Starting phenix.real_space_refine on Thu Jul 2 01:38:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8a8m_15233/07_2026/8a8m_15233.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a8m_15233/07_2026/8a8m_15233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a8m_15233/07_2026/8a8m_15233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a8m_15233/07_2026/8a8m_15233.map" model { file = "/net/cci-nas-00/data/ceres_data/8a8m_15233/07_2026/8a8m_15233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a8m_15233/07_2026/8a8m_15233.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8a8m_15233/07_2026/8a8m_15233.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8a8m_15233/07_2026/8a8m_15233.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 4 5.21 5 S 29 5.16 5 C 3348 2.51 5 N 886 2.21 5 O 973 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5244 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2816 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 17, 'TRANS': 331} Chain: "B" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2370 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 18, 'TRANS': 279} Chain breaks: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'AP2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'AP2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASP A 177 " occ=0.78 ... (6 atoms not shown) pdb=" OD2 ASP A 177 " occ=0.78 Time building chain proxies: 1.10, per 1000 atoms: 0.21 Number of scatterers: 5244 At special positions: 0 Unit cell: (61.248, 81.026, 102.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 29 16.00 P 4 15.00 Mg 4 11.99 O 973 8.00 N 886 7.00 C 3348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 116.7 milliseconds 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1228 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 42.7% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 62 through 76 Processing helix chain 'A' and resid 113 through 120 removed outlier: 4.298A pdb=" N LYS A 118 " --> pdb=" O ASN A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 145 Processing helix chain 'A' and resid 189 through 195 removed outlier: 3.807A pdb=" N ILE A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 218 removed outlier: 3.866A pdb=" N ASP A 205 " --> pdb=" O ASN A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 240 removed outlier: 4.118A pdb=" N LEU A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 278 through 289 removed outlier: 3.556A pdb=" N VAL A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 311 removed outlier: 6.710A pdb=" N TYR A 307 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 308 " --> pdb=" O HIS A 305 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLN A 310 " --> pdb=" O TYR A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 326 through 330 removed outlier: 3.650A pdb=" N ARG A 330 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 346 removed outlier: 4.059A pdb=" N SER A 339 " --> pdb=" O ASP A 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 89 through 106 removed outlier: 4.447A pdb=" N ARG B 95 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 147 removed outlier: 3.659A pdb=" N ASP B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 146 " --> pdb=" O GLN B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 173 removed outlier: 3.745A pdb=" N LYS B 164 " --> pdb=" O VAL B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 235 through 253 Processing helix chain 'B' and resid 262 through 273 Processing helix chain 'B' and resid 284 through 295 Processing helix chain 'B' and resid 304 through 311 Processing helix chain 'B' and resid 311 through 320 removed outlier: 3.550A pdb=" N THR B 315 " --> pdb=" O HIS B 311 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER B 319 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 3.544A pdb=" N LEU A 13 " --> pdb=" O THR A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA4, first strand: chain 'A' and resid 111 through 112 Processing sheet with id=AA5, first strand: chain 'B' and resid 39 through 41 removed outlier: 3.684A pdb=" N ILE B 41 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN B 44 " --> pdb=" O ILE B 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 58 removed outlier: 7.376A pdb=" N LYS B 69 " --> pdb=" O ILE B 56 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 134 through 135 removed outlier: 4.148A pdb=" N THR B 134 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 187 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 175 through 176 192 hydrogen bonds defined for protein. 