Starting phenix.real_space_refine on Sat Aug 23 08:47:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hpf_34931/08_2025/8hpf_34931.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hpf_34931/08_2025/8hpf_34931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hpf_34931/08_2025/8hpf_34931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hpf_34931/08_2025/8hpf_34931.map" model { file = "/net/cci-nas-00/data/ceres_data/8hpf_34931/08_2025/8hpf_34931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hpf_34931/08_2025/8hpf_34931.cif" } resolution = 2.34 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= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3142 atoms to isotropic. 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 34 5.16 5 C 5217 2.51 5 N 1387 2.21 5 O 1630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8268 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1542 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 12, 'TRANS': 180} Chain: "L" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain: "H" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1756 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 214} Chain: "M" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1656 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain: "N" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1642 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.07, per 1000 atoms: 0.25 Number of scatterers: 8268 At special positions: 0 Unit cell: (110.04, 126, 120.96, 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 34 16.00 O 1630 8.00 N 1387 7.00 C 5217 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 377 " distance=2.03 Simple disulfide: pdb=" SG CYS A 395 " - pdb=" SG CYS A 448 " distance=2.05 Simple disulfide: pdb=" SG CYS A 407 " - pdb=" SG CYS A 541 " distance=2.03 Simple disulfide: pdb=" SG CYS A 496 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS L 215 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.03 Simple disulfide: pdb=" SG CYS M 149 " - pdb=" SG CYS M 205 " distance=2.03 Simple disulfide: pdb=" SG CYS M 225 " - pdb=" SG CYS N 216 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 136 " - pdb=" SG CYS N 196 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1201 " - " ASN A 359 " Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 421.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1992 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 24 sheets defined 10.0% alpha, 42.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 381 through 387 removed outlier: 3.677A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 426 removed outlier: 4.279A pdb=" N SER A 424 " --> pdb=" O ASN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 454 through 459 removed outlier: 3.558A pdb=" N SER A 459 " --> pdb=" O ASN A 455 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.595A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 128 Processing helix chain 'L' and resid 184 through 189 Processing helix chain 'H' and resid 63 through 66 Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 200 through 204 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 86 through 90 Processing helix chain 'M' and resid 194 through 199 removed outlier: 4.030A pdb=" N GLY M 199 " --> pdb=" O SER M 196 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.082A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 128 Processing helix chain 'N' and resid 184 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 370 through 374 Processing sheet with id=AA2, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.067A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 115 through 119 removed outlier: 6.003A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER L 175 " --> pdb=" O THR L 165 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 146 through 151 Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.495A pdb=" N VAL H 36 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU H 52 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.566A pdb=" N PHE H 101 " --> pdb=" O TRP H 114 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.711A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.711A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 