Starting phenix.real_space_refine on Sun May 11 04:03:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qk3_18455/05_2025/8qk3_18455.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qk3_18455/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qk3_18455/05_2025/8qk3_18455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qk3_18455/05_2025/8qk3_18455.map" model { file = "/net/cci-nas-00/data/ceres_data/8qk3_18455/05_2025/8qk3_18455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qk3_18455/05_2025/8qk3_18455.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.97, per 1000 atoms: 0.66 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: 1.86 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.93 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: 2.07 Time building geometry restraints manager: 2.21 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: 0.950 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.990 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.470 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (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 TRP 0.018 0.002 TRP B 296 HIS 0.004 0.001 HIS A 218 PHE 0.016 0.001 PHE C 172 TYR 0.012 0.001 TYR D 172 ARG 0.003 0.000 ARG C 280 Details of bonding type rmsd hydrogen bonds : bond 0.11977 ( 212) hydrogen bonds : angle 6.96756 ( 528) SS BOND : bond 0.32439 ( 4) SS BOND : angle 13.44483 ( 8) covalent geometry : bond 0.00310 ( 7700) covalent geometry : angle 0.59717 (10497) *********************** 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 : 0.886 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: symmetry clash REVERT: B 319 TYR cc_start: 0.8172 (m-80) cc_final: 0.7945 (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: 0.7949 (m-80) REVERT: C 280 ARG cc_start: 0.8287 (mtt-85) cc_final: 0.7837 (mtt-85) REVERT: E 99 LEU cc_start: 0.8643 (tp) cc_final: 0.7805 (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: 0.7310 (p90) outliers start: 1 outliers final: 1 residues processed: 238 average time/residue: 0.2602 time to fit residues: 77.0402 Evaluate side-chains 157 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 77 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 0.0020 chunk 43 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.071503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.047542 restraints weight = 25223.009| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 4.28 r_work: 0.2719 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7704 Z= 0.173 Angle : 0.651 10.539 10505 Z= 0.345 Chirality : 0.047 0.280 1201 Planarity : 0.005 0.051 1360 Dihedral : 4.914 27.393 1035 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.77 % Allowed : 15.57 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.27), residues: 945 helix: -0.28 (1.25), residues: 21 sheet: -0.54 (0.26), residues: 345 loop : -0.26 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 116 HIS 0.002 0.001 HIS A 218 PHE 0.022 0.002 PHE E 85 TYR 0.025 0.002 TYR D 186 ARG 0.011 0.001 ARG E 48 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 212) hydrogen bonds : angle 6.19567 ( 528) SS BOND : bond 0.00304 ( 4) SS BOND : angle 0.49850 ( 8) covalent geometry : bond 0.00399 ( 7700) covalent geometry : angle 0.65122 (10497) *********************** 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 200 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.890 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: B 196 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8204 (mt-10) REVERT: B 285 GLU cc_start: 0.9104 (mp0) cc_final: 0.8799 (mp0) REVERT: B 300 ASP cc_start: 0.9189 (t0) cc_final: 0.8982 (t0) REVERT: B 319 TYR cc_start: 0.8518 (m-80) cc_final: 0.8235 (m-80) REVERT: B 323 GLU cc_start: 0.9238 (tp30) cc_final: 0.8828 (tp30) REVERT: A 285 GLU cc_start: 0.8871 (mp0) cc_final: 0.8329 (mp0) REVERT: A 319 TYR cc_start: 0.8839 (m-80) cc_final: 0.8423 (m-80) REVERT: A 323 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8516 (tp30) REVERT: C 155 ASP cc_start: 0.7486 (p0) cc_final: 0.7203 (p0) REVERT: C 275 VAL cc_start: 0.9107 (t) cc_final: 0.8867 (p) REVERT: C 276 MET cc_start: 