534 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: 0.49 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1709 1.35 - 1.48: 1265 1.48 - 1.61: 2331 1.61 - 1.74: 2 1.74 - 1.87: 53 Bond restraints: 5360 Sorted by residual: bond pdb=" CA VAL A 89 " pdb=" CB VAL A 89 " ideal model delta sigma weight residual 1.553 1.539 0.014 7.40e-03 1.83e+04 3.55e+00 bond pdb=" CA LEU A 74 " pdb=" C LEU A 74 " ideal model delta sigma weight residual 1.524 1.505 0.018 1.27e-02 6.20e+03 2.06e+00 bond pdb=" N HIS A 312 " pdb=" CA HIS A 312 " ideal model delta sigma weight residual 1.456 1.474 -0.018 1.44e-02 4.82e+03 1.49e+00 bond pdb=" CB LYS B 329 " pdb=" CG LYS B 329 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.34e+00 bond pdb=" N VAL A 83 " pdb=" CA VAL A 83 " ideal model delta sigma weight residual 1.459 1.445 0.014 1.25e-02 6.40e+03 1.32e+00 ... (remaining 5355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 6978 1.91 - 3.82: 233 3.82 - 5.73: 36 5.73 - 7.65: 19 7.65 - 9.56: 6 Bond angle restraints: 7272 Sorted by residual: angle pdb=" N LEU A 74 " pdb=" CA LEU A 74 " pdb=" C LEU A 74 " ideal model delta sigma weight residual 111.07 105.64 5.43 1.07e+00 8.73e-01 2.57e+01 angle pdb=" CA LYS B 329 " pdb=" CB LYS B 329 " pdb=" CG LYS B 329 " ideal model delta sigma weight residual 114.10 122.34 -8.24 2.00e+00 2.50e-01 1.70e+01 angle pdb=" N SER B 275 " pdb=" CA SER B 275 " pdb=" C SER B 275 " ideal model delta sigma weight residual 109.81 118.62 -8.81 2.21e+00 2.05e-01 1.59e+01 angle pdb=" CA GLU B 68 " pdb=" CB GLU B 68 " pdb=" CG GLU B 68 " ideal model delta sigma weight residual 114.10 121.53 -7.43 2.00e+00 2.50e-01 1.38e+01 angle pdb=" C ILE A 235 " pdb=" N LEU A 236 " pdb=" CA LEU A 236 " ideal model delta sigma weight residual 120.28 125.16 -4.88 1.34e+00 5.57e-01 1.33e+01 ... (remaining 7267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 2731 17.80 - 35.61: 378 35.61 - 53.41: 88 53.41 - 71.21: 20 71.21 - 89.02: 9 Dihedral angle restraints: 3226 sinusoidal: 1331 harmonic: 1895 Sorted by residual: dihedral pdb=" CA LEU A 108 " pdb=" C LEU A 108 " pdb=" N MET A 109 " pdb=" CA MET A 109 " ideal model delta harmonic sigma weight residual -180.00 -155.02 -24.98 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA LEU A 234 " pdb=" C LEU A 234 " pdb=" N ILE A 235 " pdb=" CA ILE A 235 " ideal model delta harmonic sigma weight residual 180.00 156.46 23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA LEU B 131 " pdb=" C LEU B 131 " pdb=" N MET B 132 " pdb=" CA MET B 132 " ideal model delta harmonic sigma weight residual 180.00 157.05 22.95 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 3223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 565 0.043 - 0.087: 186 0.087 - 0.130: 49 0.130 - 0.173: 10 0.173 - 0.217: 4 Chirality restraints: 814 Sorted by residual: chirality pdb=" CA LEU B 267 " pdb=" N LEU B 267 " pdb=" C LEU B 267 " pdb=" CB LEU B 267 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB ILE B 84 " pdb=" CA ILE B 84 " pdb=" CG1 ILE B 84 " pdb=" CG2 ILE B 84 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CA TYR B 305 " pdb=" N TYR B 305 " pdb=" C TYR B 305 " pdb=" CB TYR B 305 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.93e-01 ... (remaining 811 not shown) Planarity restraints: 920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 68 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" CD GLU B 68 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU B 68 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU B 68 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 152 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.94e+00 pdb=" N PRO A 153 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 150 " 0.028 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO B 151 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 151 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 151 " 0.024 5.00e-02 4.00e+02 ... (remaining 917 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 720 2.75 - 3.29: 5782 3.29 - 3.83: 9180 3.83 - 4.36: 10880 4.36 - 4.90: 16814 Nonbonded interactions: 43376 Sorted by model distance: nonbonded pdb=" O SER B 235 " pdb=" OG SER B 238 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR B 140 " pdb=" OE1 GLU B 249 " model vdw 2.230 3.040 nonbonded pdb=" OE2 GLU A 215 " pdb=" OG1 THR A 221 " model vdw 2.233 3.040 nonbonded pdb=" O ASP A 205 " pdb=" OG SER A 208 " model vdw 2.240 3.040 nonbonded pdb=" NH2 ARG B 178 " pdb=" O TYR B 203 " model vdw 2.243 3.120 ... (remaining 43371 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=0.78 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.040 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.060 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5380 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 : 0.004 0.037 5360 Z= 0.182 Angle : 0.888 9.558 7272 Z= 0.471 Chirality : 0.048 0.217 814 Planarity : 0.005 0.050 920 Dihedral : 17.750 89.016 1998 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 29.