166 through 169 removed outlier: 4.260A pdb=" N TYR H 209 " --> pdb=" O VAL H 226 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.634A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.391A pdb=" N GLY M 10 " --> pdb=" O THR M 119 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR M 33 " --> pdb=" O GLU M 98 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.391A pdb=" N GLY M 10 " --> pdb=" O THR M 119 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE M 111 " --> pdb=" O ARG M 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 129 through 133 removed outlier: 5.954A pdb=" N TYR M 185 " --> pdb=" O ASP M 153 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 129 through 133 removed outlier: 5.954A pdb=" N TYR M 185 " --> pdb=" O ASP M 153 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 160 through 163 removed outlier: 4.638A pdb=" N TYR M 203 " --> pdb=" O VAL M 220 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.622A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.972A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.717A pdb=" N SER N 99 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 116 through 120 removed outlier: 5.778A pdb=" N TYR N 175 " --> pdb=" O ASN N 140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 147 through 152 367 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.55 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 2661 1.36 - 1.49: 2300 1.49 - 1.62: 3471 1.62 - 1.75: 1 1.75 - 1.88: 40 Bond restraints: 8473 Sorted by residual: bond pdb=" CB PRO H 89 " pdb=" CG PRO H 89 " ideal model delta sigma weight residual 1.492 1.664 -0.172 5.00e-02 4.00e+02 1.19e+01 bond pdb=" C ASP H 116 " pdb=" N PRO H 117 " ideal model delta sigma weight residual 1.331 1.367 -0.036 1.27e-02 6.20e+03 8.21e+00 bond pdb=" CG PRO H 89 " pdb=" CD PRO H 89 " ideal model delta sigma weight residual 1.503 1.414 0.089 3.40e-02 8.65e+02 6.91e+00 bond pdb=" N PRO H 89 " pdb=" CD PRO H 89 " ideal model delta sigma weight residual 1.473 1.509 -0.036 1.40e-02 5.10e+03 6.67e+00 bond pdb=" N PRO H 89 " pdb=" CA PRO H 89 " ideal model delta sigma weight residual 1.469 1.440 0.028 1.28e-02 6.10e+03 4.87e+00 ... (remaining 8468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 11482 3.53 - 7.07: 41 7.07 - 10.60: 6 10.60 - 14.13: 2 14.13 - 17.66: 1 Bond angle restraints: 11532 Sorted by residual: angle pdb=" CA PRO H 89 " pdb=" N PRO H 89 " pdb=" CD PRO H 89 " ideal model delta sigma weight residual 112.00 94.34 17.66 1.40e+00 5.10e-01 1.59e+02 angle pdb=" CA CYS A 448 " pdb=" CB CYS A 448 " pdb=" SG CYS A 448 " ideal model delta sigma weight residual 114.40 128.38 -13.98 2.30e+00 1.89e-01 3.69e+01 angle pdb=" N PRO H 89 " pdb=" CD PRO H 89 " pdb=" CG PRO H 89 " ideal model delta sigma weight residual 103.20 94.70 8.50 1.50e+00 4.44e-01 3.21e+01 angle pdb=" C GLU M 157 " pdb=" N PRO M 158 " pdb=" CD PRO M 158 " ideal model delta sigma weight residual 120.60 108.52 12.08 2.20e+00 2.07e-01 3.01e+01 angle pdb=" C GLY A 447 " pdb=" N CYS A 448 " pdb=" CA CYS A 448 " ideal model delta sigma weight residual 122.09 114.51 7.58 1.86e+00 2.89e-01 1.66e+01 ... (remaining 11527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4326 17.31 - 34.61: 509 34.61 - 51.92: 178 51.92 - 69.22: 47 69.22 - 86.53: 16 Dihedral angle restraints: 5076 sinusoidal: 1959 harmonic: 3117 Sorted by residual: dihedral pdb=" CB CYS A 395 " pdb=" SG CYS A 395 " pdb=" SG CYS A 448 " pdb=" CB CYS A 448 " ideal model delta sinusoidal sigma weight residual 93.00 20.69 72.31 1 1.00e+01 1.00e-02 6.68e+01 dihedral pdb=" CB CYS N 136 " pdb=" SG CYS N 136 " pdb=" SG CYS N 196 " pdb=" CB CYS N 196 " ideal model delta sinusoidal sigma weight residual 93.00 45.14 47.86 1 1.00e+01 1.00e-02 3.16e+01 dihedral pdb=" CA ASP H 116 " pdb=" C ASP H 116 " pdb=" N PRO H 117 " pdb=" CA PRO H 117 " ideal model delta harmonic sigma weight residual -180.00 -157.68 -22.32 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 5073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1038 0.050 - 0.099: 186 0.099 - 0.149: 59 0.149 - 0.198: 3 0.198 - 0.248: 2 Chirality restraints: 1288 Sorted by residual: chirality pdb=" CA PRO H 