Starting phenix.real_space_refine on Thu Oct 22 18:01:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/26qi_80826/10_2026/26qi_80826.cif Found real_map, /net/cci-nas-00/data/ceres_data/26qi_80826/10_2026/26qi_80826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/26qi_80826/10_2026/26qi_80826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/26qi_80826/10_2026/26qi_80826.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/26qi_80826/10_2026/26qi_80826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/26qi_80826/10_2026/26qi_80826.map" } resolution = 3.43 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= 0.002 sd= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 29 5.16 5 C 2049 2.51 5 N 516 2.21 5 O 535 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3130 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3103 Classifications: {'peptide': 388} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 15, 'TRANS': 372} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'KYF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.88, per 1000 atoms: 0.28 Number of scatterers: 3130 At special positions: 0 Unit cell: (65.92, 61.8, 84.048, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 F 1 9.00 O 535 8.00 N 516 7.00 C 2049 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 323 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 114.3 milliseconds 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 1 sheets defined 59.5% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 2 through 36 Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 93 through 105 Processing helix chain 'A' and resid 122 through 134 Proline residue: A 130 - end of helix removed outlier: 3.616A pdb=" N VAL A 134 " --> pdb=" O PRO A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 179 through 192 Processing helix chain 'A' and resid 192 through 203 Processing helix chain 'A' and resid 217 through 223 Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.766A pdb=" N ALA A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 224 through 229' Processing helix chain 'A' and resid 234 through 246 removed outlier: 3.766A pdb=" N PHE A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 284 Processing helix chain 'A' and resid 286 through 294 removed outlier: 3.815A pdb=" N CYS A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 295 through 311 removed outlier: 4.559A pdb=" N LEU A 301 " --> pdb=" O PHE A 297 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 339 Processing helix chain 'A' and resid 345 through 370 Processing sheet with id=AA1, first strand: chain 'A' and resid 110 through 114 removed outlier: 8.881A pdb=" N ARG A 111 " --> pdb=" O TYR A 81 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL A 83 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N PHE A 113 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU A 85 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL A 53 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU A 84 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A 55 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N CYS A 86 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS A 57 " --> pdb=" O CYS A 86 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER A 54 " --> pdb=" O TRP A 141 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N CYS A 143 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A 56 " --> pdb=" O CYS A 143 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS A 213 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N SER A 212 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N GLY A 166 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N VAL A 165 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 12.143A pdb=" N SER A 253 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 12.627A pdb=" N LEU A 167 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 12.546A pdb=" N GLN A 255 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N HIS A 169 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ALA A 257 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU A 171 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLN A 259 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR A 173 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET A 258 " --> pdb=" O ARG A 148 " (cutoff:3.500A) 165 hydrogen bonds defined for protein. 