Starting phenix.real_space_refine on Fri Aug 22 19:50:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qk3_18455/08_2025/8qk3_18455.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qk3_18455/08_2025/8qk3_18455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qk3_18455/08_2025/8qk3_18455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qk3_18455/08_2025/8qk3_18455.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qk3_18455/08_2025/8qk3_18455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qk3_18455/08_2025/8qk3_18455.map" } resolution = 3.2 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4754 2.51 5 N 1241 2.21 5 O 1500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7535 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1548 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "A" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1548 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "C" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1548 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "E" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1018 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 113} Chain: "D" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1873 Classifications: {'peptide': 238} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 227} Time building chain proxies: 2.26, per 1000 atoms: 0.30 Number of scatterers: 7535 At special positions: 0 Unit cell: (106.68, 122.64, 96.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1500 8.00 N 1241 7.00 C 4754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 1 " - pdb=" SG CYS E 46 " distance=2.03 Simple disulfide: pdb=" SG CYS E 30 " - pdb=" SG CYS E 60 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 107 " distance=1.38 Simple disulfide: pdb=" SG CYS E 93 " - pdb=" SG CYS E 123 " distance=2.03 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: 0.63 Conformation dependent library (CDL) restraints added in 471.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1814 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 18 sheets defined 6.8% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 185 through 188 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 249 through 252 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 246 through 252 removed outlier: 5.413A pdb=" N LYS A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 185 through 188 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 249 through 252 Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing sheet with id=AA1, first strand: chain 'B' and resid 133 through 135 Processing sheet with id=AA2, first strand: chain 'B' and resid 190 through 199 removed outlier: 5.674A pdb=" N ASN B 297 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 219 through 220 Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 135 Processing sheet with id=AA5, first strand: chain 'A' and resid 190 through 199 removed outlier: 6.272A pdb=" N ASN A 297 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 219 through 220 Processing sheet with id=AA7, first strand: chain 'C' and resid 133 through 135 Processing sheet with id=AA8, first strand: chain 'C' and resid 190 through 199 removed outlier: 6.419A pdb=" N ASN C 297 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 219 through 220 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AB2, first strand: chain 'E' and resid 34 through 36 Processing sheet with id=AB3, first strand: chain 'E' and resid 74 through 78 removed outlier: 3.831A pdb=" N TYR E 87 " --> pdb=" O CYS E 107 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 97 through 99 Processing sheet with id=AB5, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AB6, first strand: chain 'D' and resid 114 through 120 removed outlier: 6.739A pdb=" N PHE D 115 " --> pdb=" O GLN D 210 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ARG D 212 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLY D 117 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU D 214 " --> pdb=" O GLY D 117 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL D 119 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR D 187 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU D 154 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR D 189 " --> pdb=" O VAL D 152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.635A pdb=" N ILE D 171 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 222 through 223 removed outlier: 6.766A pdb=" N VAL D 285 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG D 243 " --> pdb=" O GLY D 283 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY D 283 " --> pdb=" O ARG D 243 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 229 through 232 removed outlier: 6.626A pdb=" N SER D 302 " --> pdb=" O ALA D 264 " (cutoff:3.500A) 212 hydrogen bonds defined for protein. 