Starting phenix.real_space_refine on Thu Jul 24 04:59:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yi8_33853/07_2025/7yi8_33853.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yi8_33853/07_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_33853/07_2025/7yi8_33853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yi8_33853/07_2025/7yi8_33853.map" model { file = "/net/cci-nas-00/data/ceres_data/7yi8_33853/07_2025/7yi8_33853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yi8_33853/07_2025/7yi8_33853.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.54, per 1000 atoms: 0.68 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: 1.28 Conformation dependent library (CDL) restraints added in 672.2 milliseconds 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: 0.57 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: 1.31 Time building geometry restraints manager: 1.40 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.530 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:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.160 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP A 107 HIS 0.003 0.001 HIS B 152 PHE 0.012 0.001 PHE A 355 TYR 0.013 0.001 TYR A 352 ARG 0.003 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.14926 ( 182) hydrogen bonds : angle 6.31944 ( 504) covalent geometry : bond 0.00297 ( 5318) covalent geometry : angle 0.60783 ( 7147) *********************** 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 : 0.557 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: 1.2301 time to fit residues: 157.9303 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 : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN D 83 ASN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.182580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.147899 restraints weight = 6136.487| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.92 r_work: 0.3645 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1865 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= 0.212 Angle : 0.663 7.305 7147 Z= 0.345 Chirality : 0.045 0.160 780 Planarity : 0.005 0.069 909 Dihedral : 5.563 55.503 676 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.12 % Allowed : 14.04 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.33), residues: 620 helix: -0.48 (0.35), residues: 209 sheet: -0.13 (0.48), residues: 103 loop : -0.68 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 252 HIS 0.003 0.001 HIS A 360 PHE 0.015 0.002 PHE B 293 TYR 0.019 0.002 TYR A 207 ARG 0.007 0.001 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.05078 ( 182) hydrogen bonds : angle 5.20858 ( 504) covalent geometry : bond 0.00501 ( 5318) covalent geometry : angle 0.66299 ( 7147) *********************** 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 98 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: D 108 ILE cc_start: 0.7386 (mp) cc_final: 0.7068 (mt) outliers start: 18 outliers final: 11 residues processed: 93 average time/residue: 1.1042 time to fit residues: 107.7271 Evaluate side-chains 80 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 389 VAL 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 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 Chi-restraints excluded: chain D residue 62 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.0870 chunk 49 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4305 r_free = 0.4305 target = 0.186537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.151596 restraints weight = 6141.551| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.60 r_work: 0.3701 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5318 Z= 0.109 Angle : 0.520 5.601 7147 Z= 0.273 Chirality : 0.040 0.145 780 Planarity : 0.004 0.053 909 Dihedral : 4.993 50.566 676 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.60 % Allowed : 16.98 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.33), residues: 620 helix: -0.05 (0.36), residues: 211 sheet: -0.08 (0.52), residues: 94 loop : -0.66 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 365 HIS 0.001 0.000 HIS C 169 PHE 0.009 0.001 PHE B 158 TYR 0.019 0.001 TYR A 207 ARG 0.005 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03724 ( 182) hydrogen bonds : angle 4.67710 ( 504) covalent geometry : bond 0.00245 ( 5318) covalent geometry : angle 0.52010 ( 7147) *********************** 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 94 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.639 Fit side-chains REVERT: A 409 MET cc_start: 0.6708 (tmm) cc_final: 0.6463 (tmm) REVERT: B 171 MET cc_start: 0.7338 (mtm) cc_final: 0.6921 (mmp) REVERT: D 21 MET cc_start: 0.7906 (mmm) cc_final: 0.7706 (mmm) outliers start: 15 outliers final: 9 residues processed: 87 average time/residue: 0.9804 time to fit residues: 89.8998 Evaluate side-chains 77 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 151 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.0370 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.8464 ------------------------------------------------------------------------------- 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 = 0.4306 r_free = 0.4306 target = 0.186147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.150862 restraints weight = 6242.330| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 3.12 r_work: 0.3663 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2017 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 : 0.539 6.752 7147 Z= 0.280 Chirality : 0.041 0.143 780 Planarity : 0.004 0.052 909 Dihedral : 4.976 50.947 676 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.29 % Allowed : 18.02 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.33), residues: 620 helix: 0.01 (0.36), residues: 211 sheet: 0.00 (0.52), residues: 93 loop : -0.75 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 365 HIS 0.002 0.000 HIS A 360 PHE 0.010 0.001 PHE B 158 TYR 0.017 0.001 TYR A 207 ARG 0.003 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 182) hydrogen bonds : angle 4.60732 ( 504) covalent geometry : bond 0.00281 ( 5318) covalent geometry : angle 