495 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: 0.38 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 482 1.32 - 1.44: 919 1.44 - 1.57: 1767 1.57 - 1.70: 3 1.70 - 1.82: 45 Bond restraints: 3216 Sorted by residual: bond pdb=" C07 KYF A 401 " pdb=" N06 KYF A 401 " ideal model delta sigma weight residual 1.460 1.248 0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C09 KYF A 401 " pdb=" C10 KYF A 401 " ideal model delta sigma weight residual 1.531 1.322 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C05 KYF A 401 " pdb=" N06 KYF A 401 " ideal model delta sigma weight residual 1.453 1.276 0.177 2.00e-02 2.50e+03 7.85e+01 bond pdb=" C16 KYF A 401 " pdb=" N20 KYF A 401 " ideal model delta sigma weight residual 1.363 1.487 -0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" C02 KYF A 401 " pdb=" N12 KYF A 401 " ideal model delta sigma weight residual 1.351 1.472 -0.121 2.00e-02 2.50e+03 3.68e+01 ... (remaining 3211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 4344 3.90 - 7.81: 16 7.81 - 11.71: 2 11.71 - 15.61: 0 15.61 - 19.51: 1 Bond angle restraints: 4363 Sorted by residual: angle pdb=" C04 KYF A 401 " pdb=" C09 KYF A 401 " pdb=" C08 KYF A 401 " ideal model delta sigma weight residual 109.92 90.41 19.51 3.00e+00 1.11e-01 4.23e+01 angle pdb=" N VAL A 119 " pdb=" CA VAL A 119 " pdb=" C VAL A 119 " ideal model delta sigma weight residual 113.20 108.87 4.33 9.60e-01 1.09e+00 2.03e+01 angle pdb=" C17 KYF A 401 " pdb=" S18 KYF A 401 " pdb=" C19 KYF A 401 " ideal model delta sigma weight residual 89.42 99.24 -9.82 3.00e+00 1.11e-01 1.07e+01 angle pdb=" N12 KYF A 401 " pdb=" C02 KYF A 401 " pdb=" O03 KYF A 401 " ideal model delta sigma weight residual 110.49 119.75 -9.26 3.00e+00 1.11e-01 9.53e+00 angle pdb=" N VAL A 298 " pdb=" CA VAL A 298 " pdb=" C VAL A 298 " ideal model delta sigma weight residual 111.90 109.59 2.31 8.10e-01 1.52e+00 8.13e+00 ... (remaining 4358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 1722 17.98 - 35.96: 141 35.96 - 53.94: 27 53.94 - 71.92: 7 71.92 - 89.91: 3 Dihedral angle restraints: 1900 sinusoidal: 775 harmonic: 1125 Sorted by residual: dihedral pdb=" CB GLU A 163 " pdb=" CG GLU A 163 " pdb=" CD GLU A 163 " pdb=" OE1 GLU A 163 " ideal model delta sinusoidal sigma weight residual 0.00 -85.15 85.15 1 3.00e+01 1.11e-03 9.77e+00 dihedral pdb=" CA LYS A 217 " pdb=" CB LYS A 217 " pdb=" CG LYS A 217 " pdb=" CD LYS A 217 " ideal model delta sinusoidal sigma weight residual -60.00 -107.89 47.89 3 1.50e+01 4.44e-03 8.56e+00 dihedral pdb=" CA ILE A 227 " pdb=" CB ILE A 227 " pdb=" CG1 ILE A 227 " pdb=" CD1 ILE A 227 " ideal model delta sinusoidal sigma weight residual 60.00 107.49 -47.49 3 1.50e+01 4.44e-03 8.50e+00 ... (remaining 1897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 444 0.076 - 0.153: 31 0.153 - 0.229: 1 0.229 - 0.305: 0 0.305 - 0.382: 1 Chirality restraints: 477 Sorted by residual: chirality pdb=" C09 KYF A 401 " pdb=" C04 KYF A 401 " pdb=" C08 KYF A 401 " pdb=" C10 KYF A 401 " both_signs ideal model delta sigma weight residual False -2.85 -2.47 -0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" C04 KYF A 401 " pdb=" C05 KYF A 401 " pdb=" C09 KYF A 401 " pdb=" O03 KYF A 401 " both_signs ideal model delta sigma weight residual False 2.66 2.50 0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" CB VAL A 134 " pdb=" CA VAL A 134 " pdb=" CG1 VAL A 134 " pdb=" CG2 VAL A 134 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 474 not shown) Planarity restraints: 540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 150 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO A 151 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 151 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 151 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 92 " 0.016 5.00e-02 4.00e+02 2.42e-02 9.35e-01 pdb=" N PRO A 93 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 63 " 0.014 5.00e-02 4.00e+02 2.14e-02 7.32e-01 pdb=" N PRO A 64 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " 0.012 5.00e-02 4.00e+02 ... (remaining 537 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 851 2.80 - 3.33: 2955 3.33 - 3.85: 5304 3.85 - 4.38: 5869 4.38 - 4.90: 10248 Nonbonded interactions: 25227 Sorted by model distance: nonbonded