Starting phenix.real_space_refine on Tue Mar 3 11:50:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ji0_22341/03_2026/7ji0_22341.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ji0_22341/03_2026/7ji0_22341.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ji0_22341/03_2026/7ji0_22341.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ji0_22341/03_2026/7ji0_22341.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ji0_22341/03_2026/7ji0_22341.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ji0_22341/03_2026/7ji0_22341.map" } resolution = 2.95 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= 0.099 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 16 5.16 5 C 2298 2.51 5 N 558 2.21 5 O 684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3556 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1722 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 2, 'TRANS': 205} Chain breaks: 1 Chain: "B" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1722 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 2, 'TRANS': 205} Chain breaks: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 56 Classifications: {'peptide': 8} Modifications used: {'COO': 1} Link IDs: {'TRANS': 7} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 56 Classifications: {'peptide': 8} Modifications used: {'COO': 1} Link IDs: {'TRANS': 7} Time building chain proxies: 0.87, per 1000 atoms: 0.24 Number of scatterers: 3556 At special positions: 0 Unit cell: (78.888, 73.698, 63.318, 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 16 16.00 O 684 8.00 N 558 7.00 C 2298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 92.1 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 836 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 73.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 74 through 89 removed outlier: 3.854A pdb=" N ASN A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 123 removed outlier: 3.701A pdb=" N THR A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET A 114 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET A 122 " --> pdb=" O ILE A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 141 Processing helix chain 'A' and resid 147 through 156 removed outlier: 3.511A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 174 removed outlier: 3.698A pdb=" N LEU A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 204 removed outlier: 3.950A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 221 removed outlier: 3.513A pdb=" N PHE A 211 " --> pdb=" O PHE A 207 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 245 removed outlier: 3.518A pdb=" N TRP A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 264 Processing helix chain 'A' and resid 266 through 282 removed outlier: 3.873A pdb=" N LEU A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N HIS A 272 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS A 276 " --> pdb=" O HIS A 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 89 removed outlier: 3.754A pdb=" N ASN B 78 " --> pdb=" O GLU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.757A pdb=" N ILE B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN B 96 " --> pdb=" O ILE B 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 91 through 96' Processing helix chain 'B' and resid 108 through 120 Processing helix chain 'B' and resid 129 through 142 removed outlier: 3.677A pdb=" N TYR B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 156 removed outlier: 3.787A pdb=" N ILE B 152 " --> pdb=" O TYR B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.717A pdb=" N LEU B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 204 removed outlier: 3.983A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 190 " --> pdb=" O ASN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 221 removed outlier: 3.631A pdb=" N PHE B 211 " --> pdb=" O PHE B 207 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 245 Processing helix chain 'B' and resid 247 through 264 removed outlier: 4.151A pdb=" N ILE B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU B 252 " --> pdb=" O THR B 248 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 282 removed outlier: 3.503A pdb=" N LYS B 279 " --> pdb=" O ILE B 275 " (cutoff:3.500A) 193 hydrogen bonds defined for protein. 