0.53902 ( 7147) *********************** 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 92 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.564 Fit side-chains REVERT: B 171 MET cc_start: 0.7401 (mtm) cc_final: 0.7009 (mmp) outliers start: 19 outliers final: 12 residues processed: 86 average time/residue: 1.0059 time to fit residues: 91.0093 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 : 0.610 ------------------------------------------------------------------------------- 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 264 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 322 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 47 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.0870 chunk 61 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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 = 0.4316 r_free = 0.4316 target = 0.187511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.153375 restraints weight = 6079.639| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.59 r_work: 0.3719 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5318 Z= 0.108 Angle : 0.521 6.563 7147 Z= 0.269 Chirality : 0.040 0.138 780 Planarity : 0.004 0.051 909 Dihedral : 4.841 50.237 676 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.12 % Allowed : 19.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.33), residues: 620 helix: 0.11 (0.37), residues: 210 sheet: 0.04 (0.53), residues: 94 loop : -0.75 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 365 HIS 0.001 0.000 HIS D 39 PHE 0.011 0.001 PHE B 158 TYR 0.017 0.001 TYR A 207 ARG 0.003 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.03493 ( 182) hydrogen bonds : angle 4.50143 ( 504) covalent geometry : bond 0.00243 ( 5318) covalent geometry : angle 0.52059 ( 7147) *********************** 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 88 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 173 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7307 (mmtm) REVERT: B 171 MET cc_start: 0.7505 (mtm) cc_final: 0.7079 (mmp) REVERT: D 86 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6641 (mm-30) outliers start: 18 outliers final: 12 residues processed: 83 average time/residue: 0.9456 time to fit residues: 82.9113 Evaluate side-chains 85 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain D residue 86 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.184026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.148408 restraints weight = 6135.628| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 3.23 r_work: 0.3628 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2315 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= 0.175 Angle : 0.595 6.423 7147 Z= 0.306 Chirality : 0.042 0.147 780 Planarity : 0.004 0.055 909 Dihedral : 5.139 47.294 676 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.51 % Allowed : 19.58 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.33), residues: 620 helix: -0.07 (0.36), residues: 209 sheet: -0.03 (0.53), residues: 93 loop : -0.89 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 365 HIS 0.003 0.001 HIS A 360 PHE 0.012 0.002 PHE D 14 TYR 0.020 0.002 TYR A 352 ARG 0.003 0.000 ARG D 22 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 182) hydrogen bonds : angle 4.80611 ( 504) covalent geometry : bond 0.00408 ( 5318) covalent geometry : angle 0.59463 ( 7147) *********************** 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 102 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 173 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7345 (mmtm) REVERT: B 171 MET cc_start: 0.7497 (mtm) cc_final: 0.7100 (mmp) REVERT: B 353 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8204 (tt0) outliers start: 26 outliers final: 12 residues processed: 95 average time/residue: 0.9931 time to fit residues: 99.1286 Evaluate side-chains 90 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 B residue 353 GLU Chi-restraints excluded: chain B residue 359 ASN 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 8 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 43 optimal weight: 0.0570 chunk 22 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 48 optimal weight: 0.4980 chunk 56 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.4319 r_free = 0.4319 target = 0.187945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.153234 restraints weight = 6038.967| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.46 r_work: 0.3725 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5318 Z= 0.108 Angle : 0.539 7.267 7147 Z= 0.278 Chirality : 0.041 0.134 780 Planarity : 0.004 0.052 909 Dihedral : 4.771 47.270 676 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.12 % Allowed : 21.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.33), residues: 620 helix: 0.08 (0.36), residues: 210 sheet: 0.04 (0.54), residues: 94 loop : -0.82 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 365 HIS 0.002 0.000 HIS C 169 PHE 0.011 0.001 PHE B 203 TYR 0.017 0.001 TYR A 207 ARG 0.004 0.000 ARG B 169 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 182) hydrogen bonds : angle 4.51308 ( 504) covalent geometry : bond 0.00243 ( 5318) covalent geometry : angle 0.53947 ( 7147) *********************** 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 98 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 173 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7315 (mmtm) REVERT: B 171 MET cc_start: 0.7436 (mtm) cc_final: 0.7044 (mmp) REVERT: C 165 GLU cc_start: 0.5779 (tp30) cc_final: 0.5458 (tt0) REVERT: D 86 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6428 (mm-30) outliers start: 18 outliers final: 10 residues processed: 95 average time/residue: 1.0862 time to fit residues: 108.2891 Evaluate side-chains 83 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 277 THR 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 40 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 86 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.4272 r_free = 0.4272 target = 0.183247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.148571 