pdb=" OH TYR A 196 " pdb=" OG SER A 294 " model vdw 2.280 3.040 nonbonded pdb=" OD2 ASP A 156 " pdb=" OG1 THR A 254 " model vdw 2.285 3.040 nonbonded pdb=" O PRO A 51 " pdb=" OH TYR A 78 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR A 173 " pdb=" OE1 GLN A 338 " model vdw 2.323 3.040 nonbonded pdb=" O GLN A 178 " pdb=" OH TYR A 264 " model vdw 2.331 3.040 ... (remaining 25222 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.560 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.400 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 : 0.009 0.212 3217 Z= 0.441 Angle : 0.662 19.515 4365 Z= 0.352 Chirality : 0.041 0.382 477 Planarity : 0.003 0.026 540 Dihedral : 14.152 89.905 1177 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.91 % Allowed : 8.16 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.39), residues: 386 helix: 0.30 (0.32), residues: 214 sheet: -1.45 (0.82), residues: 37 loop : -2.09 (0.48), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 195 TYR 0.004 0.001 TYR A 188 PHE 0.010 0.001 PHE A 19 TRP 0.004 0.000 TRP A 326 HIS 0.001 0.000 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00871 / 0.44 ( 3216) covalent geometry : angle 0.66202 / 0.35 ( 4363) SS BOND : bond 0.00418 / 0.22 ( 1) SS BOND : angle 1.20410 / 0.71 ( 2) hydrogen bonds : bond 0.12589 / 8.85 ( 165) hydrogen bonds : angle 5.65232 / 4.52 ( 495) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.121 Fit side-chains REVERT: A 111 ARG cc_start: 0.7945 (ptm160) cc_final: 0.7437 (ptm160) REVERT: A 122 ASN cc_start: 0.8159 (t0) cc_final: 0.7235 (t0) REVERT: A 159 ASN cc_start: 0.8171 (m-40) cc_final: 0.7485 (m-40) REVERT: A 273 MET cc_start: 0.8236 (mmm) cc_final: 0.7852 (mmm) outliers start: 3 outliers final: 2 residues processed: 83 average time/residue: 0.0886 time to fit residues: 8.5294 Evaluate side-chains 64 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 296 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 37] chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN A 255 GLN A 270 GLN A 282 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.172701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.129673 restraints weight = 3647.035| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.12 r_work: 0.3205 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3217 Z= 0.141 Angle : 0.493 5.421 4365 Z= 0.260 Chirality : 0.040 0.122 477 Planarity : 0.004 0.038 540 Dihedral : 9.763 84.683 459 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.21 % Allowed : 12.39 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.42), residues: 386 helix: 1.48 (0.34), residues: 217 sheet: -0.17 (1.04), residues: 27 loop : -1.99 (0.46), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 280 TYR 0.012 0.001 TYR A 132 PHE 0.014 0.002 PHE A 238 TRP 0.010 0.001 TRP A 23 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 3216) covalent geometry : angle 0.48721 / 0.26 ( 4363) SS BOND : bond 0.01001 / 0.53 ( 1) SS BOND : angle 3.41735 / 1.87 ( 2) hydrogen bonds : bond 0.04225 / 2.80 ( 165) hydrogen bonds : angle 4.00845 / 2.95 ( 495) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.113 Fit side-chains REVERT: A 96 ASP cc_start: 0.7725 (m-30) cc_final: 0.7269 (m-30) REVERT: A 159 ASN cc_start: 0.8216 (m-40) cc_final: 0.7581 (m-40) REVERT: A 226 LEU cc_start: 0.7620 (mt) cc_final: 0.7246 (mt) REVERT: A 246 ARG cc_start: 0.8278 (mpt180) cc_final: 0.8035 (mpt180) REVERT: A 369 TRP cc_start: 0.7263 (t-100) cc_final: 0.7030 (t-100) outliers start: 4 outliers final: 2 residues processed: 69 average time/residue: 0.0637 time to fit residues: 5.4348 Evaluate side-chains 58 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 368 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: [9, 32, 8, 7, 21, 0, 20, 37, 4, 5, 23] chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 4 optimal weight: 0.0670 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 169 HIS A 201 ASN A 259 GLN A 260 ASN A 282 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.167602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.124443 restraints weight = 3682.714| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.20 r_work: 0.3188 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3217 Z= 0.116 Angle : 0.472 5.243 4365 Z= 0.244 Chirality : 0.041 0.237 477 Planarity : 