528 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1355 1.32 - 1.45: 2045 1.45 - 1.57: 4240 1.57 - 1.69: 0 1.69 - 1.82: 60 Bond restraints: 7700 Sorted by residual: bond pdb=" C PRO E 4 " pdb=" O PRO E 4 " ideal model delta sigma weight residual 1.240 1.207 0.033 1.12e-02 7.97e+03 8.67e+00 bond pdb=" N TYR E 20 " pdb=" CA TYR E 20 " ideal model delta sigma weight residual 1.457 1.490 -0.034 1.24e-02 6.50e+03 7.32e+00 bond pdb=" C PRO E 5 " pdb=" O PRO E 5 " ideal model delta sigma weight residual 1.233 1.202 0.031 1.19e-02 7.06e+03 6.86e+00 bond pdb=" N TRP E 52 " pdb=" CA TRP E 52 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.22e-02 6.72e+03 4.85e+00 bond pdb=" C TYR B 242 " pdb=" N PRO B 243 " ideal model delta sigma weight residual 1.328 1.353 -0.025 1.25e-02 6.40e+03 4.09e+00 ... (remaining 7695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 10032 1.28 - 2.56: 371 2.56 - 3.85: 82 3.85 - 5.13: 10 5.13 - 6.41: 2 Bond angle restraints: 10497 Sorted by residual: angle pdb=" N PRO E 4 " pdb=" CA PRO E 4 " pdb=" C PRO E 4 " ideal model delta sigma weight residual 110.70 105.76 4.94 1.22e+00 6.72e-01 1.64e+01 angle pdb=" N GLU E 2 " pdb=" CA GLU E 2 " pdb=" C GLU E 2 " ideal model delta sigma weight residual 113.89 108.62 5.27 1.58e+00 4.01e-01 1.11e+01 angle pdb=" C GLU E 2 " pdb=" N GLU E 3 " pdb=" CA GLU E 3 " ideal model delta sigma weight residual 122.26 118.69 3.57 1.10e+00 8.26e-01 1.06e+01 angle pdb=" N VAL D 129 " pdb=" CA VAL D 129 " pdb=" C VAL D 129 " ideal model delta sigma weight residual 111.45 108.49 2.96 9.30e-01 1.16e+00 1.01e+01 angle pdb=" N ASN A 278 " pdb=" CA ASN A 278 " pdb=" C ASN A 278 " ideal model delta sigma weight residual 111.30 115.56 -4.26 1.36e+00 5.41e-01 9.83e+00 ... (remaining 10492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 4287 17.61 - 35.22: 241 35.22 - 52.83: 52 52.83 - 70.44: 16 70.44 - 88.05: 5 Dihedral angle restraints: 4601 sinusoidal: 1790 harmonic: 2811 Sorted by residual: dihedral pdb=" CA SER A 153 " pdb=" C SER A 153 " pdb=" N ASN A 154 " pdb=" CA ASN A 154 " ideal model delta harmonic sigma weight residual -180.00 -154.57 -25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASN B 154 " pdb=" C ASN B 154 " pdb=" N ASP B 155 " pdb=" CA ASP B 155 " ideal model delta harmonic sigma weight residual 180.00 -156.27 -23.73 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA SER B 153 " pdb=" C SER B 153 " pdb=" N ASN B 154 " pdb=" CA ASN B 154 " ideal model delta harmonic sigma weight residual 180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 4598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 734 0.031 - 0.062: 315 0.062 - 0.093: 58 0.093 - 0.124: 74 0.124 - 0.155: 20 Chirality restraints: 1201 Sorted by residual: chirality pdb=" CA PRO E 4 " pdb=" N PRO E 4 " pdb=" C PRO E 4 " pdb=" CB PRO E 4 " both_signs ideal model delta sigma weight residual False 2.72 2.87 -0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA ILE D 324 " pdb=" N ILE D 324 " pdb=" C ILE D 324 " pdb=" CB ILE D 324 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CA ASN A 278 " pdb=" N ASN A 278 " pdb=" C ASN A 278 " pdb=" CB ASN A 278 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.78e-01 ... (remaining 1198 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 158 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.14e+00 pdb=" N PRO D 159 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 159 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 159 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 53 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO E 54 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 54 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 54 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 324 " 0.031 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO D 325 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 325 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 325 " 0.027 5.00e-02 4.00e+02 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 58 2.51 - 3.11: 5735 3.11 - 3.71: 11235 3.71 - 4.30: 16926 4.30 - 4.90: 28155 Nonbonded interactions: 62109 Sorted by model distance: nonbonded pdb=" OE1 GLU D 170 " pdb=" OH TYR D 172 " model vdw 1.913 3.040 nonbonded pdb=" O GLU D 120 " pdb=" OG SER D 123 " model vdw 1.931 3.040 nonbonded pdb=" OG1 THR D 280 " pdb=" OE2 GLU D 282 " model vdw 2.075 3.040 nonbonded pdb=" OG SER A 264 " pdb=" OE2 GLU A 303 " model vdw 2.115 3.040 nonbonded pdb=" NZ LYS A 233 " pdb=" OH TYR A 288 " model vdw 2.136 3.120 ... (remaining 62104 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.340 Find NCS groups from input model: 0.090 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 : 0.008 0.649 7704 Z= 0.406 Angle : 0.703 37.629 10505 Z= 0.397 Chirality : 0.045 0.155 1201 Planarity : 0.004 0.051 1360 Dihedral : 12.490 88.050 2775 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.12 % Allowed : 12.50 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.27), residues: 945 helix: -0.25 (1.26), residues: 21 