restraints weight = 6054.413| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.70 r_work: 0.3656 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5318 Z= 0.198 Angle : 0.644 7.947 7147 Z= 0.331 Chirality : 0.043 0.148 780 Planarity : 0.005 0.095 909 Dihedral : 5.147 43.384 676 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.81 % Allowed : 20.80 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.33), residues: 620 helix: -0.17 (0.35), residues: 210 sheet: -0.04 (0.54), residues: 93 loop : -0.96 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 365 HIS 0.003 0.001 HIS D 39 PHE 0.015 0.002 PHE B 158 TYR 0.021 0.002 TYR A 352 ARG 0.004 0.000 ARG D 22 Details of bonding type rmsd hydrogen bonds : bond 0.04460 ( 182) hydrogen bonds : angle 4.90766 ( 504) covalent geometry : bond 0.00466 ( 5318) covalent geometry : angle 0.64431 ( 7147) *********************** 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 97 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: B 171 MET cc_start: 0.7622 (mtm) cc_final: 0.7227 (mmp) REVERT: C 165 GLU cc_start: 0.6302 (tp30) cc_final: 0.5985 (tt0) REVERT: D 86 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7125 (mm-30) outliers start: 22 outliers final: 14 residues processed: 91 average time/residue: 1.0298 time to fit residues: 98.5690 Evaluate side-chains 89 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain D residue 86 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 42 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4303 r_free = 0.4303 target = 0.186158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.150811 restraints weight = 6083.384| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.43 r_work: 0.3713 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2427 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= 0.125 Angle : 0.583 8.793 7147 Z= 0.298 Chirality : 0.041 0.168 780 Planarity : 0.005 0.093 909 Dihedral : 4.921 45.964 676 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.12 % Allowed : 22.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.33), residues: 620 helix: -0.00 (0.36), residues: 210 sheet: -0.01 (0.54), residues: 93 loop : -0.89 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 365 HIS 0.002 0.000 HIS D 39 PHE 0.013 0.001 PHE B 203 TYR 0.015 0.001 TYR A 207 ARG 0.004 0.000 ARG A 359 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 182) hydrogen bonds : angle 4.66702 ( 504) covalent geometry : bond 0.00289 ( 5318) covalent geometry : angle 0.58320 ( 7147) *********************** 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 93 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: B 171 MET cc_start: 0.7521 (mtm) cc_final: 0.7144 (mmp) REVERT: C 165 GLU cc_start: 0.6026 (tp30) cc_final: 0.5711 (tt0) REVERT: D 112 GLU cc_start: 0.7819 (tp30) cc_final: 0.7525 (tp30) outliers start: 18 outliers final: 11 residues processed: 88 average time/residue: 1.0255 time to fit residues: 95.0456 Evaluate side-chains 84 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 277 THR 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 14 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4309 r_free = 0.4309 target = 0.186806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.151754 restraints weight = 6165.906| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.62 r_work: 0.3712 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5318 Z= 0.124 Angle : 0.590 9.314 7147 Z= 0.299 Chirality : 0.041 0.180 780 Planarity : 0.005 0.091 909 Dihedral : 4.881 47.813 676 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.25 % Allowed : 22.36 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.33), residues: 620 helix: 0.04 (0.36), residues: 210 sheet: -0.01 (0.55), residues: 93 loop : -0.93 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 365 HIS 0.002 0.000 HIS D 39 PHE 0.014 0.001 PHE B 203 TYR 0.014 0.001 TYR A 207 ARG 0.003 0.000 ARG B 169 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 182) hydrogen bonds : angle 4.59120 ( 504) covalent geometry : bond 0.00288 ( 5318) covalent geometry : angle 0.58953 ( 7147) ********************** 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 87 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: B 171 MET cc_start: 0.7526 (mtm) cc_final: 0.7152 (mmp) REVERT: D 112 GLU cc_start: 0.7809 (tp30) cc_final: 0.7436 (tp30) outliers start: 13 outliers final: 11 residues processed: 85 average time/residue: 0.9709 time to fit residues: 87.2944 Evaluate side-chains 83 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 277 THR 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 20 optimal weight: 0.0670 chunk 54 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 0.0870 chunk 3 optimal weight: 0.0020 chunk 1 optimal weight: 0.0770 chunk 46 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 0.0970 overall best weight: 0.0660 ------------------------------------------------------------------------------- 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 = 0.4368 r_free = 0.4368 target = 0.193364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.159157 restraints weight = 6169.029| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 2.79 r_work: 0.3820 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 5318 Z= 0.100 Angle : 0.556 9.842 7147 Z= 0.285 Chirality : 0.040 0.133 780 Planarity : 0.004 0.061 909 Dihedral : 4.593 53.423 676 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.56 % Allowed : 23.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.34), residues: 620 helix: 0.29 (0.37), residues: 211 sheet: 0.11 (0.57), residues: 94 loop : -0.86 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 365 HIS 0.001 0.000 HIS C 169 PHE 0.010 0.001 PHE B 203 TYR 0.021 0.001 TYR A 207 ARG 0.005 0.001 ARG B 329 Details of bonding type rmsd hydrogen bonds : bond 0.02824 ( 182) hydrogen bonds : angle 4.22379 ( 504) covalent geometry : bond 0.00227 ( 5318) covalent geometry : angle 0.55559 ( 7147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4674.82 seconds wall clock time: 80 minutes 22.59 seconds (4822.59 seconds total)