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.45 % Favored : 91.39 % Rotamer: Outliers : 1.56 % Allowed : 26.39 % Favored : 72.05 % 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: -2.63 (0.31), residues: 639 helix: -0.84 (0.34), residues: 219 sheet: -2.27 (0.64), residues: 53 loop : -2.31 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 85 TYR 0.012 0.001 TYR B 140 PHE 0.013 0.002 PHE B 313 TRP 0.021 0.002 TRP A 18 HIS 0.013 0.002 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 ( 5360) covalent geometry : angle 0.88783 / 0.47 ( 7272) hydrogen bonds : bond 0.19056 / 12.39 ( 192) hydrogen bonds : angle 8.79042 / 6.06 ( 534) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: -0.1395 (ttm) cc_final: -0.3125 (tmm) REVERT: B 79 MET cc_start: 0.3563 (tmm) cc_final: 0.3055 (tpp) REVERT: B 141 LYS cc_start: 0.9204 (tptt) cc_final: 0.8769 (tptp) REVERT: B 179 ASP cc_start: 0.8562 (m-30) cc_final: 0.8253 (m-30) REVERT: B 184 ASN cc_start: 0.7238 (OUTLIER) cc_final: 0.6935 (p0) outliers start: 9 outliers final: 3 residues processed: 91 average time/residue: 0.0639 time to fit residues: 7.9188 Evaluate side-chains 73 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 184 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 0.0970 chunk 25 optimal weight: 6.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS ** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 45 ASN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS B 177 HIS B 184 ASN B 226 ASN B 265 GLN B 266 GLN B 269 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.135201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.097269 restraints weight = 21347.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.098366 restraints weight = 19720.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.099002 restraints weight = 18292.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.099384 restraints weight = 17456.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.099385 restraints weight = 16641.518| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4056 r_free = 0.4056 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4053 r_free = 0.4053 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.4053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5360 Z= 0.171 Angle : 0.802 9.338 7272 Z= 0.405 Chirality : 0.049 0.205 814 Planarity : 0.005 0.053 920 Dihedral : 7.110 53.838 712 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 24.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.47 % Allowed : 25.52 % Favored : 71.01 % 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: -2.62 (0.30), residues: 639 helix: -0.88 (0.32), residues: 222 sheet: -2.49 (0.71), residues: 46 loop : -2.27 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 186 TYR 0.010 0.001 TYR A 9 PHE 0.012 0.002 PHE B 313 TRP 0.013 0.002 TRP A 187 HIS 0.009 0.002 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 ( 5360) covalent geometry : angle 0.80233 / 0.40 ( 7272) hydrogen bonds : bond 0.05323 / 3.26 ( 192) hydrogen bonds : angle 7.30676 / 4.98 ( 534) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: -0.0215 (tpt) cc_final: -0.0759 (tpt) REVERT: A 186 ARG cc_start: 0.7968 (ttp-110) cc_final: 0.7669 (tmm-80) REVERT: B 70 MET cc_start: 0.1136 (ttt) cc_final: 0.0567 (ttt) REVERT: B 79 MET cc_start: 0.5193 (tmm) cc_final: 0.4394 (tpp) REVERT: B 129 MET cc_start: 0.8638 (mmm) cc_final: 0.7994 (mmm) REVERT: B 132 MET cc_start: 0.8375 (mpp) cc_final: 0.7950 (mpp) REVERT: B 141 LYS cc_start: 0.9289 (tptt) cc_final: 0.8899 (tptp) REVERT: B 155 LEU cc_start: 0.8519 (mt) cc_final: 0.8269 (mt) REVERT: B 184 ASN cc_start: 0.9175 (OUTLIER) cc_final: 0.8555 (p0) REVERT: B 247 MET cc_start: 0.9745 (mmm) cc_final: 0.9506 (mmm) REVERT: B 257 TYR cc_start: 0.6604 (OUTLIER) cc_final: 0.6323 (m-80) REVERT: B 317 HIS cc_start: 0.7606 (OUTLIER) cc_final: 0.7322 (t-90) outliers start: 20 outliers final: 7 residues processed: 85 average time/residue: 0.0680 time to fit residues: 7.8595 Evaluate side-chains 78 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 36 optimal weight: 0.0070 chunk 46 optimal weight: 0.2980 chunk 5 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 overall best weight: 1.6604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 GLN ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.130925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.091536 restraints weight = 20901.