0.003 0.035 540 Dihedral : 9.731 86.458 457 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.11 % Allowed : 15.41 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.42), residues: 386 helix: 1.71 (0.35), residues: 217 sheet: -0.15 (1.06), residues: 26 loop : -1.68 (0.47), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 148 TYR 0.008 0.001 TYR A 32 PHE 0.012 0.001 PHE A 238 TRP 0.011 0.001 TRP A 23 HIS 0.002 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 3216) covalent geometry : angle 0.46735 / 0.24 ( 4363) SS BOND : bond 0.00929 / 0.49 ( 1) SS BOND : angle 3.22515 / 1.79 ( 2) hydrogen bonds : bond 0.04140 / 2.72 ( 165) hydrogen bonds : angle 3.80025 / 2.78 ( 495) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.079 Fit side-chains REVERT: A 55 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8126 (tt) REVERT: A 80 LYS cc_start: 0.6745 (mtmt) cc_final: 0.6178 (ptmt) REVERT: A 196 TYR cc_start: 0.8336 (m-10) cc_final: 0.8046 (m-10) REVERT: A 226 LEU cc_start: 0.7308 (mt) cc_final: 0.6862 (mt) REVERT: A 258 MET cc_start: 0.8046 (tpp) cc_final: 0.7825 (mmt) REVERT: A 369 TRP cc_start: 0.7332 (t-100) cc_final: 0.6992 (t-100) outliers start: 7 outliers final: 3 residues processed: 62 average time/residue: 0.0718 time to fit residues: 5.3600 Evaluate side-chains 57 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 320 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: [26, 19, 28, 21, 1, 35, 24, 6, 17, 2, 3] chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 ASN A 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.163766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.119395 restraints weight = 3691.688| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.23 r_work: 0.3105 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3217 Z= 0.140 Angle : 0.490 5.386 4365 Z= 0.256 Chirality : 0.040 0.130 477 Planarity : 0.004 0.035 540 Dihedral : 9.759 88.501 457 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.32 % Allowed : 16.31 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.42), residues: 386 helix: 1.80 (0.35), residues: 217 sheet: -0.17 (1.01), residues: 26 loop : -1.50 (0.49), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 148 TYR 0.009 0.001 TYR A 331 PHE 0.015 0.002 PHE A 327 TRP 0.011 0.001 TRP A 23 HIS 0.002 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 3216) covalent geometry : angle 0.48397 / 0.25 ( 4363) SS BOND : bond 0.00985 / 0.52 ( 1) SS BOND : angle 3.53820 / 1.96 ( 2) hydrogen bonds : bond 0.04514 / 2.95 ( 165) hydrogen bonds : angle 3.83064 / 2.79 ( 495) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.117 Fit side-chains REVERT: A 55 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8247 (tt) REVERT: A 71 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7768 (mt-10) REVERT: A 196 TYR cc_start: 0.8461 (m-10) cc_final: 0.8197 (m-10) REVERT: A 226 LEU cc_start: 0.7519 (mt) cc_final: 0.7035 (mt) REVERT: A 273 MET cc_start: 0.8238 (mmm) cc_final: 0.7958 (mmm) REVERT: A 275 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7695 (ttm-80) outliers start: 11 outliers final: 6 residues processed: 61 average time/residue: 0.0669 time to fit residues: 4.9602 Evaluate side-chains 55 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 368 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: [8, 22, 29, 20, 3, 5, 12, 37, 0, 26, 17] chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 HIS A 126 ASN A 260 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.159919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.115594 restraints weight = 3685.160| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.08 r_work: 0.3058 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3217 Z= 0.188 Angle : 0.537 5.465 4365 Z= 0.282 Chirality : 0.042 0.121 477 Planarity : 0.004 0.036 540 Dihedral : 9.619 83.147 457 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.93 % Allowed : 17.52 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.42), residues: 386 helix: 1.60 (0.34), residues: 218 sheet: -0.26 (0.98), residues: 26 loop : -1.38 (0.49), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 148 TYR 0.011 0.001 TYR A 331 PHE 0.015 0.002 PHE A 327 TRP 0.011 0.001 TRP A 23 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 ( 3216) covalent geometry : angle 0.53135 / 0.28 ( 4363) SS