89 " pdb=" N PRO H 89 " pdb=" C PRO H 89 " pdb=" CB PRO H 89 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C1 NAG A1201 " pdb=" ND2 ASN A 359 " pdb=" C2 NAG A1201 " pdb=" O5 NAG A1201 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA THR N 94 " pdb=" N THR N 94 " pdb=" C THR N 94 " pdb=" CB THR N 94 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 1285 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP H 88 " 0.089 5.00e-02 4.00e+02 1.20e-01 2.31e+01 pdb=" N PRO H 89 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO H 89 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO H 89 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU M 157 " -0.078 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO M 158 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO M 158 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO M 158 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR N 94 " -0.046 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO N 95 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO N 95 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO N 95 " -0.040 5.00e-02 4.00e+02 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1502 2.78 - 3.31: 7347 3.31 - 3.84: 14187 3.84 - 4.37: 16529 4.37 - 4.90: 28271 Nonbonded interactions: 67836 Sorted by model distance: nonbonded pdb=" O HIS N 191 " pdb=" NH2 ARG N 213 " model vdw 2.244 3.120 nonbonded pdb=" OD2 ASP A 436 " pdb=" OG SER M 56 " model vdw 2.247 3.040 nonbonded pdb=" N ASN A 503 " pdb=" OD1 ASN A 503 " model vdw 2.267 3.120 nonbonded pdb=" O SER H 128 " pdb=" OG SER H 128 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR H 110 " pdb=" OG SER H 113 " model vdw 2.277 3.040 ... (remaining 67831 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 12.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.360 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 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 : 0.003 0.172 8488 Z= 0.137 Angle : 0.688 17.663 11563 Z= 0.361 Chirality : 0.044 0.248 1288 Planarity : 0.007 0.120 1484 Dihedral : 17.785 86.530 3042 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 7.09 % Allowed : 26.42 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: -0.06 (0.27), residues: 1069 helix: -1.87 (0.76), residues: 33 sheet: 0.96 (0.25), residues: 439 loop : -0.71 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 78 TYR 0.015 0.001 TYR H 111 PHE 0.023 0.001 PHE L 117 TRP 0.026 0.001 TRP L 149 HIS 0.008 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8473) covalent geometry : angle 0.68385 (11532) SS BOND : bond 0.00715 ( 14) SS BOND : angle 1.47188 ( 28) hydrogen bonds : bond 0.13495 ( 324) hydrogen bonds : angle 7.01705 ( 888) link_NAG-ASN : bond 0.00391 ( 1) link_NAG-ASN : angle 2.44816 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 92 time to evaluate : 0.331 Fit side-chains outliers start: 66 outliers final: 56 residues processed: 156 average time/residue: 0.4008 time to fit residues: 68.2649 Evaluate side-chains 140 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 84 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 GLN N 162 GLN N 212 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.153978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.122644 restraints weight = 17399.073| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.11 r_work: 0.3884 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 8488 Z= 0.158 Angle : 0.651 12.780 11563 Z= 0.334 Chirality : 0.045 0.236 1288 Planarity : 0.006 0.091 1484 Dihedral : 9.310 73.856 1260 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 7.52 % Allowed : 24.49 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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 aren not related in a simple way. whole: -0.11 (0.26), residues: 1069 helix: -2.08 (0.66), residues: 41 sheet: 1.04 (0.25), residues: 442 loop : -0.83 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 373 TYR 0.015 0.001 TYR N 188 PHE 0.015 0.002 PHE L 117 TRP 0.014 0.001 TRP M 163 HIS 0.004 0.001 HIS N 191 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8473) covalent geometry : angle 0.64578 (11532) SS BOND : bond 0.00819 ( 14) SS BOND : angle 1.66514 ( 28) hydrogen