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.092970 restraints weight = 18864.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.093627 restraints weight = 17242.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.094673 restraints weight = 16203.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.095089 restraints weight = 15309.721| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5360 Z= 0.176 Angle : 0.783 8.733 7272 Z= 0.392 Chirality : 0.047 0.170 814 Planarity : 0.005 0.057 920 Dihedral : 6.474 51.143 707 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 27.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 4.69 % Allowed : 26.04 % Favored : 69.27 % 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: -2.57 (0.31), residues: 639 helix: -0.71 (0.33), residues: 218 sheet: -2.86 (0.65), residues: 46 loop : -2.24 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 237 TYR 0.014 0.002 TYR B 257 PHE 0.010 0.002 PHE A 169 TRP 0.023 0.003 TRP B 260 HIS 0.006 0.002 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 ( 5360) covalent geometry : angle 0.78318 / 0.39 ( 7272) hydrogen bonds : bond 0.04921 / 2.99 ( 192) hydrogen bonds : angle 7.01092 / 4.73 ( 534) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: -0.1123 (ttt) cc_final: -0.1430 (tpt) REVERT: A 186 ARG cc_start: 0.8271 (ttp-110) cc_final: 0.7739 (tmm-80) REVERT: B 70 MET cc_start: 0.0856 (ttt) cc_final: 0.0452 (ttt) REVERT: B 79 MET cc_start: 0.5197 (tmm) cc_final: 0.4944 (tmm) REVERT: B 129 MET cc_start: 0.8923 (mmm) cc_final: 0.8191 (mmm) REVERT: B 132 MET cc_start: 0.8727 (mpp) cc_final: 0.7693 (mpp) REVERT: B 141 LYS cc_start: 0.9313 (tptt) cc_final: 0.8910 (tptp) REVERT: B 184 ASN cc_start: 0.9169 (OUTLIER) cc_final: 0.8895 (p0) REVERT: B 220 MET cc_start: 0.5980 (mmm) cc_final: 0.5530 (tmm) REVERT: B 247 MET cc_start: 0.9789 (mmm) cc_final: 0.9556 (mmm) REVERT: B 255 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.7165 (p90) REVERT: B 257 TYR cc_start: 0.6637 (OUTLIER) cc_final: 0.4964 (m-80) REVERT: B 309 MET cc_start: 0.9261 (ptp) cc_final: 0.9054 (mmm) outliers start: 27 outliers final: 14 residues processed: 89 average time/residue: 0.0661 time to fit residues: 8.0159 Evaluate side-chains 84 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 275 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 77 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.130291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.091338 restraints weight = 21487.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.092402 restraints weight = 19694.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.093200 restraints weight = 18390.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.093845 restraints weight = 17420.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.094176 restraints weight = 16693.352| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5360 Z= 0.164 Angle : 0.781 10.489 7272 Z= 0.384 Chirality : 0.047 0.209 814 Planarity : 0.005 0.055 920 Dihedral : 6.429 50.791 707 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 25.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 6.08 % Allowed : 26.22 % Favored : 67.71 % 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: -2.60 (0.31), residues: 639 helix: -0.76 (0.33), residues: 224 sheet: -2.99 (0.64), residues: 46 loop : -2.25 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 85 TYR 0.011 0.001 TYR A 132 PHE 0.011 0.001 PHE B 255 TRP 0.013 0.002 TRP A 187 HIS 0.005 0.002 HIS A 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 5360) covalent geometry : angle 0.78072 / 0.38 ( 7272) hydrogen bonds : bond 0.04657 / 2.86 ( 192) hydrogen bonds : angle 6.82102 / 4.60 ( 534) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 66 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: -0.1073 (ttt) cc_final: -0.1516 (tpt) REVERT: A 179 MET cc_start: 0.0350 (tpt) cc_final: -0.0129 (tpt) REVERT: A 186 