579 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.38 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1120 1.34 - 1.46: 699 1.46 - 1.57: 1771 1.57 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 3616 Sorted by residual: bond pdb=" CB ILE B 189 " pdb=" CG2 ILE B 189 " ideal model delta sigma weight residual 1.521 1.502 0.019 3.30e-02 9.18e+02 3.40e-01 bond pdb=" CG PRO A 109 " pdb=" CD PRO A 109 " ideal model delta sigma weight residual 1.503 1.486 0.017 3.40e-02 8.65e+02 2.45e-01 bond pdb=" CA LEU A 269 " pdb=" CB LEU A 269 " ideal model delta sigma weight residual 1.537 1.528 0.008 1.67e-02 3.59e+03 2.44e-01 bond pdb=" CZ ARG A 159 " pdb=" NH2 ARG A 159 " ideal model delta sigma weight residual 1.330 1.324 0.006 1.30e-02 5.92e+03 2.40e-01 bond pdb=" CZ ARG B 159 " pdb=" NH2 ARG B 159 " ideal model delta sigma weight residual 1.330 1.324 0.006 1.30e-02 5.92e+03 2.34e-01 ... (remaining 3611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 4662 0.98 - 1.95: 193 1.95 - 2.93: 20 2.93 - 3.90: 9 3.90 - 4.88: 4 Bond angle restraints: 4888 Sorted by residual: angle pdb=" N LEU A 269 " pdb=" CA LEU A 269 " pdb=" C LEU A 269 " ideal model delta sigma weight residual 114.04 109.16 4.88 1.24e+00 6.50e-01 1.55e+01 angle pdb=" C ILE A 92 " pdb=" N ASN A 93 " pdb=" CA ASN A 93 " ideal model delta sigma weight residual 121.54 126.27 -4.73 1.91e+00 2.74e-01 6.14e+00 angle pdb=" C ASN B 104 " pdb=" N TYR B 105 " pdb=" CA TYR B 105 " ideal model delta sigma weight residual 121.54 125.17 -3.63 1.91e+00 2.74e-01 3.61e+00 angle pdb=" CA LEU A 269 " pdb=" C LEU A 269 " pdb=" N LYS A 270 " ideal model delta sigma weight residual 118.58 116.45 2.13 1.26e+00 6.30e-01 2.86e+00 angle pdb=" C GLY B 155 " pdb=" N ASN B 156 " pdb=" CA ASN B 156 " ideal model delta sigma weight residual 122.27 119.22 3.05 1.85e+00 2.92e-01 2.71e+00 ... (remaining 4883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 2004 17.23 - 34.45: 121 34.45 - 51.68: 34 51.68 - 68.90: 3 68.90 - 86.13: 6 Dihedral angle restraints: 2168 sinusoidal: 880 harmonic: 1288 Sorted by residual: dihedral pdb=" CA ASN A 94 " pdb=" C ASN A 94 " pdb=" N ILE A 95 " pdb=" CA ILE A 95 " ideal model delta harmonic sigma weight residual 180.00 163.46 16.54 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CB GLU B 74 " pdb=" CG GLU B 74 " pdb=" CD GLU B 74 " pdb=" OE1 GLU B 74 " ideal model delta sinusoidal sigma weight residual 0.00 86.13 -86.13 1 3.00e+01 1.11e-03 9.95e+00 dihedral pdb=" CB GLU A 74 " pdb=" CG GLU A 74 " pdb=" CD GLU A 74 " pdb=" OE1 GLU A 74 " ideal model delta sinusoidal sigma weight residual 0.00 84.80 -84.80 1 3.00e+01 1.11e-03 9.70e+00 ... (remaining 2165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 292 0.026 - 0.053: 179 0.053 - 0.079: 77 0.079 - 0.105: 15 0.105 - 0.132: 5 Chirality restraints: 568 Sorted by residual: chirality pdb=" CA PRO B 109 " pdb=" N PRO B 109 " pdb=" C PRO B 109 " pdb=" CB PRO B 109 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA PRO A 109 " pdb=" N PRO A 109 " pdb=" C PRO A 109 " pdb=" CB PRO A 109 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE A 92 " pdb=" N ILE A 92 " pdb=" C ILE A 92 " pdb=" CB ILE A 92 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 565 not shown) Planarity restraints: 610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 127 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO A 128 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 128 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 128 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 273 " 0.005 2.00e-02 2.50e+03 1.03e-02 1.05e+00 pdb=" C TYR B 273 " -0.018 2.00e-02 2.50e+03 pdb=" O TYR B 273 " 0.007 2.00e-02 2.50e+03 pdb=" N THR B 274 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 232 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" C VAL A 232 " -0.017 2.00e-02 2.50e+03 pdb=" O VAL A 232 " 0.006 2.00e-02 2.50e+03 pdb=" N PHE A 233 " 0.006 2.00e-02 2.50e+03 ... (remaining 607 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 651 2.77 - 3.30: 3491 3.30 - 3.83: 5341 3.83 - 4.37: 6765 4.37 - 4.90: 11609 Nonbonded interactions: 27857 Sorted by model distance: nonbonded pdb=" O LYS B 279 " pdb=" ND2 ASN B 283 " model vdw 2.233 3.120 nonbonded pdb=" O LYS A 279 " pdb=" ND2 ASN A 283 " model vdw 2.249 3.120 nonbonded pdb=" OD2 ASP B 123 " pdb=" OG SER B 125 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR A 82 " pdb=" ND2 ASN A 94 " model vdw 2.303 3.120 nonbonded pdb=" O ASP B 278 " pdb=" ND2 ASN B 282 " model vdw 2.335 3.120 ... (remaining 27852 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.440 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.120 Find NCS groups from input model: 0.050 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:9.