sheet: -0.33 (0.26), residues: 354 loop : -0.22 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 280 TYR 0.012 0.001 TYR D 172 PHE 0.016 0.001 PHE C 172 TRP 0.018 0.002 TRP B 296 HIS 0.004 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 7700) covalent geometry : angle 0.59717 (10497) SS BOND : bond 0.32439 ( 4) SS BOND : angle 13.44483 ( 8) hydrogen bonds : bond 0.11977 ( 212) hydrogen bonds : angle 6.96756 ( 528) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 TYR cc_start: 0.8172 (m-80) cc_final: 0.7944 (m-80) REVERT: B 324 ASP cc_start: 0.7534 (m-30) cc_final: 0.7331 (m-30) REVERT: A 182 PHE cc_start: 0.8180 (t80) cc_final: 0.7947 (t80) REVERT: A 184 MET cc_start: 0.8364 (ppp) cc_final: 0.8090 (ppp) REVERT: A 319 TYR cc_start: 0.8224 (m-80) cc_final: 0.7950 (m-80) REVERT: C 280 ARG cc_start: 0.8287 (mtt-85) cc_final: 0.7820 (mtt-85) REVERT: E 99 LEU cc_start: 0.8643 (tp) cc_final: 0.7804 (mt) REVERT: D 231 MET cc_start: 0.7852 (tpp) cc_final: 0.7530 (tpt) REVERT: D 301 PHE cc_start: 0.7552 (p90) cc_final: 0.7311 (p90) outliers start: 1 outliers final: 1 residues processed: 238 average time/residue: 0.1255 time to fit residues: 37.2756 Evaluate side-chains 155 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 90 HIS ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.069682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.045125 restraints weight = 25991.546| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 4.41 r_work: 0.2661 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 7704 Z= 0.263 Angle : 0.671 10.528 10505 Z= 0.356 Chirality : 0.047 0.275 1201 Planarity : 0.005 0.048 1360 Dihedral : 5.128 26.382 1035 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.01 % Allowed : 15.21 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.27), residues: 945 helix: -0.35 (1.25), residues: 21 sheet: -0.61 (0.26), residues: 347 loop : -0.35 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 48 TYR 0.024 0.002 TYR D 186 PHE 0.021 0.002 PHE E 85 TRP 0.017 0.003 TRP E 116 HIS 0.005 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00592 ( 7700) covalent geometry : angle 0.67097 (10497) SS BOND : bond 0.00362 ( 4) SS BOND : angle 0.64548 ( 8) hydrogen bonds : bond 0.03619 ( 212) hydrogen bonds : angle 6.25284 ( 528) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8135 (mt-10) REVERT: B 231 ASN cc_start: 0.7093 (t0) cc_final: 0.6177 (t0) REVERT: B 285 GLU cc_start: 0.9018 (mp0) cc_final: 0.8535 (mp0) REVERT: B 300 ASP cc_start: 0.9212 (t0) cc_final: 0.8979 (t0) REVERT: B 323 GLU cc_start: 0.9273 (tp30) cc_final: 0.8864 (tp30) REVERT: B 325 ASP cc_start: 0.7874 (m-30) cc_final: 0.7536 (t0) REVERT: A 285 GLU cc_start: 0.8933 (mp0) cc_final: 0.8385 (mp0) REVERT: C 280 ARG cc_start: 0.8611 (mtt-85) cc_final: 0.8363 (mtt-85) REVERT: C 285 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8853 (mp0) REVERT: E 11 GLU cc_start: 0.9182 (tt0) cc_final: 0.8597 (pm20) REVERT: E 116 TRP cc_start: 0.7688 (m100) cc_final: 0.7375 (m100) REVERT: E 122 ILE cc_start: 0.9212 (pt) cc_final: 0.8932 (tp) REVERT: D 170 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8810 (pt0) REVERT: D 186 TYR cc_start: 0.7930 (m-10) cc_final: 0.7340 (m-10) REVERT: D 210 GLN cc_start: 0.8253 (tp40) cc_final: 0.7967 (tp40) REVERT: D 211 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8581 (mm) REVERT: D 231 MET cc_start: 0.8514 (tpp) cc_final: 0.8294 (tpp) REVERT: D 255 ASP cc_start: 0.9412 (OUTLIER) cc_final: 0.8558 (t70) REVERT: D 301 PHE cc_start: 0.9035 (p90) cc_final: 0.8791 (p90) outliers start: 34 outliers final: 19 residues processed: 173 average time/residue: 0.1076 time to fit residues: 23.9418 Evaluate side-chains 155 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 44 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 69 optimal weight: 30.0000 chunk 52 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 ASN A 146 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS E 50 HIS ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.068332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.043807 restraints weight = 26026.737| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 4.46 r_work: 0.2635 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 7704 Z= 0.269 Angle : 0.646 10.694 10505 Z= 0.340 Chirality : 0.046 0.243 1201 Planarity : 0.004 0.034 1360 Dihedral : 5.126 25.892 1034 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.54 % Allowed : 15.57 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.27), residues: 945 helix: -0.90 (0.85), residues: 36 sheet: -0.71 (0.26), residues: 351 loop : -0.24 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 266 TYR 0.015 0.002 TYR A 319 PHE 0.017 0.002 PHE E 85 TRP 0.011 0.002 TRP A 296 HIS 0.008 0.002 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00599 ( 7700) covalent geometry : angle 0.64631 (10497) SS BOND : bond 0.00240 ( 4) SS BOND : angle 0.57149 ( 8) hydrogen bonds : bond 0.03375 ( 