ARG cc_start: 0.8282 (ttp-110) cc_final: 0.7744 (tmm-80) REVERT: A 213 MET cc_start: 0.9402 (OUTLIER) cc_final: 0.9091 (ppp) REVERT: A 265 MET cc_start: 0.0379 (ttp) cc_final: 0.0111 (ptt) REVERT: B 79 MET cc_start: 0.5174 (tmm) cc_final: 0.4838 (tmm) REVERT: B 129 MET cc_start: 0.9013 (mmm) cc_final: 0.8270 (mmm) REVERT: B 141 LYS cc_start: 0.9315 (tptt) cc_final: 0.8905 (tptp) REVERT: B 155 LEU cc_start: 0.8500 (mt) cc_final: 0.8208 (mt) REVERT: B 184 ASN cc_start: 0.9197 (OUTLIER) cc_final: 0.8899 (p0) REVERT: B 220 MET cc_start: 0.5969 (mmm) cc_final: 0.4937 (tmm) REVERT: B 247 MET cc_start: 0.9785 (mmm) cc_final: 0.9557 (mmm) REVERT: B 255 PHE cc_start: 0.7357 (p90) cc_final: 0.6882 (p90) outliers start: 35 outliers final: 19 residues processed: 92 average time/residue: 0.0640 time to fit residues: 7.8883 Evaluate side-chains 85 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 324 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 2 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 GLN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.124830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.086252 restraints weight = 22397.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.087631 restraints weight = 20246.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.088311 restraints weight = 18588.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.088331 restraints weight = 17258.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.089316 restraints weight = 17246.790| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5360 Z= 0.200 Angle : 0.796 9.475 7272 Z= 0.398 Chirality : 0.046 0.160 814 Planarity : 0.005 0.054 920 Dihedral : 6.395 49.187 707 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 32.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.14 % Favored : 91.71 % Rotamer: Outliers : 6.08 % Allowed : 27.26 % Favored : 66.67 % 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: -2.63 (0.31), residues: 639 helix: -0.74 (0.33), residues: 225 sheet: -3.07 (0.68), residues: 46 loop : -2.30 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 237 TYR 0.017 0.002 TYR B 140 PHE 0.016 0.002 PHE B 283 TRP 0.012 0.002 TRP B 260 HIS 0.006 0.002 HIS A 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 ( 5360) covalent geometry : angle 0.79595 / 0.40 ( 7272) hydrogen bonds : bond 0.04807 / 2.98 ( 192) hydrogen bonds : angle 6.81842 / 4.62 ( 534) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 67 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.1686 (OUTLIER) cc_final: 0.1265 (mmm160) REVERT: A 179 MET cc_start: 0.1099 (tpt) cc_final: 0.0819 (tpt) REVERT: A 186 ARG cc_start: 0.8392 (ttp-110) cc_final: 0.7902 (tmm-80) REVERT: A 213 MET cc_start: 0.9395 (OUTLIER) cc_final: 0.8942 (ppp) REVERT: B 79 MET cc_start: 0.5431 (tmm) cc_final: 0.5013 (tmm) REVERT: B 129 MET cc_start: 0.9161 (mmm) cc_final: 0.8387 (mmm) REVERT: B 141 LYS cc_start: 0.9372 (tptt) cc_final: 0.8974 (tptp) REVERT: B 184 ASN cc_start: 0.9182 (OUTLIER) cc_final: 0.8917 (p0) REVERT: B 220 MET cc_start: 0.6220 (mmm) cc_final: 0.5259 (tmm) REVERT: B 255 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.7134 (p90) REVERT: B 257 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.5578 (m-80) outliers start: 35 outliers final: 21 residues processed: 93 average time/residue: 0.0754 time to fit residues: 9.3413 Evaluate side-chains 90 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 324 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 7 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 56 optimal weight: 0.0370 chunk 1 optimal weight: 0.9980 chunk 55 optimal weight: 0.0270 chunk 54 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 148 GLN B 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.130744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.094236 restraints weight = 22003.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.095039 restraints weight = 20894.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.095608 restraints weight = 19868.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.096350 restraints weight = 18807.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.096350 restraints weight = 18121.904| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5360 Z= 0.139 Angle : 0.802 10.855 7272 Z= 0.385 Chirality : 0.047 0.215 814 Planarity : 0.004 0.047 920 Dihedral : 6.319 47.780 707 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 23.