Starting phenix.real_space_refine on Fri Aug 22 15:46:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yi8_33853/08_2025/7yi8_33853.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yi8_33853/08_2025/7yi8_33853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yi8_33853/08_2025/7yi8_33853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yi8_33853/08_2025/7yi8_33853.map" model { file = "/net/cci-nas-00/data/ceres_data/7yi8_33853/08_2025/7yi8_33853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yi8_33853/08_2025/7yi8_33853.cif" } resolution = 2.7 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= 0.064 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 3334 2.51 5 N 892 2.21 5 O 972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s 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: 5225 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2117 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain breaks: 2 Chain: "B" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1819 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain breaks: 1 Chain: "C" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 269 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "D" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 994 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 1.40, per 1000 atoms: 0.27 Number of scatterers: 5225 At special positions: 0 Unit cell: (70.55, 73.1, 119.85, 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 27 16.00 O 972 8.00 N 892 7.00 C 3334 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 225.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1206 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 39.7% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.965A pdb=" N ASN A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 192 through 204 Processing helix chain 'A' and resid 218 through 227 Processing helix chain 'A' and resid 320 through 334 Processing helix chain 'A' and resid 337 through 341 removed outlier: 4.275A pdb=" N SER A 340 " --> pdb=" O ILE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 402 through 414 removed outlier: 3.721A pdb=" N LEU A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 418 removed outlier: 3.618A pdb=" N GLN A 418 " --> pdb=" O PRO A 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 415 through 418' Processing helix chain 'B' and resid 141 through 165 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 231 through 237 Processing helix chain 'B' and resid 239 through 244 removed outlier: 3.690A pdb=" N GLN B 244 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 257 through 268 Processing helix chain 'B' and resid 336 through 346 removed outlier: 3.752A pdb=" N GLN B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 168 removed outlier: 3.910A pdb=" N LEU C 167 " --> pdb=" O LEU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 183 removed outlier: 4.377A pdb=" N ALA C 175 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 26 removed outlier: 3.567A pdb=" N TYR D 17 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS D 19 " --> pdb=" O THR D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 43 Processing helix chain 'D' and resid 51 through 65 Processing helix chain 'D' and resid 71 through 75 Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'D' and resid 91 through 96 removed outlier: 3.693A pdb=" N LEU D 95 " --> pdb=" O THR D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 removed outlier: 4.214A pdb=" N TYR D 104 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 removed outlier: 4.309A pdb=" N ILE D 116 " --> pdb=" O GLU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 129 removed outlier: 3.637A pdb=" N ASN D 128 " --> pdb=" O LYS D 125 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 129 removed outlier: 6.619A pdb=" N LYS A 125 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE A 447 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL A 127 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN A 145 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 183 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP A 187 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N HIS A 360 " --> pdb=" O SER A 212 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER A 212 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU A 362 " --> pdb=" O ASN A 210 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASN A 210 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET A 364 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 176 through 180 removed outlier: 4.061A pdb=" N SER B 301 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU B 300 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR B 277 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N CYS B 302 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU B 275 " --> pdb=" O CYS B 302 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE B 304 " --> pdb=" O VAL B 273 " (cutoff:3.500A) 182 hydrogen bonds defined for protein. 