212) hydrogen bonds : angle 6.09164 ( 528) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8120 (mt-10) REVERT: B 202 THR cc_start: 0.9468 (OUTLIER) cc_final: 0.9137 (p) REVERT: B 300 ASP cc_start: 0.9231 (t0) cc_final: 0.8762 (t0) REVERT: B 319 TYR cc_start: 0.8642 (m-80) cc_final: 0.8205 (m-80) REVERT: B 320 TYR cc_start: 0.9540 (p90) cc_final: 0.9257 (p90) REVERT: B 323 GLU cc_start: 0.9365 (tp30) cc_final: 0.8898 (tp30) REVERT: A 285 GLU cc_start: 0.9000 (mp0) cc_final: 0.8425 (mp0) REVERT: A 323 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8377 (mm-30) REVERT: C 196 GLU cc_start: 0.8283 (mm-30) cc_final: 0.8043 (mm-30) REVERT: C 250 GLU cc_start: 0.8468 (pm20) cc_final: 0.8186 (pm20) REVERT: C 256 TYR cc_start: 0.9181 (m-80) cc_final: 0.8958 (m-80) REVERT: C 280 ARG cc_start: 0.8582 (mtt-85) cc_final: 0.8304 (mtt-85) REVERT: C 285 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8988 (mm-30) REVERT: C 319 TYR cc_start: 0.8694 (m-80) cc_final: 0.8126 (m-80) REVERT: E 11 GLU cc_start: 0.9087 (tt0) cc_final: 0.8510 (pm20) REVERT: E 90 HIS cc_start: 0.9031 (m-70) cc_final: 0.8814 (m-70) REVERT: E 104 ILE cc_start: 0.8786 (mm) cc_final: 0.8398 (mm) REVERT: E 116 TRP cc_start: 0.7683 (m100) cc_final: 0.7458 (m100) REVERT: E 122 ILE cc_start: 0.9219 (pt) cc_final: 0.8924 (tp) REVERT: D 170 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8774 (pt0) REVERT: D 186 TYR cc_start: 0.8085 (m-80) cc_final: 0.7477 (m-10) REVERT: D 210 GLN cc_start: 0.8283 (tp40) cc_final: 0.7932 (tp40) REVERT: D 224 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7281 (pm20) REVERT: D 255 ASP cc_start: 0.9434 (m-30) cc_final: 0.8638 (t70) REVERT: D 279 GLN cc_start: 0.9077 (tm-30) cc_final: 0.8614 (tm-30) REVERT: D 301 PHE cc_start: 0.9100 (p90) cc_final: 0.8894 (p90) outliers start: 30 outliers final: 21 residues processed: 155 average time/residue: 0.1140 time to fit residues: 22.6791 Evaluate side-chains 160 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 72 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 231 ASN E 49 ASN E 75 GLN ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.067389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.042871 restraints weight = 26550.790| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 4.32 r_work: 0.2603 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 7704 Z= 0.308 Angle : 0.656 10.499 10505 Z= 0.345 Chirality : 0.046 0.200 1201 Planarity : 0.004 0.078 1360 Dihedral : 5.292 25.379 1034 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.25 % Allowed : 15.80 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.27), residues: 945 helix: 0.44 (1.42), residues: 18 sheet: -0.62 (0.26), residues: 349 loop : -0.49 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 266 TYR 0.020 0.002 TYR E 106 PHE 0.017 0.002 PHE E 85 TRP 0.011 0.002 TRP B 296 HIS 0.010 0.002 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00681 ( 7700) covalent geometry : angle 0.65571 (10497) SS BOND : bond 0.00249 ( 4) SS BOND : angle 0.66237 ( 8) hydrogen bonds : bond 0.03413 ( 212) hydrogen bonds : angle 5.98849 ( 528) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8150 (mt-10) REVERT: B 202 THR cc_start: 0.9498 (OUTLIER) cc_final: 0.9150 (p) REVERT: B 300 ASP cc_start: 0.9229 (t0) cc_final: 0.8723 (t0) REVERT: B 323 GLU cc_start: 0.9379 (tp30) cc_final: 0.8925 (tp30) REVERT: A 284 ASP cc_start: 0.9032 (p0) cc_final: 0.8755 (p0) REVERT: A 285 GLU cc_start: 0.9020 (mp0) cc_final: 0.8428 (mp0) REVERT: A 323 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8379 (mm-30) REVERT: C 196 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8049 (mm-30) REVERT: C 250 GLU cc_start: 0.8543 (pm20) cc_final: 0.8168 (pm20) REVERT: C 285 GLU cc_start: 0.9246 (mm-30) cc_final: 0.9014 (mm-30) REVERT: E 11 GLU cc_start: 0.9064 (tt0) cc_final: 0.8452 (pm20) REVERT: E 70 ASP cc_start: 0.9385 (m-30) cc_final: 0.9153 (t0) REVERT: E 116 TRP cc_start: 0.7706 (m100) cc_final: 0.7400 (m100) REVERT: D 112 GLN cc_start: 0.8513 (tm-30) cc_final: 0.7989 (tm-30) REVERT: D 120 GLU cc_start: 0.9349 (pt0) cc_final: 0.9037 (pm20) REVERT: D 170 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8866 (pt0) REVERT: D 186 TYR cc_start: 0.8165 (m-80) cc_final: 0.7445 (m-10) REVERT: D 210 GLN cc_start: 0.8302 (tp40) cc_final: 0.7966 (tp40) REVERT: D 243 ARG cc_start: 0.8646 (tpp80) cc_final: 0.8176 (tpp80) REVERT: D 255 ASP cc_start: 0.9440 (m-30) cc_final: 0.8627 (t70) REVERT: D 279 GLN cc_start: 0.9155 (tm-30) cc_final: 0.8702 (tm-30) outliers start: 36 outliers final: 23 residues processed: 158 average time/residue: 0.1056 time to fit residues: 21.5719 Evaluate side-chains 153 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 51 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 69 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 GLN E 75 GLN ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.068161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.043782 