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3616 Z= 0.151 Angle : 0.475 4.879 4888 Z= 0.281 Chirality : 0.038 0.132 568 Planarity : 0.003 0.029 610 Dihedral : 12.973 86.129 1332 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.91 % Allowed : 4.93 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.33), residues: 420 helix: -1.46 (0.24), residues: 330 sheet: None (None), residues: 0 loop : -3.52 (0.47), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 84 TYR 0.011 0.001 TYR A 149 PHE 0.009 0.001 PHE B 277 TRP 0.003 0.001 TRP A 245 HIS 0.002 0.000 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 3616) covalent geometry : angle 0.47536 ( 4888) hydrogen bonds : bond 0.13570 ( 193) hydrogen bonds : angle 4.36158 ( 579) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6804 (tp30) REVERT: A 94 ASN cc_start: 0.7643 (OUTLIER) cc_final: 0.7348 (t0) REVERT: A 107 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8053 (mp) REVERT: A 141 PHE cc_start: 0.8272 (m-80) cc_final: 0.8063 (m-80) REVERT: A 142 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7683 (mptt) REVERT: A 185 THR cc_start: 0.8570 (t) cc_final: 0.8293 (m) REVERT: A 189 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8003 (tt) REVERT: B 94 ASN cc_start: 0.7879 (OUTLIER) cc_final: 0.7635 (t0) REVERT: B 122 MET cc_start: 0.8162 (mtp) cc_final: 0.7911 (mtp) REVERT: B 173 MET cc_start: 0.8153 (mmm) cc_final: 0.7740 (tpp) REVERT: B 186 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7987 (t0) REVERT: B 252 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7226 (mm-30) outliers start: 24 outliers final: 5 residues processed: 74 average time/residue: 0.5208 time to fit residues: 39.7571 Evaluate side-chains 54 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 252 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.0050 chunk 37 optimal weight: 0.0970 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 186 ASN A 230 GLN B 175 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.125813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.110662 restraints weight = 4490.546| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.74 r_work: 0.3283 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 3616 Z= 0.100 Angle : 0.435 3.554 4888 Z= 0.242 Chirality : 0.037 0.126 568 Planarity : 0.003 0.028 610 Dihedral : 10.780 86.953 493 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.19 % Allowed : 8.37 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.39), residues: 420 helix: -0.02 (0.28), residues: 328 sheet: None (None), residues: 0 loop : -2.79 (0.51), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 188 TYR 0.009 0.001 TYR B 87 PHE 0.009 0.001 PHE B 277 TRP 0.002 0.000 TRP B 146 HIS 0.001 0.000 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 3616) covalent geometry : angle 0.43512 ( 4888) hydrogen bonds : bond 0.03753 ( 193) hydrogen bonds : angle 3.10544 ( 579) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7207 (tm-30) REVERT: A 94 ASN cc_start: 0.7656 (OUTLIER) cc_final: 0.7436 (t0) REVERT: A 141 PHE cc_start: 0.8325 (m-80) cc_final: 0.8069 (m-80) REVERT: A 142 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7814 (mptt) REVERT: A 185 THR cc_start: 0.8687 (t) cc_final: 0.8461 (m) REVERT: A 189 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.7970 (tt) REVERT: B 94 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7547 (t0) REVERT: B 173 MET cc_start: 0.8647 (mmm) cc_final: 0.8181 (tpp) REVERT: B 252 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7906 (mm-30) outliers start: 17 outliers final: 4 residues processed: 62 average time/residue: 0.5067 time to fit residues: 32.4177 Evaluate side-chains 49 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 252 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN B 209 ASN B 223 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.109424 restraints weight = 4499.829| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.73 r_work: 0.3263 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3616 Z= 0.124 Angle : 0.440 3.669 4888 Z= 0.241 Chirality : 0.038 0.124 568 Planarity : 0.003 0.030 610 Dihedral : 10.303 86.196 488 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.69 % Allowed : 9.36 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.40), residues: 420 helix: 0.56 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -2.19 (0.57), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 188 TYR 0.020 0.002 TYR B 148 PHE 0.008 0.001 PHE B 277 TRP 0.003 0.001 TRP A 245 HIS 0.001 0.000 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 3616) covalent geometry : angle 0.44000 ( 4888) hydrogen bonds : bond 0.04041 ( 193) hydrogen bonds : angle 3.03903 ( 579) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7280 (tm-30) REVERT: A 94 ASN cc_start: 0.7550 (OUTLIER) cc_final: 0.7347 (t0) REVERT: A 141 PHE cc_start: 0.8389 (m-80) cc_final: 0.8124 (m-80) REVERT: A 142 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7702 (mptm) REVERT: A 185 THR cc_start: 0.8700 (t) cc_final: 0.8474 (m) REVERT: A 189 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7956 (tt) REVERT: B 94 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7587 (t0) REVERT: B 111 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8144 (mt-10) REVERT: B 131 ASP cc_start: 