bonds : bond 0.03591 ( 324) hydrogen bonds : angle 6.18755 ( 888) link_NAG-ASN : bond 0.00252 ( 1) link_NAG-ASN : angle 2.44703 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 93 time to evaluate : 0.338 Fit side-chains REVERT: A 394 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7739 (ptpp) REVERT: A 502 PHE cc_start: 0.7265 (t80) cc_final: 0.6961 (t80) REVERT: L 30 ASP cc_start: 0.7594 (t0) cc_final: 0.7281 (t0) REVERT: M 215 LYS cc_start: 0.5596 (mtmm) cc_final: 0.5310 (mmtt) REVERT: N 212 ASN cc_start: 0.4398 (t0) cc_final: 0.4161 (t0) outliers start: 70 outliers final: 36 residues processed: 159 average time/residue: 0.4168 time to fit residues: 72.1827 Evaluate side-chains 126 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain L residue 195 CYS Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 90 optimal weight: 0.0050 chunk 38 optimal weight: 5.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN L 125 GLN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 GLN N 162 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.154676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.123492 restraints weight = 17281.984| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.20 r_work: 0.3880 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 8488 Z= 0.135 Angle : 0.642 13.925 11563 Z= 0.326 Chirality : 0.045 0.238 1288 Planarity : 0.006 0.084 1484 Dihedral : 8.218 74.963 1222 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 6.12 % Allowed : 26.53 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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 aren not related in a simple way. whole: 0.02 (0.26), residues: 1069 helix: -1.92 (0.75), residues: 33 sheet: 1.24 (0.25), residues: 423 loop : -0.80 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 373 TYR 0.015 0.001 TYR N 188 PHE 0.012 0.001 PHE N 141 TRP 0.013 0.001 TRP M 163 HIS 0.004 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8473) covalent geometry : angle 0.63521 (11532) SS BOND : bond 0.00799 ( 14) SS BOND : angle 1.81072 ( 28) hydrogen bonds : bond 0.03373 ( 324) hydrogen bonds : angle 5.97889 ( 888) link_NAG-ASN : bond 0.00389 ( 1) link_NAG-ASN : angle 2.51988 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 95 time to evaluate : 0.323 Fit side-chains REVERT: A 502 PHE cc_start: 0.7281 (t80) cc_final: 0.6953 (t80) REVERT: M 210 LYS cc_start: 0.6689 (OUTLIER) cc_final: 0.6259 (pttt) REVERT: M 215 LYS cc_start: 0.5583 (mtmm) cc_final: 0.5315 (mmtt) outliers start: 57 outliers final: 28 residues processed: 149 average time/residue: 0.4787 time to fit residues: 76.7685 Evaluate side-chains 121 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 210 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 165 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 105 optimal weight: 0.0980 chunk 58 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN L 125 GLN L 156 GLN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN N 157 GLN N 162 GLN N 212 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.152546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.121373 restraints weight = 17563.687| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.17 r_work: 0.3862 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 8488 Z= 0.280 Angle : 0.782 15.613 11563 Z= 0.401 Chirality : 0.049 0.302 1288 Planarity : 0.007 0.091 1484 Dihedral : 8.590 79.362 1208 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 7.73 % Allowed : 25.24 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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 aren not related in a simple way. whole: -0.41 (0.26), residues: 1069 helix: -2.15 (0.75), residues: 33 sheet: 0.83 (0.25), residues: 430 loop : -1.02 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 373 TYR 0.025 0.002 TYR N 188 PHE 0.015 0.003 PHE M 175 TRP 0.019 0.002 TRP M 163 HIS 0.010 0.002 HIS N 191 Details of bonding type rmsd covalent geometry : bond 0.00647 ( 8473) covalent geometry : angle 0.77421 (11532) SS BOND : bond 0.01110 ( 14) SS BOND : angle 2.14265 ( 28) hydrogen bonds : bond 0.04054 ( 324) hydrogen bonds : angle 6.64781 ( 888) link_NAG-ASN : bond 0.00058 ( 1) link_NAG-ASN : angle 2.75534 