0.8206 (ttp) cc_final: 0.7471 (ttp) REVERT: C 280 ARG cc_start: 0.8688 (mtt-85) cc_final: 0.8367 (mtt-85) REVERT: C 285 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8818 (mp0) REVERT: C 291 ARG cc_start: 0.7237 (mtt90) cc_final: 0.7019 (mtp-110) REVERT: C 319 TYR cc_start: 0.8471 (m-80) cc_final: 0.7773 (m-80) REVERT: E 11 GLU cc_start: 0.9199 (tt0) cc_final: 0.8629 (pm20) REVERT: E 37 ILE cc_start: 0.8703 (mt) cc_final: 0.8488 (mp) REVERT: E 104 ILE cc_start: 0.9204 (mt) cc_final: 0.8997 (mm) REVERT: E 116 TRP cc_start: 0.7652 (m100) cc_final: 0.7428 (m100) REVERT: E 122 ILE cc_start: 0.9212 (pt) cc_final: 0.8923 (tp) REVERT: D 170 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8823 (pt0) REVERT: D 186 TYR cc_start: 0.7858 (m-10) cc_final: 0.7266 (m-10) REVERT: D 206 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7736 (mm-40) REVERT: D 210 GLN cc_start: 0.8203 (tp40) cc_final: 0.7932 (tp40) REVERT: D 211 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8631 (mm) REVERT: D 231 MET cc_start: 0.8482 (tpp) cc_final: 0.8281 (tpp) REVERT: D 255 ASP cc_start: 0.9367 (OUTLIER) cc_final: 0.8476 (t70) REVERT: D 301 PHE cc_start: 0.9047 (p90) cc_final: 0.8789 (p90) outliers start: 32 outliers final: 20 residues processed: 187 average time/residue: 0.2353 time to fit residues: 56.3520 Evaluate side-chains 175 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 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 156 CYS Chi-restraints excluded: chain A residue 284 ASP 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 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 90 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 231 ASN ** 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 = 0.3520 r_free = 0.3520 target = 0.070743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.046115 restraints weight = 25782.624| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 4.40 r_work: 0.2701 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7704 Z= 0.166 Angle : 0.619 11.094 10505 Z= 0.325 Chirality : 0.046 0.239 1201 Planarity : 0.004 0.033 1360 Dihedral : 4.870 26.513 1034 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.42 % Allowed : 14.74 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.27), residues: 945 helix: -0.28 (1.28), residues: 21 sheet: -0.57 (0.26), residues: 351 loop : -0.27 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 296 HIS 0.004 0.001 HIS E 90 PHE 0.019 0.002 PHE E 91 TYR 0.022 0.001 TYR B 256 ARG 0.006 0.001 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03116 ( 212) hydrogen bonds : angle 5.97762 ( 528) SS BOND : bond 0.00156 ( 4) SS BOND : angle 0.41172 ( 8) covalent geometry : bond 0.00370 ( 7700) covalent geometry : angle 0.61915 (10497) *********************** 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 194 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8146 (mt-10) REVERT: B 202 THR cc_start: 0.9489 (OUTLIER) cc_final: 0.9202 (p) REVERT: B 224 MET cc_start: 0.8952 (mtm) cc_final: 0.8600 (mtp) REVERT: B 300 ASP cc_start: 0.9225 (t0) cc_final: 0.8773 (t0) REVERT: B 323 GLU cc_start: 0.9289 (tp30) cc_final: 0.8849 (tp30) REVERT: A 285 GLU cc_start: 0.8974 (mp0) cc_final: 0.8410 (mp0) REVERT: A 319 TYR cc_start: 0.8856 (m-80) cc_final: 0.8525 (m-80) REVERT: A 323 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8490 (mm-30) REVERT: C 155 ASP cc_start: 0.7614 (p0) cc_final: 0.7308 (p0) REVERT: C 250 GLU cc_start: 0.8422 (pm20) cc_final: 0.8153 (pm20) REVERT: C 276 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7767 (ttp) REVERT: C 280 ARG cc_start: 0.8619 (mtt-85) cc_final: 0.8313 (mtt-85) REVERT: C 285 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8858 (mm-30) REVERT: C 291 ARG cc_start: 0.7530 (mtt90) cc_final: 0.7289 (mtp-110) REVERT: C 319 TYR cc_start: 0.8560 (m-80) cc_final: 0.7774 (m-80) REVERT: E 11 GLU cc_start: 0.9151 (tt0) cc_final: 0.8596 (pm20) REVERT: D 110 PHE cc_start: 0.8653 (p90) cc_final: 0.8287 (p90) REVERT: D 112 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8249 (tm-30) REVERT: D 170 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8672 (pt0) REVERT: D 