0.7629 (t0) cc_final: 0.7400 (t0) REVERT: B 173 MET cc_start: 0.8640 (mmm) cc_final: 0.8172 (tpp) REVERT: B 252 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7790 (mm-30) outliers start: 15 outliers final: 4 residues processed: 54 average time/residue: 0.5444 time to fit residues: 30.3546 Evaluate side-chains 47 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 252 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.124126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.108930 restraints weight = 4531.302| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.76 r_work: 0.3250 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3616 Z= 0.142 Angle : 0.473 7.673 4888 Z= 0.253 Chirality : 0.040 0.205 568 Planarity : 0.003 0.030 610 Dihedral : 10.337 86.927 488 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.69 % Allowed : 10.10 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.41), residues: 420 helix: 0.76 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.81 (0.60), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 84 TYR 0.010 0.001 TYR B 87 PHE 0.008 0.001 PHE B 277 TRP 0.002 0.001 TRP B 146 HIS 0.001 0.000 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 3616) covalent geometry : angle 0.47256 ( 4888) hydrogen bonds : bond 0.04199 ( 193) hydrogen bonds : angle 3.06167 ( 579) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7876 (pttm) cc_final: 0.7138 (tmtm) REVERT: A 74 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7248 (tp30) REVERT: A 81 GLN cc_start: 0.8274 (mt0) cc_final: 0.8066 (mp10) REVERT: A 94 ASN cc_start: 0.7543 (OUTLIER) cc_final: 0.7309 (t0) REVERT: A 141 PHE cc_start: 0.8414 (m-80) cc_final: 0.8161 (m-80) REVERT: A 142 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7679 (mptm) REVERT: B 94 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7547 (t0) REVERT: B 131 ASP cc_start: 0.7672 (t0) cc_final: 0.7469 (t0) REVERT: B 173 MET cc_start: 0.8720 (mmm) cc_final: 0.8268 (tpp) REVERT: B 252 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7795 (mm-30) outliers start: 15 outliers final: 3 residues processed: 51 average time/residue: 0.6247 time to fit residues: 32.6521 Evaluate side-chains 45 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 252 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.124559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.109493 restraints weight = 4512.890| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.77 r_work: 0.3262 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3616 Z= 0.119 Angle : 0.445 6.412 4888 Z= 0.240 Chirality : 0.039 0.187 568 Planarity : 0.002 0.030 610 Dihedral : 9.928 86.493 483 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.46 % Allowed : 11.08 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.41), residues: 420 helix: 1.02 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.32 (0.63), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 84 TYR 0.010 0.001 TYR B 87 PHE 0.009 0.001 PHE B 277 TRP 0.002 0.000 TRP B 146 HIS 0.001 0.000 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 3616) covalent geometry : angle 0.44462 ( 4888) hydrogen bonds : bond 0.03913 ( 193) hydrogen bonds : angle 2.94009 ( 579) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7858 (pttm) cc_final: 0.7007 (tmtm) REVERT: A 74 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7176 (tp30) REVERT: A 81 GLN cc_start: 0.8233 (mt0) cc_final: 0.8002 (mp10) REVERT: A 94 ASN cc_start: 0.7499 (OUTLIER) cc_final: 0.7183 (t160) REVERT: A 141 PHE cc_start: 0.8385 (m-80) cc_final: 0.8127 (m-80) REVERT: A 142 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7646 (mptm) REVERT: B 131 ASP cc_start: 0.7603 (t0) cc_final: 0.7387 (t0) REVERT: B 252 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7825 (mm-30) outliers start: 10 outliers final: 3 residues processed: 47 average time/residue: 0.6638 time to fit residues: 32.0742 Evaluate side-chains 43 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 252 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.0270 chunk 29 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.0570 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 0.0870 chunk 24 optimal weight: 0.9980 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.126188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.109090 restraints weight = 4421.880| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.08 r_work: 0.3198 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3616 Z= 0.079 Angle : 0.418 9.424 4888 Z= 0.222 Chirality : 0.037 0.171 568 Planarity : 0.002 0.032 610 Dihedral : 9.628 85.746 481 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.46 % Allowed : 11.33 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.42), residues: 420 helix: 1.40 