504 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.72 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1406 1.33 - 1.45: 870 1.45 - 1.57: 2995 1.57 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 5318 Sorted by residual: bond pdb=" C2 SAH B 401 " pdb=" N3 SAH B 401 " ideal model delta sigma weight residual 1.322 1.381 -0.059 2.00e-02 2.50e+03 8.61e+00 bond pdb=" C8 SAH B 401 " pdb=" N7 SAH B 401 " ideal model delta sigma weight residual 1.299 1.351 -0.052 2.00e-02 2.50e+03 6.66e+00 bond pdb=" C2 SAH B 401 " pdb=" N1 SAH B 401 " ideal model delta sigma weight residual 1.330 1.379 -0.049 2.00e-02 2.50e+03 5.89e+00 bond pdb=" C6 SAH B 401 " pdb=" N1 SAH B 401 " ideal model delta sigma weight residual 1.338 1.378 -0.040 2.00e-02 2.50e+03 4.10e+00 bond pdb=" C1' SAH B 401 " pdb=" N9 SAH B 401 " ideal model delta sigma weight residual 1.440 1.476 -0.036 2.00e-02 2.50e+03 3.24e+00 ... (remaining 5313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 7036 2.07 - 4.14: 96 4.14 - 6.21: 10 6.21 - 8.27: 2 8.27 - 10.34: 3 Bond angle restraints: 7147 Sorted by residual: angle pdb=" CG SAH B 401 " pdb=" SD SAH B 401 " pdb=" C5' SAH B 401 " ideal model delta sigma weight residual 101.77 91.43 10.34 3.00e+00 1.11e-01 1.19e+01 angle pdb=" O SAH B 401 " pdb=" C SAH B 401 " pdb=" OXT SAH B 401 " ideal model delta sigma weight residual 126.79 117.95 8.84 3.00e+00 1.11e-01 8.67e+00 angle pdb=" C LYS B 317 " pdb=" N ASN B 318 " pdb=" CA ASN B 318 " ideal model delta sigma weight residual 121.54 126.99 -5.45 1.91e+00 2.74e-01 8.14e+00 angle pdb=" C2 SAH B 401 " pdb=" N3 SAH B 401 " pdb=" C4 SAH B 401 " ideal model delta sigma weight residual 111.67 120.13 -8.46 3.00e+00 1.11e-01 7.96e+00 angle pdb=" N1 SAH B 401 " pdb=" C2 SAH B 401 " pdb=" N3 SAH B 401 " ideal model delta sigma weight residual 128.45 120.52 7.93 3.00e+00 1.11e-01 6.99e+00 ... (remaining 7142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 2895 17.61 - 35.23: 266 35.23 - 52.84: 60 52.84 - 70.45: 10 70.45 - 88.07: 6 Dihedral angle restraints: 3237 sinusoidal: 1382 harmonic: 1855 Sorted by residual: dihedral pdb=" CA MET A 401 " pdb=" C MET A 401 " pdb=" N MET A 402 " pdb=" CA MET A 402 " ideal model delta harmonic sigma weight residual 180.00 163.78 16.22 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CG ARG B 357 " pdb=" CD ARG B 357 " pdb=" NE ARG B 357 " pdb=" CZ ARG B 357 " ideal model delta sinusoidal sigma weight residual -90.00 -134.61 44.61 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CB GLU A 201 " pdb=" CG GLU A 201 " pdb=" CD GLU A 201 " pdb=" OE1 GLU A 201 " ideal model delta sinusoidal sigma weight residual 0.00 -88.07 88.07 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 3234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 489 0.034 - 0.068: 212 0.068 - 0.102: 50 0.102 - 0.136: 26 0.136 - 0.170: 3 Chirality restraints: 780 Sorted by residual: chirality pdb=" CB VAL B 310 " pdb=" CA VAL B 310 " pdb=" CG1 VAL B 310 " pdb=" CG2 VAL B 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CA GLN B 155 " pdb=" N GLN B 155 " pdb=" C GLN B 155 " pdb=" CB GLN B 155 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CA ILE A 112 " pdb=" N ILE A 112 " pdb=" C ILE A 112 " pdb=" CB ILE A 112 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 777 not shown) Planarity restraints: 909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 151 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.22e+00 pdb=" C LEU B 151 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU B 151 " -0.015 2.00e-02 2.50e+03 pdb=" N HIS B 152 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 352 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO A 353 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 353 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 353 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 51 " 0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO D 52 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 52 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 52 " 0.023 5.00e-02 4.00e+02 ... (remaining 906 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 200 2.72 - 3.27: 5149 3.27 - 3.81: 8125 3.81 - 4.36: 10477 4.36 - 4.90: 17641 Nonbonded interactions: 41592 Sorted by model distance: nonbonded pdb=" OG SER B 326 " pdb=" OE2 GLU B 337 " model vdw 2.179 3.040 nonbonded pdb=" O LYS B 257 " pdb=" OG1 THR B 261 " model vdw 2.204 3.040 nonbonded pdb=" OG SER A 383 " pdb=" NZ LYS B 289 " model vdw 2.257 3.120 nonbonded pdb=" O CYS B 346 " pdb=" OH TYR B 351 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR A 407 " pdb=" OE1 GLU A 431 " model vdw 2.286 3.040 ... (remaining 41587 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.040 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 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 0.059 