186 TYR cc_start: 0.7990 (m-80) cc_final: 0.7502 (m-10) REVERT: D 210 GLN cc_start: 0.8306 (tp40) cc_final: 0.7892 (tp40) REVERT: D 224 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7494 (pm20) REVERT: D 251 GLU cc_start: 0.9383 (tt0) cc_final: 0.8776 (tm-30) REVERT: D 255 ASP cc_start: 0.9387 (m-30) cc_final: 0.8523 (t70) REVERT: D 279 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8553 (tm-30) outliers start: 29 outliers final: 19 residues processed: 182 average time/residue: 0.2152 time to fit residues: 50.4879 Evaluate side-chains 169 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 163 VAL 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 C residue 145 CYS Chi-restraints excluded: chain C residue 276 MET 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 E residue 105 LEU Chi-restraints excluded: chain D residue 171 ILE 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 48 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 E 43 HIS E 49 ASN E 50 HIS ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.067849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.043293 restraints weight = 26503.972| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 4.43 r_work: 0.2613 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 7704 Z= 0.336 Angle : 0.688 10.718 10505 Z= 0.363 Chirality : 0.047 0.193 1201 Planarity : 0.004 0.036 1360 Dihedral : 5.237 28.080 1034 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.54 % Allowed : 15.80 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.27), residues: 945 helix: -0.88 (0.86), residues: 36 sheet: -0.72 (0.26), residues: 356 loop : -0.30 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 116 HIS 0.006 0.002 HIS E 90 PHE 0.026 0.002 PHE E 91 TYR 0.021 0.002 TYR B 256 ARG 0.005 0.001 ARG A 266 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 212) hydrogen bonds : angle 6.04786 ( 528) SS BOND : bond 0.00266 ( 4) SS BOND : angle 0.75783 ( 8) covalent geometry : bond 0.00744 ( 7700) covalent geometry : angle 0.68771 (10497) *********************** 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 164 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8150 (mt-10) REVERT: B 202 THR cc_start: 0.9510 (OUTLIER) cc_final: 0.9164 (p) REVERT: B 300 ASP cc_start: 0.9228 (t0) cc_final: 0.8749 (t0) REVERT: B 319 TYR cc_start: 0.8738 (m-80) cc_final: 0.8341 (m-80) REVERT: B 323 GLU cc_start: 0.9387 (tp30) cc_final: 0.8884 (tp30) REVERT: A 284 ASP cc_start: 0.9023 (p0) cc_final: 0.8759 (p0) REVERT: A 285 GLU cc_start: 0.9031 (mp0) cc_final: 0.8470 (mp0) REVERT: A 319 TYR cc_start: 0.8876 (m-80) cc_final: 0.8576 (m-80) REVERT: A 323 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8369 (mm-30) REVERT: C 196 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8157 (mm-30) REVERT: C 250 GLU cc_start: 0.8506 (pm20) cc_final: 0.8148 (pm20) REVERT: C 256 TYR cc_start: 0.9213 (m-80) cc_final: 0.8989 (m-80) REVERT: C 285 GLU cc_start: 0.9231 (mm-30) cc_final: 0.9010 (mm-30) REVERT: C 319 TYR cc_start: 0.8819 (m-80) cc_final: 0.8139 (m-80) REVERT: E 11 GLU cc_start: 0.9116 (tt0) cc_final: 0.8498 (pm20) REVERT: E 122 ILE cc_start: 0.9263 (pt) cc_final: 0.8983 (tp) REVERT: D 110 PHE cc_start: 0.8828 (p90) cc_final: 0.8450 (p90) REVERT: D 112 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8188 (tm-30) REVERT: D 170 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8752 (pt0) REVERT: D 186 TYR cc_start: 0.8155 (m-80) cc_final: 0.7487 (m-10) REVERT: D 210 GLN cc_start: 0.8228 (tp40) cc_final: 0.7896 (tp40) REVERT: D 251 GLU cc_start: 0.9387 (tt0) cc_final: 0.8777 (tm-30) REVERT: D 255 ASP cc_start: 0.9435 (m-30) cc_final: 0.8656 (t70) REVERT: D 279 GLN cc_start: 0.9117 (tm-30) cc_final: 0.8667 (tm-30) REVERT: D 301 PHE cc_start: 0.9150 (p90) cc_final: 0.8949 (p90) outliers start: 30 outliers final: 22 residues processed: 153 average time/residue: 0.2286 time to fit residues: 45.5863 Evaluate side-chains 154 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 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 64 THR Chi-restraints excluded: chain E residue 105 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 