BOND : bond 0.01004 / 0.53 ( 1) SS BOND : angle 3.81737 / 2.11 ( 2) hydrogen bonds : bond 0.05054 / 3.31 ( 165) hydrogen bonds : angle 4.00240 / 2.90 ( 495) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.118 Fit side-chains REVERT: A 55 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8220 (tt) REVERT: A 69 ASN cc_start: 0.8158 (m-40) cc_final: 0.7780 (m110) REVERT: A 80 LYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6441 (ptmt) REVERT: A 196 TYR cc_start: 0.8392 (m-10) cc_final: 0.8111 (m-10) REVERT: A 226 LEU cc_start: 0.7664 (mt) cc_final: 0.7139 (mt) REVERT: A 273 MET cc_start: 0.8260 (mmm) cc_final: 0.7873 (mmm) REVERT: A 275 ARG cc_start: 0.7941 (ttp80) cc_final: 0.7679 (ttm-80) outliers start: 13 outliers final: 7 residues processed: 61 average time/residue: 0.0717 time to fit residues: 5.3054 Evaluate side-chains 57 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 368 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: [11, 25, 30, 7, 17, 26, 4, 35, 32, 24, 23] chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.161375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.116447 restraints weight = 3651.904| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.18 r_work: 0.3075 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3217 Z= 0.141 Angle : 0.498 5.680 4365 Z= 0.260 Chirality : 0.041 0.131 477 Planarity : 0.003 0.033 540 Dihedral : 9.682 86.038 457 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.72 % Allowed : 19.03 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.42), residues: 386 helix: 1.74 (0.35), residues: 218 sheet: -0.24 (0.98), residues: 26 loop : -1.30 (0.48), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 280 TYR 0.008 0.001 TYR A 331 PHE 0.017 0.002 PHE A 327 TRP 0.012 0.001 TRP A 23 HIS 0.002 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 3216) covalent geometry : angle 0.49219 / 0.26 ( 4363) SS BOND : bond 0.00932 / 0.49 ( 1) SS BOND : angle 3.54222 / 1.97 ( 2) hydrogen bonds : bond 0.04674 / 3.04 ( 165) hydrogen bonds : angle 3.81625 / 2.76 ( 495) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.115 Fit side-chains REVERT: A 55 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8199 (tt) REVERT: A 67 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7573 (mm) REVERT: A 69 ASN cc_start: 0.8167 (m-40) cc_final: 0.7759 (m110) REVERT: A 71 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7744 (mt-10) REVERT: A 80 LYS cc_start: 0.7106 (OUTLIER) cc_final: 0.6487 (ptmt) REVERT: A 196 TYR cc_start: 0.8338 (m-10) cc_final: 0.8086 (m-10) REVERT: A 226 LEU cc_start: 0.7517 (mt) cc_final: 0.6991 (mt) REVERT: A 273 MET cc_start: 0.8304 (mmm) cc_final: 0.7855 (mmm) REVERT: A 275 ARG cc_start: 0.7931 (ttp80) cc_final: 0.7677 (ttm-80) outliers start: 9 outliers final: 5 residues processed: 61 average time/residue: 0.0738 time to fit residues: 5.4430 Evaluate side-chains 59 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 320 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: [2, 17, 33, 6, 4, 14, 28, 8, 24, 12, 23] chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 0.0030 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.0870 overall best weight: 0.5570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.173778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.131091 restraints weight = 3659.391| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.07 r_work: 0.3166 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3217 Z= 0.116 Angle : 0.473 5.666 4365 Z= 0.246 Chirality : 0.040 0.132 477 Planarity : 0.003 0.033 540 Dihedral : 9.773 89.618 457 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.02 % Allowed : 19.03 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.42), residues: 386 helix: 1.90 (0.35), residues: 218 sheet: -0.17 (0.99), residues: 26 loop : -1.23 (0.48), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 246 TYR 0.018 0.001 TYR A 362 PHE 0.016 0.001 PHE A 327 TRP 0.012 0.001 TRP A 23 HIS 0.002 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 3216) covalent geometry : angle 0.46757 / 0.24 ( 4363) SS BOND : bond 0.00849 / 0.45 ( 1) SS BOND : angle 3.24034 / 1.80 ( 2) hydrogen bonds : bond 0.04333 / 2.83 ( 165) hydrogen bonds : angle 3.66015 / 2.65 ( 495) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.094 Fit side-chains