5318 Z= 0.139 Angle : 0.608 10.344 7147 Z= 0.301 Chirality : 0.043 0.170 780 Planarity : 0.004 0.047 909 Dihedral : 14.732 88.067 2031 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.33), residues: 620 helix: 0.07 (0.37), residues: 193 sheet: -0.33 (0.47), residues: 104 loop : -0.51 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 108 TYR 0.013 0.001 TYR A 352 PHE 0.012 0.001 PHE A 355 TRP 0.005 0.001 TRP A 107 HIS 0.003 0.001 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 5318) covalent geometry : angle 0.60783 ( 7147) hydrogen bonds : bond 0.14926 ( 182) hydrogen bonds : angle 6.31944 ( 504) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.177 Fit side-chains REVERT: A 384 ASP cc_start: 0.7231 (t70) cc_final: 0.6985 (t0) REVERT: A 405 TYR cc_start: 0.7434 (t80) cc_final: 0.7153 (t80) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.5674 time to fit residues: 72.6173 Evaluate side-chains 80 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN B 343 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN D 83 ASN D 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.182982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.148222 restraints weight = 6181.130| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.77 r_work: 0.3655 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5318 Z= 0.203 Angle : 0.648 7.225 7147 Z= 0.338 Chirality : 0.044 0.157 780 Planarity : 0.005 0.067 909 Dihedral : 5.474 55.256 676 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.95 % Allowed : 14.04 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.33), residues: 620 helix: -0.43 (0.35), residues: 209 sheet: -0.10 (0.48), residues: 103 loop : -0.66 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 108 TYR 0.019 0.002 TYR A 207 PHE 0.014 0.002 PHE B 293 TRP 0.009 0.002 TRP B 252 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 5318) covalent geometry : angle 0.64795 ( 7147) hydrogen bonds : bond 0.05033 ( 182) hydrogen bonds : angle 5.18857 ( 504) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: B 353 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8358 (tt0) REVERT: D 108 ILE cc_start: 0.7379 (mp) cc_final: 0.7073 (mt) outliers start: 17 outliers final: 9 residues processed: 92 average time/residue: 0.5466 time to fit residues: 52.5650 Evaluate side-chains 79 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 51 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 0.0970 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.184699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.148974 restraints weight = 6129.075| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.73 r_work: 0.3678 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5318 Z= 0.130 Angle : 0.552 6.047 7147 Z= 0.288 Chirality : 0.041 0.148 780 Planarity : 0.004 0.057 909 Dihedral : 5.124 51.030 676 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.12 % Allowed : 16.64 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.33), residues: 620 helix: -0.13 (0.36), residues: 209 sheet: -0.03 (0.52), residues: 93 loop : -0.70 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 108 TYR 0.019 0.002 TYR A 207 PHE 0.009 0.001 PHE D 14 TRP 0.007 0.001 TRP B 252 HIS 0.002 0.000 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5318) covalent geometry : angle 0.55154 ( 7147) hydrogen bonds : bond 0.04057 ( 182) hydrogen bonds : angle 4.78638 ( 504) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.220 Fit side-chains REVERT: A 429 MET cc_start: 0.8230 (mtt) cc_final: 0.7958 (mtt) REVERT: B 171 MET cc_start: 0.7647 (mtm) cc_final: 0.7181 (mmp) REVERT: D 21 MET cc_start: 0.7957 (mmm) cc_final: 0.7749 (mmm) outliers start: 18 outliers final: 11 residues processed: 85 average time/residue: 0.4904 time to fit residues: 43.8994 Evaluate side-chains 78 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 9 optimal weight: 0.0970 chunk 51 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN A 380 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN D 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.182855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.148123 restraints weight = 6109.039| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.58 r_work: 0.3662 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5318 Z= 0.181 Angle : 0.605 6.444 7147 Z= 0.312 Chirality : 0.042 0.154 780 Planarity : 0.005 0.063 909 Dihedral : 5.288 49.204 676 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.16 % Allowed : 16.98 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.33), residues: 620 helix: -0.28 (0.35), residues: 211 sheet: -0.24 (0.51), residues: 93 loop : -0.86 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 108 TYR 0.018 0.002 TYR A 352 PHE 0.014 0.002 PHE B 203 TRP 0.008 0.002 TRP B 252 HIS 0.002 0.001 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 5318) covalent geometry : angle 0.60455 ( 7147) hydrogen bonds : bond 0.04519 ( 182) hydrogen bonds : angle 4.92171 ( 504) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.258 Fit side-chains REVERT: B 171 MET cc_start: 0.7684 (mtm) cc_final: 0.7266 (mmp) REVERT: B 310 VAL cc_start: 0.7356 (OUTLIER) cc_final: 0.7131 (t) outliers start: 24 outliers final: 16 residues processed: 89 average time/residue: 0.4878 time to fit residues: 45.7370 Evaluate side-chains 88 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN A 380 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.185775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.150547 restraints weight = 6194.835| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.90 r_work: 0.3661 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5318 Z= 0.123 Angle : 0.547 6.408 7147 Z= 0.283 Chirality : 0.041 0.142 780 Planarity : 0.004 0.054 909 Dihedral : 4.986 47.140 676 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.29 % Allowed : 18.89 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.33), residues: 620 helix: -0.06 (0.36), residues: 211 sheet: -0.12 (0.52), residues: 93 loop : -0.86 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 108 TYR 0.017 0.001 TYR A 207 PHE 0.012 0.001 PHE B 203 TRP 0.008 0.001 TRP B 365 HIS 0.002 0.000 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 5318) covalent geometry : angle 0.54666 ( 7147) hydrogen bonds : bond 0.03779 ( 182) hydrogen bonds : angle 4.64297 ( 504) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 173 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7273 (mmtm) REVERT: B 171 MET cc_start: 0.7369 (mtm) cc_final: 0.6976 (mmp) outliers start: 19 outliers final: 10 residues processed: 93 average time/residue: 0.5430 time to fit residues: 52.9467 Evaluate side-chains 87 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 51 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 52 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN A 226 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.186754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.151951 restraints weight = 6229.666| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 3.10 r_work: 0.3673 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5318 Z= 0.113 Angle : 0.536 6.692 7147 Z= 0.277 Chirality : 0.040 0.139 780 Planarity : 0.004 0.053 909 Dihedral : 4.862 47.601 676 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.81 % Allowed : 19.58 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.33), residues: 620 helix: 0.05 (0.36), residues: 211 sheet: -0.03 (0.53), residues: 93 loop : -0.87 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 169 TYR 0.016 0.001 TYR A 207 PHE 0.012 0.001 PHE B 158 TRP 0.011 0.001 TRP B 365 HIS 0.002 0.000 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 5318) covalent geometry : angle 0.53644 ( 7147) hydrogen bonds : bond 0.03562 ( 182) hydrogen bonds : angle 4.50775 ( 504) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: B 171 MET cc_start: 0.7291 (mtm) cc_final: 0.6910 (mmp) outliers start: 22 outliers final: 13 residues processed: 95 average time/residue: 0.5277 time to fit residues: 52.5968 Evaluate side-chains 87 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 52 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.185189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.149648 restraints weight = 6180.703| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 3.08 r_work: 0.3650 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5318 Z= 0.145 Angle : 0.582 7.603 7147 Z= 0.300 Chirality : 0.041 0.143 780 Planarity : 0.005 0.085 909 Dihedral : 4.978 45.599 676 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.12 % Allowed : 20.28 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.33), residues: 620 helix: -0.02 (0.36), residues: 210 sheet: -0.03 (0.54), residues: 93 loop : -0.92 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 169 TYR 0.016 0.002 TYR A 352 PHE 0.010 0.002 PHE D 14 TRP 0.015 0.001 TRP B 365 HIS 0.002 0.001 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 5318) covalent geometry : angle 0.58227 ( 7147) hydrogen bonds : bond 0.03994 ( 182) hydrogen bonds : angle 4.67631 ( 504) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: B 171 MET cc_start: 0.7380 (mtm) cc_final: 0.6986 (mmp) REVERT: C 165 GLU cc_start: 0.5941 (tp30) cc_final: 0.5632 (tt0) outliers start: 18 outliers final: 12 residues processed: 90 average time/residue: 0.5024 time to fit residues: 47.6364 Evaluate side-chains 85 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.182865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.147197 restraints weight = 6195.988| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 3.03 r_work: 0.3612 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5318 Z= 0.196 Angle : 0.647 7.681 7147 Z= 0.331 Chirality : 0.043 0.150 780 Planarity : 0.005 0.103 909 Dihedral : 5.206 42.777 676 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.81 % Allowed : 20.10 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.33), residues: 620 helix: -0.25 (0.35), residues: 210 sheet: -0.25 (0.54), residues: 94 loop : -0.98 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 22 TYR 0.024 0.002 TYR A 352 PHE 0.015 0.002 PHE B 203 TRP 0.018 0.002 TRP B 365 HIS 0.002 0.001 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 5318) covalent geometry : angle 0.64704 ( 7147) hydrogen bonds : bond 0.04505 ( 182) hydrogen bonds : angle 4.94979 ( 504) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.224 Fit side-chains REVERT: A 173 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7439 (mmtm) REVERT: B 171 MET cc_start: 0.7491 (mtm) cc_final: 0.7107 (mmp) REVERT: C 165 GLU cc_start: 0.6195 (tp30) cc_final: 0.5944 (tt0) outliers start: 22 outliers final: 13 residues processed: 89 average time/residue: 0.4861 time to fit residues: 45.5672 Evaluate side-chains 83 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 57 optimal weight: 0.1980 chunk 20 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.186168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.152320 restraints weight = 6156.203| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.57 r_work: 0.3713 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5318 Z= 0.118 Angle : 0.573 8.801 7147 Z= 0.293 Chirality : 0.041 0.165 780 Planarity : 0.005 0.086 909 Dihedral : 4.905 47.339 676 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.60 % Allowed : 22.18 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.33), residues: 620 helix: -0.01 (0.36), residues: 210 sheet: 0.03 (0.54), residues: 91 loop : -0.95 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 359 TYR 0.015 0.001 TYR A 207 PHE 0.012 0.001 PHE B 203 TRP 0.021 0.001 TRP B 365 HIS 0.002 0.000 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 5318) covalent geometry : angle 0.57327 ( 7147) hydrogen bonds : bond 0.03661 ( 182) hydrogen bonds : angle 4.63312 ( 504) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 173 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7374 (mmtm) REVERT: B 171 MET cc_start: 0.7490 (mtm) cc_final: 0.7099 (mmp) REVERT: C 165 GLU cc_start: 0.5966 (tp30) cc_final: 0.5714 (tt0) outliers start: 15 outliers final: 11 residues processed: 85 average time/residue: 0.4827 time to fit residues: 43.2091 Evaluate side-chains 79 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.0770 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 47 optimal weight: 0.0170 chunk 9 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.188273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.153566 restraints weight = 6149.129| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.44 r_work: 0.3747 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5318 Z= 0.106 Angle : 0.550 9.426 7147 Z= 0.280 Chirality : 0.041 0.175 780 Planarity : 0.004 0.072 909 Dihedral : 4.688 50.441 676 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.73 % Allowed : 23.40 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.33), residues: 620 helix: 0.13 (0.37), residues: 210 sheet: 0.07 (0.55), residues: 91 loop : -0.93 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 108 TYR 0.016 0.001 TYR A 207 PHE 0.010 0.001 PHE B 203 TRP 0.024 0.001 TRP B 365 HIS 0.001 0.000 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 5318) covalent geometry : angle 0.54996 ( 7147) hydrogen bonds : bond 0.03405 ( 182) hydrogen bonds : angle 4.47776 ( 504) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: B 171 MET cc_start: 0.7515 (mtm) cc_final: 0.7117 (mmp) outliers start: 10 outliers final: 8 residues processed: 84 average time/residue: 0.4339 time to fit residues: 38.5636 Evaluate side-chains 74 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 0.1980 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN A 323 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.188461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.153405 restraints weight = 6217.458| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.64 r_work: 0.3734 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5318 Z= 0.106 Angle : 0.529 7.366 7147 Z= 0.274 Chirality : 0.040 0.135 780 Planarity : 0.004 0.077 909 Dihedral : 4.648 50.225 676 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.25 % Allowed : 23.40 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.33), residues: 620 helix: 0.18 (0.37), residues: 210 sheet: 0.00 (0.56), residues: 94 loop : -0.93 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 169 TYR 0.015 0.001 TYR A 207 PHE 0.013 0.001 PHE B 203 TRP 0.031 0.001 TRP B 365 HIS 0.001 0.000 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 5318) covalent geometry : angle 0.52870 ( 7147) hydrogen bonds : bond 0.03372 ( 182) hydrogen bonds : angle 4.38862 ( 504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2316.38 seconds wall clock time: 40 minutes 17.14 seconds (2417.14 seconds total)