6 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 36 optimal weight: 0.0970 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 GLN ** 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 = 0.3501 r_free = 0.3501 target = 0.069686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.045134 restraints weight = 25733.570| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 4.45 r_work: 0.2678 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.4186 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= 0.133 Angle : 0.627 10.430 10505 Z= 0.326 Chirality : 0.046 0.184 1201 Planarity : 0.004 0.071 1360 Dihedral : 4.968 27.031 1034 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.07 % Allowed : 16.75 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.27), residues: 945 helix: 0.32 (1.34), residues: 18 sheet: -0.81 (0.27), residues: 341 loop : -0.18 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 296 HIS 0.006 0.001 HIS E 90 PHE 0.017 0.002 PHE E 85 TYR 0.015 0.001 TYR D 149 ARG 0.007 0.001 ARG C 291 Details of bonding type rmsd hydrogen bonds : bond 0.02920 ( 212) hydrogen bonds : angle 5.74693 ( 528) SS BOND : bond 0.00111 ( 4) SS BOND : angle 0.59320 ( 8) covalent geometry : bond 0.00302 ( 7700) covalent geometry : angle 0.62749 (10497) *********************** 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 171 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8097 (mt-10) REVERT: B 202 THR cc_start: 0.9501 (OUTLIER) cc_final: 0.9226 (p) REVERT: B 224 MET cc_start: 0.8976 (mtm) cc_final: 0.8693 (mtp) REVERT: B 300 ASP cc_start: 0.9185 (t0) cc_final: 0.8646 (t0) REVERT: B 320 TYR cc_start: 0.9512 (p90) cc_final: 0.9308 (p90) REVERT: B 323 GLU cc_start: 0.9367 (tp30) cc_final: 0.8919 (tp30) REVERT: A 156 CYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7272 (p) REVERT: A 284 ASP cc_start: 0.9023 (p0) cc_final: 0.8768 (p0) REVERT: A 285 GLU cc_start: 0.9003 (mp0) cc_final: 0.8423 (mp0) REVERT: A 319 TYR cc_start: 0.8824 (m-80) cc_final: 0.8611 (m-80) REVERT: A 323 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8380 (mm-30) REVERT: C 196 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8075 (mm-30) REVERT: C 250 GLU cc_start: 0.8555 (pm20) cc_final: 0.8157 (pm20) REVERT: C 280 ARG cc_start: 0.8540 (mtt-85) cc_final: 0.8257 (mtt-85) REVERT: C 285 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8843 (mm-30) REVERT: C 319 TYR cc_start: 0.8590 (m-80) cc_final: 0.7857 (m-80) REVERT: E 11 GLU cc_start: 0.9135 (tt0) cc_final: 0.8536 (pm20) REVERT: E 32 LYS cc_start: 0.9213 (tppt) cc_final: 0.8917 (tppt) REVERT: D 112 GLN cc_start: 0.8781 (tm-30) cc_final: 0.7882 (tm-30) REVERT: D 170 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8660 (pt0) REVERT: D 186 TYR cc_start: 0.8138 (m-80) cc_final: 0.7589 (m-10) REVERT: D 210 GLN cc_start: 0.8238 (tp40) cc_final: 0.7860 (tp40) REVERT: D 243 ARG cc_start: 0.8729 (tpp80) cc_final: 0.8259 (tpp80) REVERT: D 251 GLU cc_start: 0.9424 (tt0) cc_final: 0.8879 (tm-30) REVERT: D 255 ASP cc_start: 0.9419 (m-30) cc_final: 0.8670 (t70) REVERT: D 279 GLN cc_start: 0.9125 (tm-30) cc_final: 0.8679 (tm-30) outliers start: 26 outliers final: 17 residues processed: 160 average time/residue: 0.2260 time to fit residues: 46.7088 Evaluate side-chains 153 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 A residue 138 VAL Chi-restraints excluded: chain A residue 156 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 64 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain D residue 232 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 66 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 81 optimal weight: 0.0010 chunk 61 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 75 GLN ** 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 = 0.3471 r_free = 0.3471 target = 0.068272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.043773 restraints weight = 26175.405| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 4.39 r_work: 0.2638 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7704 Z= 0.233 Angle : 0.658 10.218 10505 Z= 0.340 Chirality : 0.045 0.174 1201 Planarity : 0.004 0.042 1360 