restraints weight = 26163.842| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 4.36 r_work: 0.2636 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7704 Z= 0.190 Angle : 0.634 10.443 10505 Z= 0.329 Chirality : 0.046 0.200 1201 Planarity : 0.004 0.035 1360 Dihedral : 5.114 26.433 1034 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.77 % Allowed : 16.75 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.27), residues: 945 helix: 0.43 (1.38), residues: 18 sheet: -0.70 (0.27), residues: 337 loop : -0.32 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 266 TYR 0.018 0.001 TYR A 319 PHE 0.021 0.002 PHE E 91 TRP 0.011 0.001 TRP B 296 HIS 0.007 0.001 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 7700) covalent geometry : angle 0.63427 (10497) SS BOND : bond 0.00236 ( 4) SS BOND : angle 0.53172 ( 8) hydrogen bonds : bond 0.03193 ( 212) hydrogen bonds : angle 5.86075 ( 528) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8097 (mt-10) REVERT: B 202 THR cc_start: 0.9511 (OUTLIER) cc_final: 0.9213 (p) REVERT: B 224 MET cc_start: 0.8990 (mtm) cc_final: 0.8704 (mtp) REVERT: B 300 ASP cc_start: 0.9219 (t0) cc_final: 0.8682 (t0) REVERT: B 323 GLU cc_start: 0.9391 (tp30) cc_final: 0.8912 (tp30) REVERT: A 284 ASP cc_start: 0.9042 (p0) cc_final: 0.8762 (p0) REVERT: A 285 GLU cc_start: 0.9027 (mp0) cc_final: 0.8419 (mp0) REVERT: A 323 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8563 (tp30) REVERT: C 196 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7964 (mm-30) REVERT: C 250 GLU cc_start: 0.8570 (pm20) cc_final: 0.8153 (pm20) REVERT: C 285 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8855 (mm-30) REVERT: C 320 TYR cc_start: 0.9518 (p90) cc_final: 0.9318 (p90) REVERT: E 11 GLU cc_start: 0.9068 (tt0) cc_final: 0.8454 (pm20) REVERT: E 15 LYS cc_start: 0.9029 (ttpp) cc_final: 0.8664 (pptt) REVERT: E 48 ARG cc_start: 0.8077 (tmm160) cc_final: 0.7819 (tmm160) REVERT: E 116 TRP cc_start: 0.7708 (m100) cc_final: 0.7323 (m100) REVERT: D 112 GLN cc_start: 0.8788 (tm-30) cc_final: 0.7916 (tm-30) REVERT: D 120 GLU cc_start: 0.9334 (pt0) cc_final: 0.8989 (pm20) REVERT: D 170 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8835 (pt0) REVERT: D 186 TYR cc_start: 0.8196 (m-80) cc_final: 0.7501 (m-10) REVERT: D 210 GLN cc_start: 0.8310 (tp40) cc_final: 0.8044 (tp40) REVERT: D 231 MET cc_start: 0.8778 (tpp) cc_final: 0.8266 (mpp) REVERT: D 243 ARG cc_start: 0.8691 (tpp80) cc_final: 0.8219 (tpp80) REVERT: D 255 ASP cc_start: 0.9434 (m-30) cc_final: 0.8660 (t70) REVERT: D 279 GLN cc_start: 0.9154 (tm-30) cc_final: 0.8709 (tm-30) REVERT: D 301 PHE cc_start: 0.9028 (p90) cc_final: 0.8754 (p90) outliers start: 32 outliers final: 24 residues processed: 155 average time/residue: 0.1075 time to fit residues: 21.5338 Evaluate side-chains 156 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 48 optimal weight: 0.0570 chunk 25 optimal weight: 0.5980 chunk 72 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 1 optimal weight: 0.0040 chunk 36 optimal weight: 5.9990 overall best weight: 1.1112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 307 ASN ** 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 = 0.3489 r_free = 0.3489 target = 0.068882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.044438 restraints weight = 26092.559| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 4.41 r_work: 0.2658 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7704 Z= 0.133 Angle : 0.622 10.518 10505 Z= 0.322 Chirality : 0.046 0.178 1201 Planarity : 0.004 0.034 1360 Dihedral : 4.911 26.369 1034 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.66 % Allowed : 17.92 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.27), residues: 945 helix: 0.46 (1.36), residues: 18 sheet: -0.66 (0.27), residues: 335 loop : -0.19 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 208 TYR 0.016 0.001 TYR A 319 PHE 0.025 0.002 PHE E 91 TRP 0.030 0.002 TRP E 52 HIS 0.010 0.001 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7700) covalent geometry : angle 0.62227 (10497) SS BOND : bond 0.00148 ( 4) SS BOND : angle 0.42613 ( 8) hydrogen bonds : bond 0.02971 ( 212) hydrogen bonds : angle 5.69842 ( 528) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8121 (mt-10) REVERT: B 202 THR cc_start: 0.9490 (OUTLIER) cc_final: 0.9215 (p) REVERT: B 300 ASP cc_start: 0.9186 (t0) cc_final: 0.8644 (t0) REVERT: B 320 TYR cc_start: 0.9496 (p90) cc_final: 0.9154 (p90) REVERT: B 323 GLU cc_start: 0.9400 (tp30) cc_final: 0.8923 (tp30) REVERT: A 142 GLU cc_start: 0.9070 (pm20) cc_final: 0.8798 (mp0) REVERT: A 156 CYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7475 (p) REVERT: A 284 ASP cc_start: 0.9004 (p0) cc_final: 0.8740 (p0) REVERT: A 285 GLU cc_start: 0.9045 (mp0) cc_final: 0.8452 (mp0) REVERT: A 323 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8579 (tp30) REVERT: C 196 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7915 (mm-30) REVERT: C 250 GLU