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 94 time to evaluate : 0.349 Fit side-chains REVERT: A 502 PHE cc_start: 0.7331 (t80) cc_final: 0.7042 (t80) REVERT: H 111 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.7414 (m-80) REVERT: M 104 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7475 (tm) REVERT: M 204 ILE cc_start: 0.5086 (pp) cc_final: 0.4769 (pt) REVERT: M 210 LYS cc_start: 0.6786 (OUTLIER) cc_final: 0.6467 (pttt) REVERT: M 215 LYS cc_start: 0.5551 (mtmm) cc_final: 0.5218 (mmtt) outliers start: 72 outliers final: 41 residues processed: 157 average time/residue: 0.4365 time to fit residues: 74.3030 Evaluate side-chains 137 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 93 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 111 TYR Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 210 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 178 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 98 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN A 493 ASN ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 55 GLN N 157 GLN N 162 GLN N 212 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.153971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.122274 restraints weight = 17414.882| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.00 r_work: 0.3905 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3820 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 8488 Z= 0.140 Angle : 0.662 13.680 11563 Z= 0.338 Chirality : 0.045 0.254 1288 Planarity : 0.006 0.080 1484 Dihedral : 7.865 76.990 1208 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 6.98 % Allowed : 25.78 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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 aren not related in a simple way. whole: -0.25 (0.26), residues: 1069 helix: -2.23 (0.72), residues: 33 sheet: 0.94 (0.25), residues: 431 loop : -0.90 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 78 TYR 0.018 0.001 TYR N 188 PHE 0.014 0.002 PHE L 117 TRP 0.015 0.001 TRP M 163 HIS 0.005 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8473) covalent geometry : angle 0.65579 (11532) SS BOND : bond 0.00844 ( 14) SS BOND : angle 1.70921 ( 28) hydrogen bonds : bond 0.03385 ( 324) hydrogen bonds : angle 6.14600 ( 888) link_NAG-ASN : bond 0.00475 ( 1) link_NAG-ASN : angle 2.76963 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 92 time to evaluate : 0.327 Fit side-chains REVERT: M 204 ILE cc_start: 0.4951 (pp) cc_final: 0.4707 (pt) REVERT: M 210 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6448 (pttt) REVERT: M 215 LYS cc_start: 0.5564 (mtmm) cc_final: 0.5283 (mmtt) outliers start: 65 outliers final: 33 residues processed: 151 average time/residue: 0.4814 time to fit residues: 78.3665 Evaluate side-chains 119 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 210 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 80 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 105 optimal weight: 0.0980 chunk 89 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 16 optimal weight: 0.3980 chunk 91 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN N 157 GLN N 162 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.153828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.122941 restraints weight = 17259.034| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.18 r_work: 0.3874 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 8488 Z= 0.153 Angle : 0.687 14.670 11563 Z= 0.349 Chirality : 0.045 0.248 1288 Planarity : 0.006 0.079 1484 Dihedral : 7.657 76.622 1208 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 6.23 % Allowed : 26.64 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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 aren not related in a simple way. whole: -0.23 (0.26), residues: 1069 helix: -2.28 (0.72), residues: 33 sheet: 0.95 (0.26), residues: 430 loop : -0.88 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 78 TYR 0.017 0.001 TYR N 188 PHE 0.014 0.002 PHE H 137 TRP 0.015 0.001 TRP L 149 HIS 0.007 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8473) covalent geometry : angle 0.68193 (11532) SS BOND : bond 0.00831 ( 14) SS BOND : angle 1.69539 ( 28) hydrogen bonds : bond 