Dihedral : 4.993 27.733 1034 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.18 % Allowed : 17.45 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.27), residues: 945 helix: 0.39 (1.38), residues: 18 sheet: -0.80 (0.27), residues: 341 loop : -0.27 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 52 HIS 0.006 0.001 HIS E 90 PHE 0.024 0.002 PHE E 91 TYR 0.014 0.001 TYR B 256 ARG 0.006 0.001 ARG B 208 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 212) hydrogen bonds : angle 5.77603 ( 528) SS BOND : bond 0.00348 ( 4) SS BOND : angle 0.78141 ( 8) covalent geometry : bond 0.00519 ( 7700) covalent geometry : angle 0.65818 (10497) *********************** 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 160 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8135 (mt-10) REVERT: B 202 THR cc_start: 0.9533 (OUTLIER) cc_final: 0.9244 (p) REVERT: B 300 ASP cc_start: 0.9187 (t0) cc_final: 0.8646 (t0) REVERT: B 319 TYR cc_start: 0.8570 (m-80) cc_final: 0.8141 (m-80) REVERT: B 320 TYR cc_start: 0.9536 (p90) cc_final: 0.9294 (p90) REVERT: B 323 GLU cc_start: 0.9382 (tp30) cc_final: 0.8881 (tp30) REVERT: A 284 ASP cc_start: 0.9063 (p0) cc_final: 0.8836 (p0) REVERT: A 285 GLU cc_start: 0.9062 (mp0) cc_final: 0.8481 (mp0) REVERT: A 323 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8501 (tp30) REVERT: C 196 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8184 (mm-30) REVERT: C 250 GLU cc_start: 0.8566 (pm20) cc_final: 0.8113 (pm20) REVERT: C 285 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8873 (mm-30) REVERT: C 319 TYR cc_start: 0.8740 (m-80) cc_final: 0.8178 (m-80) REVERT: E 11 GLU cc_start: 0.9113 (tt0) cc_final: 0.8495 (pm20) REVERT: E 32 LYS cc_start: 0.9221 (tppt) cc_final: 0.8918 (tppt) REVERT: E 48 ARG cc_start: 0.8161 (tmm160) cc_final: 0.7740 (tmm160) REVERT: D 170 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8721 (pt0) REVERT: D 186 TYR cc_start: 0.8217 (m-80) cc_final: 0.7629 (m-10) REVERT: D 193 ARG cc_start: 0.8190 (mtp-110) cc_final: 0.7176 (ptm160) REVERT: D 210 GLN cc_start: 0.8208 (tp40) cc_final: 0.7846 (tp40) REVERT: D 243 ARG cc_start: 0.8704 (tpp80) cc_final: 0.8348 (tpp80) REVERT: D 251 GLU cc_start: 0.9422 (tt0) cc_final: 0.8843 (tm-30) REVERT: D 255 ASP cc_start: 0.9428 (m-30) cc_final: 0.8723 (t70) REVERT: D 279 GLN cc_start: 0.9127 (tm-30) cc_final: 0.8673 (tm-30) outliers start: 27 outliers final: 21 residues processed: 151 average time/residue: 0.2263 time to fit residues: 44.0654 Evaluate side-chains 152 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 156 CYS 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 64 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain D residue 232 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN ** D 112 GLN ** 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 = 0.3493 r_free = 0.3493 target = 0.069278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.044730 restraints weight = 25830.964| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 4.43 r_work: 0.2669 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.4486 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= 0.146 Angle : 0.651 11.431 10505 Z= 0.335 Chirality : 0.045 0.179 1201 Planarity : 0.004 0.037 1360 Dihedral : 4.929 26.170 1034 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.83 % Allowed : 17.92 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.27), residues: 945 helix: 0.37 (1.35), residues: 18 sheet: -0.86 (0.26), residues: 347 loop : -0.20 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 52 HIS 0.005 0.001 HIS E 90 PHE 0.019 0.002 PHE E 91 TYR 0.013 0.001 TYR A 319 ARG 0.007 0.001 ARG A 266 Details of bonding type rmsd hydrogen bonds : bond 0.02973 ( 212) hydrogen bonds : angle 5.67850 ( 528) SS BOND : bond 0.00138 ( 4) SS BOND : angle 0.48452 ( 8) covalent geometry : bond 0.00332 ( 7700) covalent geometry : angle 0.65146 (10497) *********************** 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 165 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8123 (mt-10) REVERT: B 202 THR cc_start: 0.9499 (OUTLIER) cc_final: 0.9232 (p) REVERT: B 300 ASP cc_start: 0.9176 (t0) cc_final: 0.8621 (t0) REVERT: B 320 TYR cc_start: 0.9508 (p90) cc_final: 0.9276 (p90) REVERT: B 323 GLU cc_start: 0.9385 (tp30) cc_final: 0.8904 (tp30) REVERT: A 156 CYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7570 (p) REVERT: A 284 ASP cc_start: 0.9025 (p0) cc_final: 0.8797 (p0) REVERT: A 285 GLU cc_start: 0.9051 (mp0) cc_final: 0.8482 (mp0) REVERT: A 323 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8609 (tp30) REVERT: C 196 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8114 (mm-30) REVERT: C 250 GLU cc_start: 0.8578 (pm20) cc_final: 0.8114 (pm20) REVERT: C 285 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8848 (mm-30) REVERT: E 11 GLU cc_start: 0.9117 (tt0) cc_final: 0.8541 (pm20) REVERT: E 32 LYS cc_start: 0.9212 (tppt) cc_final: 0.8901 (tppt) REVERT: D 112 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7520 (tm-30) REVERT: D 170 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8766 (pt0) REVERT: D 186 TYR cc_start: 0.8147 (m-80) cc_final: 0.7654 (m-10) REVERT: D 210 GLN cc_start: 0.8306 (tp40) cc_final: 0.8027 (tp40) REVERT: D 243 ARG cc_start: 0.8711 (tpp80) cc_final: 0.8330 (tpp80) REVERT: D 251 GLU cc_start: 0.9430 (tt0) cc_final: 0.8924 (tm-30) REVERT: D 255 ASP cc_start: 0.9430 (m-30) cc_final: 0.8706 (t70) REVERT: D 279 GLN cc_start: 0.9163 (tm-30) cc_final: 0.8705 (tm-30) outliers start: 24 outliers final: 21 residues processed: 157 average time/residue: 0.2341 time to fit residues: 47.5637 Evaluate side-chains 155 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 156 CYS 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 70 ASP Chi-restraints excluded: chain D residue 232 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 44 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 61 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 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 = 0.3480 r_free = 0.3480 target = 0.068588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.044230 restraints weight = 26423.329| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 4.43 r_work: 0.2654 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7704 Z= 0.185 Angle : 0.666 9.997 10505 Z= 0.342 Chirality : 0.045 0.159 1201 Planarity : 0.004 0.044 1360 Dihedral : 4.885 27.084 1034 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.07 % Allowed : 18.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.27), residues: 945 helix: 0.35 (1.36), residues: 18 sheet: -0.69 (0.27), residues: 341 loop : -0.21 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 52 HIS 0.004 0.001 HIS E 90 PHE 0.016 0.002 PHE C 172 TYR 0.014 0.001 TYR D 149 ARG 0.009 0.001 ARG D 150 Details of bonding type rmsd hydrogen bonds : bond 0.02972 ( 212) hydrogen bonds : angle 5.68372 ( 528) SS BOND : bond 0.00172 ( 4) SS BOND : angle 0.46676 ( 8) covalent geometry : bond 0.00417 ( 7700) covalent geometry : angle 0.66595 (10497) *********************** 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 161 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8149 (mt-10) REVERT: B 202 THR cc_start: 0.9497 (OUTLIER) cc_final: 0.9233 (p) REVERT: B 300 ASP cc_start: 0.9166 (t0) cc_final: 0.8603 (t0) REVERT: B 320 TYR cc_start: 0.9524 (p90) cc_final: 0.9291 (p90) REVERT: B 323 GLU cc_start: 0.9382 (tp30) cc_final: 0.8866 (tp30) REVERT: A 284 ASP cc_start: 0.9067 (p0) cc_final: 0.8850 (p0) REVERT: A 285 GLU cc_start: 0.9079 (mp0) cc_final: 0.8500 (mp0) REVERT: A 323 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8543 (tp30) REVERT: C 196 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8170 (mm-30) REVERT: C 250 GLU cc_start: 0.8561 (pm20) cc_final: 0.8073 (pm20) REVERT: C 285 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8839 (mm-30) REVERT: E 11 GLU cc_start: 0.9119 (tt0) cc_final: 0.8880 (pm20) REVERT: E 29 LYS cc_start: 0.8911 (pttp) cc_final: 0.8290 (ptmm) REVERT: E 32 LYS cc_start: 0.9203 (tppt) cc_final: 0.8988 (tppt) REVERT: E 91 PHE cc_start: 0.8884 (m-10) cc_final: 0.8603 (m-10) REVERT: E 99 LEU cc_start: 0.7715 (tp) cc_final: 0.7481 (mt) REVERT: D 130 MET cc_start: 0.7761 (mmt) cc_final: 0.7297 (mtt) REVERT: D 170 