cc_start: 0.8574 (pm20) cc_final: 0.8117 (pm20) REVERT: C 285 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8850 (mm-30) REVERT: E 11 GLU cc_start: 0.9091 (tt0) cc_final: 0.8523 (pm20) REVERT: E 32 LYS cc_start: 0.9237 (tppt) cc_final: 0.8942 (tppt) REVERT: D 120 GLU cc_start: 0.9318 (pt0) cc_final: 0.8981 (pm20) REVERT: D 170 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8786 (pt0) REVERT: D 186 TYR cc_start: 0.8140 (m-80) cc_final: 0.7485 (m-10) REVERT: D 210 GLN cc_start: 0.8323 (tp40) cc_final: 0.8030 (tp40) REVERT: D 243 ARG cc_start: 0.8711 (tpp80) cc_final: 0.8206 (tpp80) REVERT: D 255 ASP cc_start: 0.9417 (m-30) cc_final: 0.8653 (t70) REVERT: D 279 GLN cc_start: 0.9181 (tm-30) cc_final: 0.8735 (tm-30) outliers start: 31 outliers final: 23 residues processed: 156 average time/residue: 0.1005 time to fit residues: 20.1170 Evaluate side-chains 161 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 20 optimal weight: 0.0270 chunk 52 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 59 optimal weight: 0.3980 chunk 22 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** 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 = 0.3498 r_free = 0.3498 target = 0.069337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.044986 restraints weight = 26066.318| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 4.37 r_work: 0.2675 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7704 Z= 0.131 Angle : 0.648 10.408 10505 Z= 0.334 Chirality : 0.045 0.167 1201 Planarity : 0.004 0.040 1360 Dihedral : 4.869 25.572 1034 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.42 % Allowed : 17.69 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.27), residues: 945 helix: 0.45 (1.36), residues: 18 sheet: -0.64 (0.27), residues: 339 loop : -0.16 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 266 TYR 0.022 0.001 TYR B 256 PHE 0.023 0.002 PHE E 91 TRP 0.018 0.002 TRP E 52 HIS 0.007 0.001 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7700) covalent geometry : angle 0.64767 (10497) SS BOND : bond 0.00151 ( 4) SS BOND : angle 0.60337 ( 8) hydrogen bonds : bond 0.02862 ( 212) hydrogen bonds : angle 5.63220 ( 528) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8113 (mt-10) REVERT: B 202 THR cc_start: 0.9516 (OUTLIER) cc_final: 0.9259 (p) REVERT: B 300 ASP cc_start: 0.9161 (t0) cc_final: 0.8603 (t0) REVERT: B 320 TYR cc_start: 0.9455 (p90) cc_final: 0.9097 (p90) REVERT: B 323 GLU cc_start: 0.9376 (tp30) cc_final: 0.8882 (tp30) REVERT: A 142 GLU cc_start: 0.9043 (pm20) cc_final: 0.8762 (mp0) REVERT: A 224 MET cc_start: 0.9394 (mpp) cc_final: 0.8996 (mpp) REVERT: A 284 ASP cc_start: 0.9025 (p0) cc_final: 0.8769 (p0) REVERT: A 285 GLU cc_start: 0.9071 (mp0) cc_final: 0.8489 (mp0) REVERT: A 323 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8541 (tp30) REVERT: C 196 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7858 (mm-30) REVERT: C 250 GLU cc_start: 0.8598 (pm20) cc_final: 0.8112 (pm20) REVERT: C 285 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8830 (mm-30) REVERT: E 11 GLU cc_start: 0.9110 (tt0) cc_final: 0.8569 (pm20) REVERT: E 32 LYS cc_start: 0.9203 (tppt) cc_final: 0.8892 (tppt) REVERT: E 116 TRP cc_start: 0.7656 (m100) cc_final: 0.7239 (m100) REVERT: D 112 GLN cc_start: 0.7989 (tm-30) cc_final: 0.7753 (tm-30) REVERT: D 120 GLU cc_start: 0.9326 (pt0) cc_final: 0.8979 (pm20) REVERT: D 130 MET cc_start: 0.8854 (mtp) cc_final: 0.8565 (mtp) REVERT: D 170 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8819 (pt0) REVERT: D 186 TYR cc_start: 0.8188 (m-80) cc_final: 0.7624 (m-10) REVERT: D 193 ARG cc_start: 0.8537 (mtp-110) cc_final: 0.7238 (ptm160) REVERT: D 210 GLN cc_start: 0.8344 (tp40) cc_final: 0.8029 (tp40) REVERT: D 243 ARG cc_start: 0.8753 (tpp80) cc_final: 0.8214 (tpp80) REVERT: D 255 ASP cc_start: 0.9430 (m-30) cc_final: 0.8681 (t70) REVERT: D 279 GLN cc_start: 0.9187 (tm-30) cc_final: 0.8790 (tm-30) REVERT: D 301 PHE cc_start: 0.9034 (p90) cc_final: 0.8815 (p90) outliers start: 29 outliers final: 24 residues processed: 163 average time/residue: 0.1004 time to fit residues: 21.0633 Evaluate side-chains 159 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 256 TYR Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 330 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 85 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 49 optimal weight: 0.4980 chunk 3 optimal weight: 7.9990 chunk 47 optimal weight: 0.4980 chunk 79 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 50 HIS ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.068128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.043688 restraints weight = 26334.843| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 4.40 r_work: 0.2639 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7704 Z= 0.172 Angle : 0.651 10.498 10505 Z= 0.333 Chirality : 0.045 0.150 1201 Planarity : 0.004 0.037 1360 Dihedral : 4.828 24.891 1034 