REVERT: A 55 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8113 (tt) REVERT: A 67 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7503 (mm) REVERT: A 69 ASN cc_start: 0.8129 (m-40) cc_final: 0.7815 (m-40) REVERT: A 71 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7702 (mt-10) REVERT: A 80 LYS cc_start: 0.7077 (mtmt) cc_final: 0.6583 (ptmt) REVERT: A 196 TYR cc_start: 0.8239 (m-10) cc_final: 0.7962 (m-10) REVERT: A 217 LYS cc_start: 0.7207 (tmtt) cc_final: 0.6745 (tptp) REVERT: A 226 LEU cc_start: 0.7440 (mt) cc_final: 0.6897 (mt) REVERT: A 273 MET cc_start: 0.8305 (mmm) cc_final: 0.7797 (mmm) REVERT: A 275 ARG cc_start: 0.7881 (ttp80) cc_final: 0.7634 (ttm-80) outliers start: 10 outliers final: 7 residues processed: 59 average time/residue: 0.0652 time to fit residues: 4.7315 Evaluate side-chains 61 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 368 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: [33, 19, 3, 12, 17, 26, 16, 2, 21, 14, 29] chunk 33 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.163334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.119062 restraints weight = 3776.212| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.12 r_work: 0.3105 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3217 Z= 0.125 Angle : 0.476 5.886 4365 Z= 0.248 Chirality : 0.041 0.138 477 Planarity : 0.003 0.034 540 Dihedral : 9.720 89.096 457 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.02 % Allowed : 19.64 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.42), residues: 386 helix: 1.90 (0.35), residues: 218 sheet: -0.20 (0.98), residues: 26 loop : -1.22 (0.48), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.007 0.001 TYR A 331 PHE 0.017 0.001 PHE A 327 TRP 0.011 0.001 TRP A 23 HIS 0.002 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 3216) covalent geometry : angle 0.47094 / 0.25 ( 4363) SS BOND : bond 0.00864 / 0.45 ( 1) SS BOND : angle 3.31086 / 1.84 ( 2) hydrogen bonds : bond 0.04413 / 2.87 ( 165) hydrogen bonds : angle 3.67722 / 2.66 ( 495) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.120 Fit side-chains REVERT: A 55 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8166 (tt) REVERT: A 67 ILE cc_start: 0.7750 (mm) cc_final: 0.7522 (mm) REVERT: A 69 ASN cc_start: 0.8167 (m-40) cc_final: 0.7851 (m-40) REVERT: A 71 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7744 (mt-10) REVERT: A 80 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6643 (ptmt) REVERT: A 196 TYR cc_start: 0.8287 (m-10) cc_final: 0.7956 (m-10) REVERT: A 217 LYS cc_start: 0.7250 (tmtt) cc_final: 0.6802 (tptp) REVERT: A 226 LEU cc_start: 0.7502 (mt) cc_final: 0.6956 (mt) REVERT: A 273 MET cc_start: 0.8340 (mmm) cc_final: 0.7836 (mmm) REVERT: A 275 ARG cc_start: 0.7920 (ttp80) cc_final: 0.7680 (ttm-80) outliers start: 10 outliers final: 7 residues processed: 61 average time/residue: 0.0660 time to fit residues: 4.9233 Evaluate side-chains 62 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 320 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: [9, 2, 22, 18, 36, 32, 17, 14, 12, 11, 25] chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.163266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.119005 restraints weight = 3731.861| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.12 r_work: 0.3102 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3217 Z= 0.126 Angle : 0.479 6.039 4365 Z= 0.249 Chirality : 0.041 0.136 477 Planarity : 0.003 0.033 540 Dihedral : 9.671 87.892 457 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.93 % Allowed : 19.03 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.42), residues: 386 helix: 1.88 (0.35), residues: 218 sheet: -0.16 (0.98), residues: 26 loop : -1.19 (0.49), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.012 0.001 TYR A 362 PHE 0.016 0.002 PHE A 327 TRP 0.011 0.001 TRP A 23 HIS 0.002 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 3216) covalent geometry : angle 0.47409 / 0.25 ( 4363) SS BOND : bond 0.00863 / 0.45 ( 1) SS BOND : angle 3.30680 / 1.84 ( 2) hydrogen bonds : bond 0.04436 / 2.88 ( 165) hydrogen bonds : angle 3.67394 / 2.66 ( 495) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.108 Fit side-chains REVERT: A 20 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7968 (mm) REVERT: A 55 