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.98 (0.64), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 84 TYR 0.024 0.001 TYR B 148 PHE 0.008 0.001 PHE B 277 TRP 0.007 0.001 TRP B 146 HIS 0.002 0.000 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00170 ( 3616) covalent geometry : angle 0.41811 ( 4888) hydrogen bonds : bond 0.03051 ( 193) hydrogen bonds : angle 2.72283 ( 579) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7154 (tp30) REVERT: A 81 GLN cc_start: 0.7990 (mt0) cc_final: 0.7784 (mp10) REVERT: A 94 ASN cc_start: 0.7495 (OUTLIER) cc_final: 0.7008 (t160) REVERT: A 141 PHE cc_start: 0.8296 (m-80) cc_final: 0.8017 (m-80) REVERT: A 142 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7362 (mptm) REVERT: A 189 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7695 (tt) REVERT: B 252 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7732 (mm-30) outliers start: 10 outliers final: 1 residues processed: 44 average time/residue: 0.6366 time to fit residues: 28.8202 Evaluate side-chains 42 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 252 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 0.0370 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.1980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.124928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.107997 restraints weight = 4458.012| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.05 r_work: 0.3181 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3616 Z= 0.088 Angle : 0.397 4.692 4888 Z= 0.216 Chirality : 0.037 0.148 568 Planarity : 0.002 0.031 610 Dihedral : 8.924 86.647 477 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.22 % Allowed : 11.82 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.42), residues: 420 helix: 1.57 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.90 (0.63), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 244 TYR 0.020 0.001 TYR B 148 PHE 0.008 0.001 PHE B 277 TRP 0.001 0.000 TRP A 245 HIS 0.001 0.000 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 3616) covalent geometry : angle 0.39654 ( 4888) hydrogen bonds : bond 0.03390 ( 193) hydrogen bonds : angle 2.72415 ( 579) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7806 (pttm) cc_final: 0.6819 (tmtm) REVERT: A 74 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7146 (tp30) REVERT: A 81 GLN cc_start: 0.8011 (mt0) cc_final: 0.7768 (mp10) REVERT: A 94 ASN cc_start: 0.7448 (OUTLIER) cc_final: 0.6994 (t0) REVERT: A 141 PHE cc_start: 0.8360 (m-80) cc_final: 0.8078 (m-80) REVERT: A 142 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7384 (mptm) REVERT: A 189 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7706 (tt) REVERT: B 252 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7753 (mm-30) outliers start: 9 outliers final: 1 residues processed: 46 average time/residue: 0.6452 time to fit residues: 30.5201 Evaluate side-chains 44 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 252 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 3 optimal weight: 0.0970 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.108348 restraints weight = 4442.902| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.04 r_work: 0.3179 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 3616 Z= 0.100 Angle : 0.413 4.412 4888 Z= 0.228 Chirality : 0.037 0.139 568 Planarity : 0.002 0.032 610 Dihedral : 8.893 86.084 477 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.72 % Allowed : 13.05 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.42), residues: 420 helix: 1.68 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -0.89 (0.62), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 188 TYR 0.008 0.001 TYR B 87 PHE 0.008 0.001 PHE B 277 TRP 0.001 0.000 TRP A 245 HIS 0.001 0.000 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 3616) covalent geometry : angle 0.41275 ( 4888) hydrogen bonds : bond 0.03414 ( 193) hydrogen bonds : angle 2.73504 ( 579) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7819 (pttm) cc_final: 0.6958 (tmtm) REVERT: A 74 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7138 (tp30) REVERT: A 81 GLN cc_start: 0.8078 (mt0) cc_final: 0.7860 (mp10) REVERT: A 94 ASN cc_start: 0.7469 (OUTLIER) cc_final: 0.7020 (t0) REVERT: A 141 PHE cc_start: 0.8397 (m-80) cc_final: 0.8105 (m-80) REVERT: A 142 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7438 (mptm) REVERT: A 189 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7711 (tt) REVERT: B 252 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7737 (mm-30) outliers start: 7 outliers final: 1 residues processed: 44 average time/residue: 0.6091 time to fit residues: 27.5402 Evaluate side-chains 42 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 252 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.0470 