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.54 % Allowed : 17.69 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.27), residues: 945 helix: 0.42 (1.37), residues: 18 sheet: -0.60 (0.28), residues: 337 loop : -0.22 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 208 TYR 0.018 0.001 TYR B 256 PHE 0.018 0.002 PHE E 91 TRP 0.012 0.002 TRP A 296 HIS 0.006 0.001 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 7700) covalent geometry : angle 0.65087 (10497) SS BOND : bond 0.00209 ( 4) SS BOND : angle 0.51794 ( 8) hydrogen bonds : bond 0.02943 ( 212) hydrogen bonds : angle 5.64966 ( 528) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8130 (mt-10) REVERT: B 202 THR cc_start: 0.9518 (OUTLIER) cc_final: 0.9241 (p) REVERT: B 300 ASP cc_start: 0.9161 (t0) cc_final: 0.8604 (t0) REVERT: B 320 TYR cc_start: 0.9499 (p90) cc_final: 0.9119 (p90) REVERT: B 323 GLU cc_start: 0.9379 (tp30) cc_final: 0.8886 (tp30) REVERT: A 142 GLU cc_start: 0.9070 (pm20) cc_final: 0.8773 (mp0) REVERT: A 284 ASP cc_start: 0.9047 (p0) cc_final: 0.8807 (p0) REVERT: A 285 GLU cc_start: 0.9090 (mp0) cc_final: 0.8524 (mp0) REVERT: A 323 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8576 (tp30) REVERT: C 196 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7916 (mm-30) REVERT: C 250 GLU cc_start: 0.8583 (pm20) cc_final: 0.8079 (pm20) REVERT: C 285 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8819 (mm-30) REVERT: E 11 GLU cc_start: 0.9100 (tt0) cc_final: 0.8533 (pm20) REVERT: E 32 LYS cc_start: 0.9180 (tppt) cc_final: 0.8860 (tppt) REVERT: E 122 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8796 (tt) REVERT: D 120 GLU cc_start: 0.9352 (pt0) cc_final: 0.9022 (pm20) REVERT: D 170 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8825 (pt0) REVERT: D 186 TYR cc_start: 0.8242 (m-80) cc_final: 0.7611 (m-10) REVERT: D 193 ARG cc_start: 0.8517 (mtp-110) cc_final: 0.7183 (ptm160) REVERT: D 210 GLN cc_start: 0.8398 (tp40) cc_final: 0.8084 (tp40) REVERT: D 231 MET cc_start: 0.8738 (tpp) cc_final: 0.7976 (mpp) REVERT: D 243 ARG cc_start: 0.8781 (tpp80) cc_final: 0.8242 (tpp80) REVERT: D 255 ASP cc_start: 0.9433 (m-30) cc_final: 0.8751 (t70) REVERT: D 279 GLN cc_start: 0.9201 (tm-30) cc_final: 0.8753 (tm-30) outliers start: 30 outliers final: 25 residues processed: 151 average time/residue: 0.1028 time to fit residues: 19.9737 Evaluate side-chains 161 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 74 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 85 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 307 ASN ** 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 = 0.3492 r_free = 0.3492 target = 0.068952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.044474 restraints weight = 26084.751| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 4.37 r_work: 0.2665 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7704 Z= 0.154 Angle : 0.683 10.586 10505 Z= 0.350 Chirality : 0.045 0.152 1201 Planarity : 0.004 0.041 1360 Dihedral : 4.850 25.266 1034 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.30 % Allowed : 18.40 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.27), residues: 945 helix: 0.33 (1.34), residues: 18 sheet: -0.58 (0.28), residues: 336 loop : -0.18 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 208 TYR 0.017 0.001 TYR A 319 PHE 0.017 0.002 PHE D 301 TRP 0.012 0.002 TRP E 52 HIS 0.005 0.001 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 7700) covalent geometry : angle 0.68288 (10497) SS BOND : bond 0.00140 ( 4) SS BOND : angle 0.59859 ( 8) hydrogen bonds : bond 0.02883 ( 212) hydrogen bonds : angle 5.67160 ( 528) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8123 (mt-10) REVERT: B 202 THR cc_start: 0.9501 (OUTLIER) cc_final: 0.9256 (p) REVERT: B 300 ASP cc_start: 0.9151 (t0) cc_final: 0.8583 (t0) REVERT: B 320 TYR cc_start: 0.9479 (p90) cc_final: 0.9107 (p90) REVERT: B 323 GLU cc_start: 0.9384 (tp30) cc_final: 0.8872 (tp30) REVERT: A 142 GLU cc_start: 0.9066 (pm20) cc_final: 0.8755 (mp0) REVERT: A 284 ASP cc_start: 0.9045 (p0) cc_final: 0.8805 (p0) REVERT: A 285 GLU cc_start: 0.9098 (mp0) cc_final: 0.8541 (mp0) REVERT: A 323 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8540 (tp30) REVERT: C 196 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7869 (mm-30) REVERT: C 250 GLU cc_start: 0.8584 (pm20) cc_final: 0.8071 (pm20) REVERT: C 285 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8813 (mm-30) REVERT: E 11 GLU cc_start: 0.9103 (tt0) cc_final: 0.8564 (pm20) REVERT: E 32 LYS cc_start: 0.9183 (tppt) cc_final: 0.8866 (tppt) REVERT: E 91 PHE cc_start: 0.8800 (m-10) cc_final: 0.8452 (m-10) REVERT: E 122 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8626 (tp) REVERT: D 120 GLU cc_start: 0.9341 (pt0) cc_final: 0.9006 (pm20) REVERT: D 170 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8829 (pt0) REVERT: D 186 TYR cc_start: 0.8226 (m-80) cc_final: 0.7559 (m-10) REVERT: D 193 ARG cc_start: 0.8486 (mtp-110) cc_final: 