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 4.34 % Allowed : 28.99 % Favored : 66.67 % 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: -2.33 (0.32), residues: 639 helix: -0.46 (0.35), residues: 226 sheet: -2.91 (0.77), residues: 36 loop : -2.18 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 61 TYR 0.012 0.001 TYR A 132 PHE 0.011 0.001 PHE B 255 TRP 0.014 0.002 TRP B 126 HIS 0.005 0.001 HIS A 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 5360) covalent geometry : angle 0.80219 / 0.39 ( 7272) hydrogen bonds : bond 0.04274 / 2.60 ( 192) hydrogen bonds : angle 6.55495 / 4.46 ( 534) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: -0.0846 (ttt) cc_final: -0.1296 (tpt) REVERT: A 186 ARG cc_start: 0.8291 (ttp-110) cc_final: 0.7946 (tmm-80) REVERT: A 209 VAL cc_start: 0.9791 (t) cc_final: 0.9479 (t) REVERT: A 213 MET cc_start: 0.9337 (OUTLIER) cc_final: 0.8929 (ppp) REVERT: A 288 MET cc_start: 0.8572 (mmp) cc_final: 0.7654 (ptm) REVERT: B 70 MET cc_start: 0.1021 (ttt) cc_final: 0.0724 (ttt) REVERT: B 79 MET cc_start: 0.5046 (tmm) cc_final: 0.4683 (tmm) REVERT: B 129 MET cc_start: 0.9128 (mmm) cc_final: 0.8374 (mmm) REVERT: B 141 LYS cc_start: 0.9328 (tptt) cc_final: 0.8921 (tptp) REVERT: B 184 ASN cc_start: 0.9144 (OUTLIER) cc_final: 0.8907 (p0) REVERT: B 220 MET cc_start: 0.6061 (mmm) cc_final: 0.5640 (tmm) REVERT: B 255 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.7031 (p90) REVERT: B 257 TYR cc_start: 0.6975 (OUTLIER) cc_final: 0.5494 (m-80) outliers start: 25 outliers final: 15 residues processed: 87 average time/residue: 0.0706 time to fit residues: 8.3297 Evaluate side-chains 85 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 267 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 0.0010 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.130074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.090801 restraints weight = 22329.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.092225 restraints weight = 20167.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.093185 restraints weight = 18321.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.094113 restraints weight = 17161.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.094793 restraints weight = 16182.115| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5360 Z= 0.140 Angle : 0.775 9.438 7272 Z= 0.375 Chirality : 0.046 0.282 814 Planarity : 0.004 0.046 920 Dihedral : 6.200 42.511 707 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 3.65 % Allowed : 30.21 % Favored : 66.15 % 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: -2.26 (0.32), residues: 639 helix: -0.51 (0.35), residues: 231 sheet: -2.87 (0.84), residues: 30 loop : -2.11 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 136 TYR 0.014 0.001 TYR B 140 PHE 0.009 0.001 PHE B 255 TRP 0.013 0.002 TRP B 126 HIS 0.005 0.001 HIS A 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 5360) covalent geometry : angle 0.77544 / 0.38 ( 7272) hydrogen bonds : bond 0.04174 / 2.56 ( 192) hydrogen bonds : angle 6.47555 / 4.38 ( 534) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8581 (OUTLIER) cc_final: 0.8180 (t60) REVERT: A 78 MET cc_start: -0.0955 (ttt) cc_final: -0.1297 (tpt) REVERT: A 186 ARG cc_start: 0.8355 (ttp-110) cc_final: 0.8050 (tmm-80) REVERT: A 209 VAL cc_start: 0.9816 (t) cc_final: 0.9452 (t) REVERT: A 213 MET cc_start: 0.9351 (OUTLIER) cc_final: 0.8951 (ppp) REVERT: A 216 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8327 (mm) REVERT: B 79 MET cc_start: 0.5110 (tmm) cc_final: 0.4830 (tmm) REVERT: B 98 MET cc_start: 0.7298 (ppp) cc_final: 0.7095 (ppp) REVERT: B 129 MET cc_start: 0.9122 (mmm) cc_final: 0.8323 (mmm) REVERT: B 141 LYS cc_start: 0.9334 (tptt) cc_final: 0.8922 (tptp) REVERT: B 184 ASN cc_start: 0.9140 (OUTLIER) cc_final: 0.8936 (p0) REVERT: B 220 MET cc_start: 0.6098 (mmm) cc_final: 0.5634 (tmm) REVERT: B 255 PHE cc_start: 0.7420 (p90) cc_final: 0.7046 (p90) REVERT: B 257 TYR cc_start: 0.6929 (OUTLIER) cc_final: 0.5475 (m-80) REVERT: B 309 MET cc_start: 0.9289 (ptp) cc_final: 0.9055 (mmm) outliers start: 21 outliers final: 14 residues processed: 84 average time/residue: 0.0784 time to fit residues: 8.5776 Evaluate side-chains 84 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 324 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.0270 chunk 43 optimal weight: 0.9980 chunk 50 optimal weight: 0.3980 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN B 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.151011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.127314 restraints weight = 35503.