0.03362 ( 324) hydrogen bonds : angle 6.13551 ( 888) link_NAG-ASN : bond 0.00368 ( 1) link_NAG-ASN : angle 2.67288 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 88 time to evaluate : 0.344 Fit side-chains REVERT: L 136 LEU cc_start: 0.5356 (OUTLIER) cc_final: 0.4958 (tp) REVERT: H 105 ASP cc_start: 0.5443 (p0) cc_final: 0.5087 (p0) REVERT: M 104 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7543 (tm) REVERT: M 204 ILE cc_start: 0.4974 (pp) cc_final: 0.4719 (pt) REVERT: M 210 LYS cc_start: 0.6889 (OUTLIER) cc_final: 0.6482 (pttt) REVERT: M 215 LYS cc_start: 0.5596 (mtmm) cc_final: 0.5300 (mmtt) REVERT: N 124 ASP cc_start: 0.4433 (OUTLIER) cc_final: 0.3572 (m-30) outliers start: 58 outliers final: 35 residues processed: 142 average time/residue: 0.4538 time to fit residues: 69.7546 Evaluate side-chains 122 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 83 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 210 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 178 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 34 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 92 optimal weight: 0.9990 chunk 16 optimal weight: 0.0000 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN L 138 ASN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN N 37 GLN N 157 GLN N 162 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.154893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.123589 restraints weight = 17512.214| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.17 r_work: 0.3887 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3793 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 8488 Z= 0.127 Angle : 0.670 14.015 11563 Z= 0.338 Chirality : 0.045 0.235 1288 Planarity : 0.006 0.075 1484 Dihedral : 7.259 75.160 1206 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.40 % Allowed : 28.57 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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 aren not related in a simple way. whole: -0.13 (0.27), residues: 1069 helix: -2.30 (0.70), residues: 33 sheet: 1.05 (0.25), residues: 425 loop : -0.82 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 78 TYR 0.015 0.001 TYR N 188 PHE 0.012 0.001 PHE N 141 TRP 0.016 0.001 TRP L 149 HIS 0.007 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8473) covalent geometry : angle 0.66526 (11532) SS BOND : bond 0.00782 ( 14) SS BOND : angle 1.59561 ( 28) hydrogen bonds : bond 0.03223 ( 324) hydrogen bonds : angle 5.96665 ( 888) link_NAG-ASN : bond 0.00466 ( 1) link_NAG-ASN : angle 2.66083 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 89 time to evaluate : 0.351 Fit side-chains REVERT: L 136 LEU cc_start: 0.5476 (OUTLIER) cc_final: 0.5055 (tp) REVERT: H 105 ASP cc_start: 0.5459 (p0) cc_final: 0.5111 (p0) REVERT: M 104 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7440 (tm) REVERT: M 152 LYS cc_start: 0.6359 (ttpp) cc_final: 0.6116 (tttt) REVERT: M 204 ILE cc_start: 0.4914 (pp) cc_final: 0.4679 (pt) REVERT: M 210 LYS cc_start: 0.6793 (OUTLIER) cc_final: 0.6339 (pttt) REVERT: M 215 LYS cc_start: 0.5464 (mtmm) cc_final: 0.5219 (mmtt) REVERT: N 124 ASP cc_start: 0.4508 (OUTLIER) cc_final: 0.3637 (m-30) REVERT: N 185 LYS cc_start: 0.5573 (tptt) cc_final: 0.4359 (tppt) outliers start: 41 outliers final: 27 residues processed: 127 average time/residue: 0.4592 time to fit residues: 63.1313 Evaluate side-chains 115 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 210 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 68 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 76 optimal weight: 0.0870 chunk 36 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN N 162 GLN N 212 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.155115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.125422 restraints weight = 17303.090| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.18 r_work: 0.3916 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3827 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 8488 Z= 0.123 Angle : 0.667 13.786 11563 Z= 0.338 Chirality : 0.044 0.225 1288 Planarity : 0.005 0.074 1484 Dihedral : 6.982 74.114 1203 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.83 % Allowed : 28.36 