0.7144 (ptm160) REVERT: D 210 GLN cc_start: 0.8377 (tp40) cc_final: 0.8091 (tp40) REVERT: D 243 ARG cc_start: 0.8786 (tpp80) cc_final: 0.8273 (tpp80) REVERT: D 255 ASP cc_start: 0.9444 (m-30) cc_final: 0.8718 (t70) REVERT: D 279 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8800 (tm-30) outliers start: 28 outliers final: 22 residues processed: 153 average time/residue: 0.1024 time to fit residues: 20.0378 Evaluate side-chains 159 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 33 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 19 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 307 ASN ** 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 = 0.3476 r_free = 0.3476 target = 0.068396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.043799 restraints weight = 26063.134| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 4.45 r_work: 0.2645 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7704 Z= 0.173 Angle : 0.689 10.498 10505 Z= 0.350 Chirality : 0.045 0.149 1201 Planarity : 0.004 0.045 1360 Dihedral : 4.835 25.525 1034 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.95 % Allowed : 18.51 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.27), residues: 945 helix: 0.31 (1.34), residues: 18 sheet: -0.63 (0.27), residues: 337 loop : -0.17 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 266 TYR 0.015 0.001 TYR A 319 PHE 0.015 0.002 PHE A 199 TRP 0.012 0.002 TRP A 296 HIS 0.004 0.001 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 7700) covalent geometry : angle 0.68898 (10497) SS BOND : bond 0.00167 ( 4) SS BOND : angle 0.80526 ( 8) hydrogen bonds : bond 0.02907 ( 212) hydrogen bonds : angle 5.68295 ( 528) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8144 (mt-10) REVERT: B 202 THR cc_start: 0.9491 (OUTLIER) cc_final: 0.9222 (p) REVERT: B 300 ASP cc_start: 0.9138 (t0) cc_final: 0.8563 (t0) REVERT: B 319 TYR cc_start: 0.8422 (m-80) cc_final: 0.7995 (m-80) REVERT: B 323 GLU cc_start: 0.9384 (tp30) cc_final: 0.8833 (tp30) REVERT: A 142 GLU cc_start: 0.9068 (pm20) cc_final: 0.8752 (mp0) REVERT: A 284 ASP cc_start: 0.9070 (p0) cc_final: 0.8844 (p0) REVERT: A 285 GLU cc_start: 0.9102 (mp0) cc_final: 0.8534 (mp0) REVERT: A 319 TYR cc_start: 0.8902 (m-80) cc_final: 0.8685 (m-80) REVERT: A 323 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8547 (tp30) REVERT: C 196 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7897 (mm-30) REVERT: C 250 GLU cc_start: 0.8583 (pm20) cc_final: 0.8073 (pm20) REVERT: C 285 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8805 (mm-30) REVERT: C 319 TYR cc_start: 0.8729 (m-80) cc_final: 0.8198 (m-80) REVERT: E 11 GLU cc_start: 0.9096 (tt0) cc_final: 0.8555 (pm20) REVERT: E 32 LYS cc_start: 0.9172 (tppt) cc_final: 0.8853 (tppt) REVERT: E 99 LEU cc_start: 0.7718 (mt) cc_final: 0.7408 (tp) REVERT: E 122 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8744 (tp) REVERT: D 120 GLU cc_start: 0.9359 (pt0) cc_final: 0.9027 (pm20) REVERT: D 170 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8854 (pt0) REVERT: D 186 TYR cc_start: 0.8309 (m-80) cc_final: 0.7627 (m-10) REVERT: D 193 ARG cc_start: 0.8482 (mtp-110) cc_final: 0.7104 (ptm160) REVERT: D 210 GLN cc_start: 0.8408 (tp40) cc_final: 0.8131 (tp40) REVERT: D 243 ARG cc_start: 0.8801 (tpp80) cc_final: 0.8294 (tpp80) REVERT: D 255 ASP cc_start: 0.9449 (m-30) cc_final: 0.8767 (t70) REVERT: D 279 GLN cc_start: 0.9224 (tm-30) cc_final: 0.8771 (tm-30) outliers start: 25 outliers final: 21 residues processed: 150 average time/residue: 0.1002 time to fit residues: 19.1378 Evaluate side-chains 156 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 21 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 63 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 307 ASN ** 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 = 0.3491 r_free = 0.3491 target = 0.068995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.044350 restraints weight = 26077.001| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 4.42 r_work: 0.2665 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7704 Z= 0.140 Angle : 0.683 10.024 10505 Z= 0.347 Chirality : 0.045 0.151 1201 Planarity : 0.004 0.045 1360 Dihedral : 4.743 26.044 1034 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.83 % Allowed : 18.51 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.28), residues: 945 helix: 0.31 (1.33), residues: 18 sheet: -0.53 (0.28), residues: 335 loop : -0.13 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 69 TYR 0.015 0.001 TYR A 319 PHE 0.022 0.002 PHE E 91 TRP 0.012 0.002 TRP A 296 HIS 0.004 0.001 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7700) covalent geometry : angle 0.68307 (10497) SS BOND : bond 0.00101 ( 4) SS BOND : angle 0.72907 ( 8) hydrogen bonds : bond 0.02798 ( 212) hydrogen bonds : angle 5.60930 ( 528) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2425.95 seconds wall clock time: 42 minutes 14.93 seconds (2534.93 seconds total)