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.129765 restraints weight = 24788.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.131308 restraints weight = 19237.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.132364 restraints weight = 16120.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.133104 restraints weight = 14215.263| |-----------------------------------------------------------------------------| r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5360 Z= 0.137 Angle : 0.811 17.528 7272 Z= 0.384 Chirality : 0.047 0.307 814 Planarity : 0.004 0.045 920 Dihedral : 6.125 38.285 707 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.45 % Favored : 91.39 % Rotamer: Outliers : 4.17 % Allowed : 30.21 % Favored : 65.62 % 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: -2.18 (0.32), residues: 639 helix: -0.41 (0.35), residues: 231 sheet: -2.95 (0.73), residues: 39 loop : -2.03 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 5 TYR 0.009 0.001 TYR B 140 PHE 0.010 0.001 PHE B 255 TRP 0.013 0.002 TRP B 126 HIS 0.006 0.001 HIS A 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 5360) covalent geometry : angle 0.81053 / 0.38 ( 7272) hydrogen bonds : bond 0.04105 / 2.55 ( 192) hydrogen bonds : angle 6.48037 / 4.38 ( 534) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8488 (OUTLIER) cc_final: 0.8111 (t60) REVERT: A 78 MET cc_start: -0.1178 (ttt) cc_final: -0.1415 (tpt) REVERT: A 186 ARG cc_start: 0.8365 (ttp-110) cc_final: 0.8018 (tmm-80) REVERT: A 209 VAL cc_start: 0.9809 (t) cc_final: 0.9452 (t) REVERT: A 213 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8877 (ppp) REVERT: A 216 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8174 (mm) REVERT: B 129 MET cc_start: 0.9143 (mmm) cc_final: 0.8317 (mmm) REVERT: B 141 LYS cc_start: 0.9305 (tptt) cc_final: 0.8882 (tptp) REVERT: B 220 MET cc_start: 0.5910 (mmm) cc_final: 0.5096 (tmm) REVERT: B 255 PHE cc_start: 0.7384 (p90) cc_final: 0.7031 (p90) REVERT: B 257 TYR cc_start: 0.6928 (OUTLIER) cc_final: 0.5474 (m-80) REVERT: B 309 MET cc_start: 0.9297 (ptp) cc_final: 0.9086 (mmm) outliers start: 24 outliers final: 16 residues processed: 85 average time/residue: 0.0763 time to fit residues: 8.5338 Evaluate side-chains 86 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 324 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 27 optimal weight: 0.0980 chunk 6 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 18 optimal weight: 0.0970 chunk 37 optimal weight: 7.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.132076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.091983 restraints weight = 22011.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.093324 restraints weight = 19973.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.093967 restraints weight = 18352.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.094948 restraints weight = 17206.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.095313 restraints weight = 16431.326| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5360 Z= 0.136 Angle : 0.823 15.892 7272 Z= 0.389 Chirality : 0.047 0.333 814 Planarity : 0.004 0.045 920 Dihedral : 6.060 35.691 705 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.61 % Favored : 91.24 % Rotamer: Outliers : 3.47 % Allowed : 30.73 % Favored : 65.80 % 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: -2.22 (0.32), residues: 639 helix: -0.42 (0.35), residues: 233 sheet: -3.33 (0.68), residues: 41 loop : -2.02 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 5 TYR 0.012 0.001 TYR B 140 PHE 0.010 0.001 PHE B 255 TRP 0.031 0.003 TRP A 197 HIS 0.005 0.001 HIS A 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 5360) covalent geometry : angle 0.82286 / 0.39 ( 7272) hydrogen bonds : bond 0.04034 / 2.48 ( 192) hydrogen bonds : angle 6.46662 / 4.37 ( 534) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8371 (OUTLIER) cc_final: 0.8034 (t60) REVERT: A 78 MET cc_start: -0.1096 (ttt) cc_final: -0.1910 (tpp) REVERT: A 186 ARG cc_start: 0.8400 (ttp-110) cc_final: 0.8057 (tmm-80) REVERT: A 209 VAL cc_start: 0.9821 (t) cc_final: 0.9549 (t) REVERT: A 213 MET cc_start: 0.9335 (OUTLIER) cc_final: 0.8984 (ppp) REVERT: A 216 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8233 (mm) REVERT: A 288 MET cc_start: 0.8527 (mmp) cc_final: 0.7478 (ptp) REVERT: B 129 MET cc_start: 0.9069 (mmm) cc_final: 0.8372 (mmm) REVERT: B 141 LYS cc_start: 0.9325 (tptt) cc_final: 0.8897 (tptp) REVERT: B 220 MET cc_start: 0.6135 (mmm) cc_final: 0.5840 (tpt) REVERT: B 255 PHE cc_start: 0.7331 (p90) cc_final: 0.6979 (p90) REVERT: B 257 TYR cc_start: 0.6872 (OUTLIER) cc_final: 0.5357 (m-80) REVERT: B 309 MET cc_start: 0.9299 (ptp) cc_final: 0.9074 (mmm) outliers start: 20 outliers final: 15 residues processed: 81 average time/residue: 0.0773 time to fit residues: 8.3135 Evaluate side-chains 85 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 324 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 45 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.147670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.123692 restraints weight = 35897.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.126047 restraints weight = 25249.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.127512 restraints weight = 19698.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.128523 restraints weight = 16551.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.129053 restraints weight = 14723.453| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5360 Z= 0.164 Angle : 0.836 15.216 7272 Z= 0.399 Chirality : 0.048 0.327 814 Planarity : 0.005 0.046 920 Dihedral : 6.098 31.948 705 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 27.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.08 % Favored : 90.77 % Rotamer: Outliers : 3.30 % Allowed : 31.25 % Favored : 65.45 % 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: -2.43 (0.32), residues: 639 helix: -0.62 (0.33), residues: 240 sheet: -3.54 (0.58), residues: 51 loop : -2.05 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 95 TYR 0.011 0.001 TYR A 132 PHE 0.010 0.001 PHE B 255 TRP 0.022 0.002 TRP A 197 HIS 0.005 0.001 HIS A 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 5360) covalent geometry : angle 0.83579 / 0.40 ( 7272) hydrogen bonds : bond 0.04311 / 2.69 ( 192) hydrogen bonds : angle 6.67815 / 4.52 ( 534) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8658 (OUTLIER) cc_final: 0.8256 (t60) REVERT: A 78 MET cc_start: -0.0928 (ttt) cc_final: -0.1443 (tpt) REVERT: A 186 ARG cc_start: 0.8468 (ttp-110) cc_final: 0.8086 (tmm-80) REVERT: A 213 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8859 (ppp) REVERT: A 216 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8232 (mm) REVERT: B 129 MET cc_start: 0.9215 (mmm) cc_final: 0.8423 (mmm) REVERT: B 141 LYS cc_start: 0.9349 (tptt) cc_final: 0.8901 (tptp) REVERT: B 155 LEU cc_start: 0.8327 (mt) cc_final: 0.8058 (mt) REVERT: B 220 MET cc_start: 0.6097 (mmm) cc_final: 0.5360 (tmm) REVERT: B 255 PHE cc_start: 0.7455 (p90) cc_final: 0.7075 (p90) REVERT: B 257 TYR cc_start: 0.7044 (OUTLIER) cc_final: 0.5517 (m-80) outliers start: 19 outliers final: 14 residues processed: 79 average time/residue: 0.0782 time to fit residues: 8.1786 Evaluate side-chains 83 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 324 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 39 optimal weight: 0.0170 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.108808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.074748 restraints weight = 26095.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.075712 restraints weight = 22223.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.077226 restraints weight = 20042.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.078106 restraints weight = 18196.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.078792 restraints weight = 16907.594| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5360 Z= 0.218 Angle : 0.895 14.572 7272 Z= 0.436 Chirality : 0.050 0.276 814 Planarity : 0.005 0.047 920 Dihedral : 6.480 35.006 705 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 36.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.23 % Favored : 90.61 % Rotamer: Outliers : 3.65 % Allowed : 30.56 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.31), residues: 639 helix: -1.09 (0.31), residues: 239 sheet: -3.92 (0.56), residues: 48 loop : -2.11 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 71 TYR 0.018 0.002 TYR A 132 PHE 0.015 0.002 PHE A 308 TRP 0.010 0.002 TRP A 197 HIS 0.008 0.002 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.22 ( 5360) covalent geometry : angle 0.89477 / 0.44 ( 7272) hydrogen bonds : bond 0.04918 / 3.09 ( 192) hydrogen bonds : angle 6.94866 / 4.73 ( 534) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1403.04 seconds wall clock time: 25 minutes 8.31 seconds (1508.31 seconds total)