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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 aren not related in a simple way. whole: -0.07 (0.27), residues: 1069 helix: -2.24 (0.70), residues: 33 sheet: 1.14 (0.26), residues: 425 loop : -0.82 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 78 TYR 0.015 0.001 TYR N 188 PHE 0.015 0.001 PHE H 137 TRP 0.017 0.001 TRP L 149 HIS 0.007 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8473) covalent geometry : angle 0.66180 (11532) SS BOND : bond 0.00744 ( 14) SS BOND : angle 1.57062 ( 28) hydrogen bonds : bond 0.03191 ( 324) hydrogen bonds : angle 5.88189 ( 888) link_NAG-ASN : bond 0.00464 ( 1) link_NAG-ASN : angle 2.60291 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 90 time to evaluate : 0.348 Fit side-chains REVERT: A 502 PHE cc_start: 0.7141 (t80) cc_final: 0.6853 (t80) REVERT: L 136 LEU cc_start: 0.5280 (OUTLIER) cc_final: 0.4872 (tp) REVERT: H 105 ASP cc_start: 0.5345 (p0) cc_final: 0.4996 (p0) REVERT: M 104 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7433 (tm) REVERT: M 130 VAL cc_start: 0.5630 (OUTLIER) cc_final: 0.5247 (p) REVERT: M 152 LYS cc_start: 0.6260 (ttpp) cc_final: 0.6042 (mttt) REVERT: M 204 ILE cc_start: 0.4900 (pp) cc_final: 0.4674 (pt) REVERT: M 210 LYS cc_start: 0.6764 (OUTLIER) cc_final: 0.6319 (pttt) REVERT: M 215 LYS cc_start: 0.5474 (mtmm) cc_final: 0.5185 (mmtt) REVERT: M 218 LYS cc_start: 0.4246 (OUTLIER) cc_final: 0.3928 (ptmm) REVERT: N 82 ASP cc_start: 0.7389 (m-30) cc_final: 0.7162 (m-30) REVERT: N 124 ASP cc_start: 0.4509 (OUTLIER) cc_final: 0.3637 (m-30) REVERT: N 185 LYS cc_start: 0.5622 (tptt) cc_final: 0.4409 (tppt) REVERT: N 212 ASN cc_start: 0.4389 (t0) cc_final: 0.4127 (t0) outliers start: 45 outliers final: 27 residues processed: 132 average time/residue: 0.4365 time to fit residues: 62.5082 Evaluate side-chains 120 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 210 LYS Chi-restraints excluded: chain M residue 218 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 79 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 94 optimal weight: 0.0670 chunk 88 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.155373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.124511 restraints weight = 17352.106| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.29 r_work: 0.3894 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 8488 Z= 0.121 Angle : 0.668 14.348 11563 Z= 0.339 Chirality : 0.044 0.217 1288 Planarity : 0.006 0.072 1484 Dihedral : 6.750 72.842 1202 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.08 % Allowed : 29.32 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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 aren not related in a simple way. whole: -0.03 (0.27), residues: 1069 helix: -2.23 (0.69), residues: 33 sheet: 1.18 (0.26), residues: 425 loop : -0.81 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 78 TYR 0.015 0.001 TYR N 188 PHE 0.012 0.001 PHE N 141 TRP 0.021 0.001 TRP L 149 HIS 0.008 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8473) covalent geometry : angle 0.66371 (11532) SS BOND : bond 0.00759 ( 14) SS BOND : angle 1.53970 ( 28) hydrogen bonds : bond 0.03172 ( 324) hydrogen bonds : angle 5.81372 ( 888) link_NAG-ASN : bond 0.00440 ( 1) link_NAG-ASN : angle 2.54143 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 86 time to evaluate : 0.350 Fit side-chains REVERT: A 502 PHE cc_start: 0.7204 (t80) cc_final: 0.6876 (t80) REVERT: L 136 LEU cc_start: 0.5336 (OUTLIER) cc_final: 0.4928 (tp) REVERT: M 104 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7488 (tm) REVERT: M 130 VAL cc_start: 0.5557 (OUTLIER) cc_final: 0.5192 (p) REVERT: M 152 LYS cc_start: 0.6188 (ttpp) cc_final: 0.5968 (mttt) REVERT: M 204 ILE cc_start: 0.4898 (pp) cc_final: 0.4638 (pt) REVERT: M 210 LYS cc_start: 0.6772 (OUTLIER) cc_final: 0.6332 (pttt) REVERT: M 215 LYS cc_start: 0.5531 (mtmm) cc_final: 0.5200 (mmtt) REVERT: N 124 ASP cc_start: 0.4527 (OUTLIER) cc_final: 0.3675 (m-30) REVERT: N 185 LYS cc_start: 0.5566 (tptt) cc_final: 0.4564 (mmpt) outliers start: 38 outliers final: 26 residues processed: 121 average time/residue: 0.4754 time to fit residues: 62.1018 Evaluate side-chains 115 