SER cc_start: 0.8480 (OUTLIER) cc_final: 0.8068 (t) REVERT: B 132 GLU cc_start: 0.7903 (tp30) cc_final: 0.7661 (mm-30) REVERT: C 60 ARG cc_start: 0.7076 (ttt-90) cc_final: 0.6805 (ttt90) REVERT: C 67 PHE cc_start: 0.7413 (m-10) cc_final: 0.6980 (m-80) REVERT: T 59 TYR cc_start: 0.7641 (m-80) cc_final: 0.7368 (m-80) outliers start: 25 outliers final: 18 residues processed: 109 average time/residue: 0.0660 time to fit residues: 9.2190 Evaluate side-chains 111 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 99 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 20 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 14 optimal weight: 0.1980 chunk 41 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 30.0000 chunk 6 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 ASN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.172741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139405 restraints weight = 6357.435| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.31 r_work: 0.3577 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.6963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5522 Z= 0.136 Angle : 0.708 9.177 7513 Z= 0.359 Chirality : 0.044 0.219 829 Planarity : 0.004 0.045 967 Dihedral : 5.714 54.017 906 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.22 % Favored : 95.33 % Rotamer: Outliers : 2.94 % Allowed : 25.04 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.30), residues: 664 helix: -1.25 (1.19), residues: 21 sheet: -1.19 (0.29), residues: 270 loop : -1.74 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 43 TYR 0.015 0.001 TYR C 37 PHE 0.013 0.001 PHE C 97 TRP 0.030 0.002 TRP B 201 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 5508) covalent geometry : angle 0.70100 ( 7477) SS BOND : bond 0.00445 ( 6) SS BOND : angle 1.31968 ( 12) hydrogen bonds : bond 0.03165 ( 186) hydrogen bonds : angle 6.21115 ( 516) link_BETA1-4 : bond 0.00470 ( 4) link_BETA1-4 : angle 2.03650 ( 12) link_BETA1-6 : bond 0.00438 ( 1) link_BETA1-6 : angle 1.48868 ( 3) link_NAG-ASN : bond 0.00150 ( 3) link_NAG-ASN : angle 1.16528 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7693 (mp) REVERT: A 107 SER cc_start: 0.8446 (OUTLIER) cc_final: 0.8089 (t) REVERT: A 181 PHE cc_start: 0.5009 (OUTLIER) cc_final: 0.4267 (p90) REVERT: B 132 GLU cc_start: 0.7787 (tp30) cc_final: 0.7542 (mm-30) REVERT: C 67 PHE cc_start: 0.7202 (m-10) cc_final: 0.6484 (m-80) REVERT: C 82 MET cc_start: 0.7593 (tpp) cc_final: 0.6481 (tpp) REVERT: T 34 TYR cc_start: 0.8728 (m-80) cc_final: 0.8487 (m-80) outliers start: 17 outliers final: 10 residues processed: 103 average time/residue: 0.0709 time to fit residues: 9.4045 Evaluate side-chains 100 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 99 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 47 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 26 optimal weight: 0.2980 chunk 63 optimal weight: 5.9990 chunk 23 optimal weight: 0.0020 chunk 40 optimal weight: 4.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.175952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142762 restraints weight = 6226.158| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.31 r_work: 0.3551 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.7062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5522 Z= 0.127 Angle : 0.696 8.974 7513 Z= 0.351 Chirality : 0.044 0.201 829 Planarity : 0.004 0.047 967 Dihedral : 5.329 53.502 904 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.97 % Favored : 94.58 % Rotamer: Outliers : 2.25 % Allowed : 25.04 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.30), residues: 664 helix: -0.93 (1.25), residues: 21 sheet: -1.07 (0.29), residues: 270 loop : -1.64 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 43 TYR 0.013 0.001 TYR C 37 PHE 0.011 0.001 PHE B 150 TRP 0.026 0.002 TRP B 201 HIS 0.005 0.001 HIS T 50 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 5508) covalent geometry : angle 0.69055 ( 7477) SS BOND : bond 0.00283 ( 6) SS BOND : angle 1.08286 ( 12) hydrogen bonds : bond 0.02994 ( 186) hydrogen bonds : angle 6.00688 ( 516) link_BETA1-4 : bond 0.00502 ( 4) link_BETA1-4 : angle 1.88336 ( 12) link_BETA1-6 : bond 0.00452 ( 1) link_BETA1-6 : angle 1.35554 ( 3) link_NAG-ASN : bond 0.00155 ( 3) link_NAG-ASN : angle 1.00850 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7651 (mp) REVERT: A 107 SER cc_start: 0.8477 (OUTLIER) cc_final: 0.8096 (t) REVERT: A 181 PHE cc_start: 0.5047 (OUTLIER) cc_final: 0.4435 (p90) REVERT: B 115 GLU cc_start: 0.8604 (tp30) cc_final: 0.8384 (tp30) REVERT: B 132 GLU cc_start: 0.7759 (tp30) cc_final: 0.7486 (mm-30) REVERT: B 175 GLN cc_start: 0.6357 (mm110) cc_final: 0.6073 (mm-40) REVERT: C 67 PHE cc_start: 0.7008 (m-10) cc_final: 0.6242 (m-80) REVERT: C 82 MET cc_start: 0.7638 (tpp) cc_final: 0.6520 (tpp) REVERT: T 59 TYR cc_start: 0.7588 (m-80) cc_final: 0.7043 (m-80) outliers start: 13 outliers final: 10 residues processed: 98 average time/residue: 0.0623 time to fit residues: 8.0641 Evaluate side-chains 98 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 99 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 14 optimal weight: 0.0570 chunk 46 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.173390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139959 restraints weight = 6273.479| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.28 r_work: 0.3491 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.7144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5522 Z= 0.161 Angle : 0.696 9.106 7513 Z= 0.351 Chirality : 0.044 0.183 829 Planarity : 0.005 0.068 967 Dihedral : 5.296 54.421 904 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.42 % Favored : 94.13 % Rotamer: Outliers : 2.42 % Allowed : 24.53 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.30), residues: 664 helix: -0.80 (1.28), residues: 21 sheet: -1.12 (0.28), residues: 280 loop : -1.60 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 43 TYR 0.016 0.002 TYR B 215 PHE 0.015 0.002 PHE B 150 TRP 0.030 0.002 TRP B 201 HIS 0.004 0.001 HIS B 154 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 5508) covalent geometry : angle 0.69072 ( 7477) SS BOND : bond 0.00404 ( 6) SS BOND : angle 1.13296 ( 12) hydrogen bonds : bond 0.03094 ( 186) hydrogen bonds : angle 5.96014 ( 516) link_BETA1-4 : bond 0.00485 ( 4) link_BETA1-4 : angle 1.81326 ( 12) link_BETA1-6 : bond 0.00546 ( 1) link_BETA1-6 : angle 1.41627 ( 3) link_NAG-ASN : bond 0.00100 ( 3) link_NAG-ASN : angle 1.03034 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1196.37 seconds wall clock time: 21 minutes 17.99 seconds (1277.99 seconds total)