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8168 (tt) REVERT: A 67 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7531 (mm) REVERT: A 69 ASN cc_start: 0.8155 (m-40) cc_final: 0.7838 (m-40) REVERT: A 71 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7751 (mt-10) REVERT: A 196 TYR cc_start: 0.8297 (m-10) cc_final: 0.7971 (m-10) REVERT: A 217 LYS cc_start: 0.7306 (tmtt) cc_final: 0.6858 (tptp) REVERT: A 226 LEU cc_start: 0.7572 (mt) cc_final: 0.7019 (mt) REVERT: A 273 MET cc_start: 0.8355 (mmm) cc_final: 0.7800 (mmm) REVERT: A 275 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7691 (ttm-80) outliers start: 13 outliers final: 8 residues processed: 62 average time/residue: 0.0590 time to fit residues: 4.5228 Evaluate side-chains 67 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 368 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: [2, 10, 8, 16, 25, 6, 23, 5, 27, 14, 20] chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.162414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.117571 restraints weight = 3720.369| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.21 r_work: 0.3089 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3217 Z= 0.127 Angle : 0.490 6.162 4365 Z= 0.252 Chirality : 0.041 0.137 477 Planarity : 0.003 0.033 540 Dihedral : 9.644 87.279 457 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.63 % Allowed : 19.94 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.42), residues: 386 helix: 1.85 (0.35), residues: 218 sheet: -0.06 (0.97), residues: 26 loop : -1.15 (0.49), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 111 TYR 0.007 0.001 TYR A 331 PHE 0.016 0.002 PHE A 327 TRP 0.011 0.001 TRP A 23 HIS 0.002 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 3216) covalent geometry : angle 0.48466 / 0.25 ( 4363) SS BOND : bond 0.00860 / 0.45 ( 1) SS BOND : angle 3.29573 / 1.83 ( 2) hydrogen bonds : bond 0.04463 / 2.89 ( 165) hydrogen bonds : angle 3.67949 / 2.66 ( 495) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.122 Fit side-chains REVERT: A 20 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7958 (mm) REVERT: A 55 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8212 (tt) REVERT: A 67 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7521 (mm) REVERT: A 69 ASN cc_start: 0.8127 (m-40) cc_final: 0.7807 (m-40) REVERT: A 71 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7775 (mt-10) REVERT: A 111 ARG cc_start: 0.8281 (ptm160) cc_final: 0.7452 (ptm160) REVERT: A 129 MET cc_start: 0.6974 (mmm) cc_final: 0.6572 (mmm) REVERT: A 196 TYR cc_start: 0.8300 (m-10) cc_final: 0.7983 (m-10) REVERT: A 217 LYS cc_start: 0.7279 (tmtt) cc_final: 0.6815 (tptp) REVERT: A 226 LEU cc_start: 0.7548 (mt) cc_final: 0.6567 (mt) REVERT: A 273 MET cc_start: 0.8348 (mmm) cc_final: 0.7802 (mmm) REVERT: A 275 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7674 (ttm-80) outliers start: 12 outliers final: 8 residues processed: 65 average time/residue: 0.0565 time to fit residues: 4.5969 Evaluate side-chains 64 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 368 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: [20, 25, 0, 35, 18, 28, 37, 12, 31, 13, 2] chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.161976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.116735 restraints weight = 3767.174| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.22 r_work: 0.3068 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3217 Z= 0.147 Angle : 0.508 6.074 4365 Z= 0.263 Chirality : 0.042 0.156 477 Planarity : 0.003 0.033 540 Dihedral : 9.728 89.207 457 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.63 % Allowed : 19.64 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.42), residues: 386 helix: 1.74 (0.35), residues: 218 sheet: -0.02 (0.98), residues: 26 loop : -1.08 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.009 0.001 TYR A 331 PHE 0.016 0.002 PHE A 327 TRP 0.011 0.001 TRP A 23 HIS 0.002 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 3216) covalent geometry : angle 0.50319 / 0.26 ( 4363) SS BOND : bond 0.00900 / 0.47 ( 1) SS BOND : angle 3.44309 / 1.91 ( 2) hydrogen bonds : bond 0.04692 / 3.02 ( 165) hydrogen bonds : angle 3.74748 / 2.70 ( 495) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1025.58 seconds wall clock time: 18 minutes 16.27 seconds (1096.27 seconds total)