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 210 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 78 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 GLN N 212 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.154778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.124830 restraints weight = 17324.437| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.02 r_work: 0.3922 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3835 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8488 Z= 0.145 Angle : 0.704 14.599 11563 Z= 0.356 Chirality : 0.045 0.222 1288 Planarity : 0.006 0.075 1484 Dihedral : 6.840 73.856 1201 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.08 % Allowed : 29.32 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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 aren not related in a simple way. whole: -0.08 (0.27), residues: 1069 helix: -2.20 (0.69), residues: 33 sheet: 1.12 (0.26), residues: 426 loop : -0.82 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 78 TYR 0.016 0.001 TYR N 188 PHE 0.018 0.002 PHE H 137 TRP 0.023 0.001 TRP L 149 HIS 0.009 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 8473) covalent geometry : angle 0.69981 (11532) SS BOND : bond 0.00824 ( 14) SS BOND : angle 1.59358 ( 28) hydrogen bonds : bond 0.03305 ( 324) hydrogen bonds : angle 5.95065 ( 888) link_NAG-ASN : bond 0.00372 ( 1) link_NAG-ASN : angle 2.49865 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 87 time to evaluate : 0.342 Fit side-chains REVERT: A 502 PHE cc_start: 0.7050 (t80) cc_final: 0.6757 (t80) REVERT: L 136 LEU cc_start: 0.5268 (OUTLIER) cc_final: 0.4820 (tp) REVERT: H 105 ASP cc_start: 0.5436 (p0) cc_final: 0.5230 (p0) REVERT: H 159 ASP cc_start: 0.6668 (m-30) cc_final: 0.6408 (m-30) REVERT: M 104 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7413 (tm) REVERT: M 152 LYS cc_start: 0.6206 (ttpp) cc_final: 0.5988 (mttt) REVERT: M 204 ILE cc_start: 0.4805 (pp) cc_final: 0.4548 (pt) REVERT: M 210 LYS cc_start: 0.6754 (OUTLIER) cc_final: 0.6331 (pttt) REVERT: M 215 LYS cc_start: 0.5526 (mtmm) cc_final: 0.5213 (mmtt) REVERT: M 218 LYS cc_start: 0.4233 (OUTLIER) cc_final: 0.3878 (ptmm) REVERT: N 124 ASP cc_start: 0.4565 (OUTLIER) cc_final: 0.3650 (m-30) outliers start: 38 outliers final: 29 residues processed: 122 average time/residue: 0.4629 time to fit residues: 61.0405 Evaluate side-chains 119 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 210 LYS Chi-restraints excluded: chain M residue 218 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 41 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 46 optimal weight: 0.0370 chunk 70 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 3 optimal weight: 0.0060 chunk 20 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.7878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 GLN N 212 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.155025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.125001 restraints weight = 17462.701| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.11 r_work: 0.3910 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3823 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8488 Z= 0.136 Angle : 0.696 14.509 11563 Z= 0.351 Chirality : 0.045 0.218 1288 Planarity : 0.006 0.074 1484 Dihedral : 6.776 73.625 1201 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.97 % Allowed : 29.54 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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 aren not related in a simple way. whole: -0.08 (0.26), residues: 1069 helix: -2.54 (0.62), residues: 39 sheet: 1.26 (0.26), residues: 417 loop : -0.87 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 78 TYR 0.017 0.001 TYR N 188 PHE 0.011 0.001 PHE N 141 TRP 0.025 0.001 TRP L 149 HIS 0.010 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8473) covalent geometry : angle 0.69123 (11532) SS BOND : bond 0.00804 ( 14) SS BOND : angle 1.57638 ( 28) hydrogen bonds : bond 0.03258 ( 324) hydrogen bonds : angle 5.91407 ( 888) link_NAG-ASN : bond 0.00384 ( 1) link_NAG-ASN : angle 2.43411 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5495.53 seconds wall clock time: 94 minutes 16.57 seconds (5656.57 seconds total)