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.123089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.106167 restraints weight = 4329.461| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.02 r_work: 0.3161 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 3616 Z= 0.120 Angle : 0.436 4.377 4888 Z= 0.239 Chirality : 0.038 0.146 568 Planarity : 0.002 0.031 610 Dihedral : 9.002 86.518 477 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.72 % Allowed : 13.05 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.41), residues: 420 helix: 1.57 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.31 (0.60), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 188 TYR 0.009 0.001 TYR B 87 PHE 0.008 0.001 PHE B 277 TRP 0.001 0.000 TRP A 146 HIS 0.001 0.000 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3616) covalent geometry : angle 0.43634 ( 4888) hydrogen bonds : bond 0.03887 ( 193) hydrogen bonds : angle 2.84408 ( 579) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7788 (pttm) cc_final: 0.6987 (tmtm) REVERT: A 74 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7151 (tp30) REVERT: A 81 GLN cc_start: 0.8102 (mt0) cc_final: 0.7870 (mp10) REVERT: A 94 ASN cc_start: 0.7470 (OUTLIER) cc_final: 0.7028 (t0) REVERT: A 141 PHE cc_start: 0.8429 (m-80) cc_final: 0.8148 (m-80) REVERT: A 142 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7420 (mptm) REVERT: A 189 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7730 (tt) REVERT: B 252 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7740 (mm-30) outliers start: 7 outliers final: 2 residues processed: 44 average time/residue: 0.6360 time to fit residues: 28.7916 Evaluate side-chains 45 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 252 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.0070 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.123384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.106354 restraints weight = 4402.281| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.03 r_work: 0.3161 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 3616 Z= 0.115 Angle : 0.430 4.316 4888 Z= 0.235 Chirality : 0.038 0.143 568 Planarity : 0.002 0.031 610 Dihedral : 8.973 85.637 477 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.72 % Allowed : 12.81 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.41), residues: 420 helix: 1.59 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.30 (0.59), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 188 TYR 0.009 0.001 TYR B 87 PHE 0.008 0.001 PHE B 277 TRP 0.001 0.000 TRP B 146 HIS 0.001 0.000 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 3616) covalent geometry : angle 0.42971 ( 4888) hydrogen bonds : bond 0.03773 ( 193) hydrogen bonds : angle 2.83081 ( 579) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7710 (pttm) cc_final: 0.6925 (tmtm) REVERT: A 74 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7106 (tp30) REVERT: A 81 GLN cc_start: 0.8105 (mt0) cc_final: 0.7882 (mp10) REVERT: A 94 ASN cc_start: 0.7384 (OUTLIER) cc_final: 0.6936 (t160) REVERT: A 141 PHE cc_start: 0.8437 (m-80) cc_final: 0.8223 (m-80) REVERT: A 142 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7436 (mptm) REVERT: A 189 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7715 (tt) REVERT: B 252 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7735 (mm-30) outliers start: 7 outliers final: 2 residues processed: 44 average time/residue: 0.5959 time to fit residues: 26.9478 Evaluate side-chains 45 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 252 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 3 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 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 = 0.3552 r_free = 0.3552 target = 0.124860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.109809 restraints weight = 4454.446| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.74 r_work: 0.3254 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 3616 Z= 0.132 Angle : 0.449 4.333 4888 Z= 0.245 Chirality : 0.039 0.150 568 Planarity : 0.003 0.031 610 Dihedral : 9.044 86.418 477 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.72 % Allowed : 12.81 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.41), residues: 420 helix: 1.56 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.32 (0.59), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 188 TYR 0.009 0.001 TYR B 87 PHE 0.008 0.001 PHE B 277 TRP 0.001 0.000 TRP A 146 HIS 0.001 0.000 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 3616) covalent geometry : angle 0.44930 ( 4888) hydrogen bonds : bond 0.04079 ( 193) hydrogen bonds : angle 2.89768 ( 579) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1244.88 seconds wall clock time: 21 minutes 53.54 seconds (1313.54 seconds total)