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8745 (pt0) REVERT: D 186 TYR cc_start: 0.8207 (m-80) cc_final: 0.7643 (m-10) REVERT: D 193 ARG cc_start: 0.8538 (mtp-110) cc_final: 0.7253 (ptm160) REVERT: D 210 GLN cc_start: 0.8394 (tp40) cc_final: 0.7978 (tp40) REVERT: D 243 ARG cc_start: 0.8735 (tpp80) cc_final: 0.8322 (tpp80) REVERT: D 251 GLU cc_start: 0.9442 (tt0) cc_final: 0.8932 (tm-30) REVERT: D 255 ASP cc_start: 0.9437 (m-30) cc_final: 0.8727 (t70) REVERT: D 279 GLN cc_start: 0.9191 (tm-30) cc_final: 0.8734 (tm-30) outliers start: 26 outliers final: 21 residues processed: 152 average time/residue: 0.2326 time to fit residues: 45.5448 Evaluate side-chains 153 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 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 70 ASP Chi-restraints excluded: chain D residue 232 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 18 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 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 = 0.3472 r_free = 0.3472 target = 0.068260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.043913 restraints weight = 26262.950| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 4.42 r_work: 0.2646 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7704 Z= 0.203 Angle : 0.675 10.513 10505 Z= 0.346 Chirality : 0.045 0.164 1201 Planarity : 0.004 0.042 1360 Dihedral : 4.942 27.133 1034 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.83 % Allowed : 18.16 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.27), residues: 945 helix: 0.24 (1.35), residues: 18 sheet: -0.62 (0.27), residues: 338 loop : -0.29 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 296 HIS 0.004 0.001 HIS E 90 PHE 0.017 0.002 PHE D 110 TYR 0.027 0.002 TYR E 106 ARG 0.007 0.001 ARG D 150 Details of bonding type rmsd hydrogen bonds : bond 0.03038 ( 212) hydrogen bonds : angle 5.70457 ( 528) SS BOND : bond 0.00187 ( 4) SS BOND : angle 0.57419 ( 8) covalent geometry : bond 0.00458 ( 7700) covalent geometry : angle 0.67481 (10497) *********************** 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 159 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8137 (mt-10) REVERT: B 300 ASP cc_start: 0.9169 (t0) cc_final: 0.8606 (t0) REVERT: B 320 TYR cc_start: 0.9529 (p90) cc_final: 0.9275 (p90) REVERT: B 323 GLU cc_start: 0.9397 (tp30) cc_final: 0.8881 (tp30) REVERT: A 284 ASP cc_start: 0.9059 (p0) cc_final: 0.8842 (p0) REVERT: A 285 GLU cc_start: 0.9071 (mp0) cc_final: 0.8479 (mp0) REVERT: A 323 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8539 (tp30) REVERT: C 196 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8216 (mm-30) REVERT: C 250 GLU cc_start: 0.8581 (pm20) cc_final: 0.8078 (pm20) REVERT: C 285 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8820 (mm-30) REVERT: E 11 GLU cc_start: 0.9111 (tt0) cc_final: 0.8891 (pm20) REVERT: E 29 LYS cc_start: 0.8923 (pttp) cc_final: 0.8292 (ptmm) REVERT: E 32 LYS cc_start: 0.9208 (tppt) cc_final: 0.8997 (tppt) REVERT: E 99 LEU cc_start: 0.7883 (tp) cc_final: 0.7627 (mt) REVERT: D 130 MET cc_start: 0.7761 (mmt) cc_final: 0.7321 (mtt) REVERT: D 170 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8768 (pt0) REVERT: D 186 TYR cc_start: 0.8230 (m-80) cc_final: 0.7633 (m-10) REVERT: D 193 ARG cc_start: 0.8571 (mtp-110) cc_final: 0.7243 (ptm160) REVERT: D 210 GLN cc_start: 0.8417 (tp40) cc_final: 0.7965 (tp40) REVERT: D 243 ARG cc_start: 0.8713 (tpp80) cc_final: 0.8309 (tpp80) REVERT: D 255 ASP cc_start: 0.9431 (m-30) cc_final: 0.8740 (t70) REVERT: D 279 GLN cc_start: 0.9225 (tm-30) cc_final: 0.8770 (tm-30) outliers start: 24 outliers final: 22 residues processed: 150 average time/residue: 0.2540 time to fit residues: 49.4636 Evaluate side-chains 154 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 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 10 MET Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain D residue 232 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 6 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 69 optimal weight: 40.0000 chunk 26 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 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 = 0.3460 r_free = 0.3460 target = 0.067767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.043209 restraints weight = 26592.587| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 4.47 r_work: 0.2626 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7704 Z= 0.222 Angle : 0.696 10.344 10505 Z= 0.356 Chirality : 0.045 0.158 1201 Planarity : 0.004 0.044 1360 Dihedral : 4.968 27.560 1034 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.95 % Allowed : 18.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.27), residues: 945 helix: -1.12 (0.84), residues: 36 sheet: -0.60 (0.27), residues: 338 loop : -0.17 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 296 HIS 0.003 0.001 HIS E 90 PHE 0.023 0.002 PHE E 91 TYR 0.025 0.002 TYR E 106 ARG 0.007 0.001 ARG A 266 Details of bonding type rmsd hydrogen bonds : bond 0.03075 ( 212) hydrogen bonds : angle 5.74486 ( 528) SS BOND : bond 0.00215 ( 4) SS BOND : angle 0.60426 ( 8) covalent geometry : bond 0.00499 ( 7700) covalent geometry : angle 0.69652 (10497) ********************** 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 157 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8150 (mt-10) REVERT: B 300 ASP cc_start: 0.9177 (t0) cc_final: 0.8605 (t0) REVERT: B 320 TYR cc_start: 0.9537 (p90) cc_final: 0.9280 (p90) REVERT: B 323 GLU cc_start: 0.9403 (tp30) cc_final: 0.8868 (tp30) REVERT: A 284 ASP cc_start: 0.9094 (p0) cc_final: 0.8882 (p0) REVERT: A 285 GLU cc_start: 0.9099 (mp0) cc_final: 0.8547 (mp0) REVERT: A 323 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8521 (tp30) REVERT: C 196 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8234 (mm-30) REVERT: C 250 GLU cc_start: 0.8599 (pm20) cc_final: 0.8096 (pm20) REVERT: C 285 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8801 (mm-30) REVERT: E 11 GLU cc_start: 0.9077 (tt0) cc_final: 0.8540 (pm20) REVERT: E 32 LYS cc_start: 0.9190 (tppt) cc_final: 0.8878 (tppt) REVERT: D 130 MET cc_start: 0.7761 (mmt) cc_final: 0.7367 (mtt) REVERT: D 170 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8761 (pt0) REVERT: D 186 TYR cc_start: 0.8250 (m-80) cc_final: 0.7607 (m-10) REVERT: D 193 ARG cc_start: 0.8523 (mtp-110) cc_final: 0.7148 (ptm160) REVERT: D 210 GLN cc_start: 0.8393 (tp40) cc_final: 0.7953 (tp40) REVERT: D 243 ARG cc_start: 0.8733 (tpp80) cc_final: 0.8365 (tpp80) REVERT: D 255 ASP cc_start: 0.9442 (m-30) cc_final: 0.8735 (t70) REVERT: D 279 GLN cc_start: 0.9240 (tm-30) cc_final: 0.8788 (tm-30) outliers start: 25 outliers final: 22 residues processed: 150 average time/residue: 0.2400 time to fit residues: 46.2178 Evaluate side-chains 153 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 147 ILE 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 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 D residue 232 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 46 optimal weight: 0.0970 chunk 67 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 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 = 0.3475 r_free = 0.3475 target = 0.068461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.044208 restraints weight = 26055.849| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 4.39 r_work: 0.2655 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7704 Z= 0.185 Angle : 0.682 10.365 10505 Z= 0.349 Chirality : 0.045 0.153 1201 Planarity : 0.004 0.046 1360 Dihedral : 4.960 28.250 1034 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.83 % Allowed : 18.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.27), residues: 945 helix: 0.15 (1.32), residues: 18 sheet: -0.63 (0.27), residues: 344 loop : -0.22 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 296 HIS 0.003 0.001 HIS E 90 PHE 0.017 0.002 PHE C 172 TYR 0.027 0.002 TYR E 106 ARG 0.007 0.001 ARG A 266 Details of bonding type rmsd hydrogen bonds : bond 0.02950 ( 212) hydrogen bonds : angle 5.71406 ( 528) SS BOND : bond 0.00173 ( 4) SS BOND : angle 0.52211 ( 8) covalent geometry : bond 0.00417 ( 7700) covalent geometry : angle 0.68250 (10497) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5018.99 seconds wall clock time: 87 minutes 25.04 seconds (5245.04 seconds total)