Starting phenix.real_space_refine on Wed Mar 5 20:57:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ji0_22341/03_2025/7ji0_22341.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ji0_22341/03_2025/7ji0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ji0_22341/03_2025/7ji0_22341.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ji0_22341/03_2025/7ji0_22341.map" model { file = "/net/cci-nas-00/data/ceres_data/7ji0_22341/03_2025/7ji0_22341.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ji0_22341/03_2025/7ji0_22341.cif" } resolution = 2.95 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= 0.099 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 2.58, per 1000 atoms: 0.73 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: 0.70 Conformation dependent library (CDL) restraints added in 349.5 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: 0.30 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: 0.86 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 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: 0.02 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: 1.360 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.900 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:14.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.840 ------------------------------------------------------------------------------- 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= 0.213 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 (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: -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 TRP 0.003 0.001 TRP A 245 HIS 0.002 0.000 HIS A 276 PHE 0.009 0.001 PHE B 277 TYR 0.011 0.001 TYR A 149 ARG 0.002 0.000 ARG B 84 *********************** 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 : 0.403 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: 0.8385 (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: 0.8569 (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: 1.1100 time to fit residues: 84.8692 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 : 0.410 ------------------------------------------------------------------------------- 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 33 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 209 ASN A 230 GLN B 175 ASN B 209 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.121878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.106723 restraints weight = 4453.930| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.72 r_work: 0.3234 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3616 Z= 0.289 Angle : 0.524 4.540 4888 Z= 0.285 Chirality : 0.041 0.144 568 Planarity : 0.003 0.030 610 Dihedral : 11.060 87.143 493 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.19 % Allowed : 8.87 % 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 (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: -1.30 (0.38), residues: 420 helix: -0.25 (0.27), residues: 330 sheet: None (None), residues: 0 loop : -2.81 (0.53), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 146 HIS 0.001 0.001 HIS A 276 PHE 0.009 0.002 PHE A 211 TYR 0.012 0.002 TYR B 87 ARG 0.002 0.000 ARG A 188 *********************** 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 63 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7837 (pttm) cc_final: 0.7176 (tmtm) REVERT: A 74 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: A 94 ASN cc_start: 0.7800 (OUTLIER) cc_final: 0.7517 (t0) REVERT: A 141 PHE cc_start: 0.8452 (m-80) cc_final: 0.8249 (m-80) REVERT: A 142 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7865 (mptt) REVERT: A 185 THR cc_start: 0.8718 (t) cc_final: 0.8453 (m) REVERT: A 189 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.7995 (tt) REVERT: B 94 ASN cc_start: 0.7763 (OUTLIER) cc_final: 0.7463 (t0) REVERT: B 173 MET cc_start: 0.8710 (mmm) cc_final: 0.8303 (tpp) REVERT: B 252 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7933 (mm-30) outliers start: 17 outliers final: 4 residues processed: 61 average time/residue: 1.0990 time to fit residues: 69.4134 Evaluate side-chains 51 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.123807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.108755 restraints weight = 4428.583| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.72 r_work: 0.3261 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3616 Z= 0.195 Angle : 0.458 3.855 4888 Z= 0.252 Chirality : 0.038 0.126 568 Planarity : 0.003 0.030 610 Dihedral : 10.484 86.361 488 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.69 % Allowed : 9.85 % 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 (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: -0.37 (0.40), residues: 420 helix: 0.37 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -2.35 (0.57), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 146 HIS 0.001 0.000 HIS A 276 PHE 0.009 0.001 PHE B 277 TYR 0.012 0.001 TYR B 148 ARG 0.002 0.000 ARG A 84 *********************** 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 61 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7237 (tm-30) REVERT: A 94 ASN cc_start: 0.7653 (OUTLIER) cc_final: 0.7435 (t0) REVERT: A 141 PHE cc_start: 0.8399 (m-80) cc_final: 0.8184 (m-80) REVERT: A 142 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7784 (mptt) REVERT: A 185 THR cc_start: 0.8716 (t) cc_final: 0.8470 (m) REVERT: A 189 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.7934 (tt) REVERT: B 94 ASN cc_start: 0.7743 (OUTLIER) cc_final: 0.7462 (t0) REVERT: B 111 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8139 (mt-10) REVERT: B 131 ASP cc_start: 0.7553 (t0) cc_final: 0.7281 (t0) REVERT: B 173 MET cc_start: 0.8702 (mmm) cc_final: 0.8264 (tpp) REVERT: B 252 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7810 (mm-30) outliers start: 15 outliers final: 4 residues processed: 59 average time/residue: 1.2402 time to fit residues: 75.5382 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 : 0.385 ------------------------------------------------------------------------------- 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 12 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN B 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.124054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.108983 restraints weight = 4524.989| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.73 r_work: 0.3263 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3616 Z= 0.194 Angle : 0.467 7.753 4888 Z= 0.252 Chirality : 0.039 0.208 568 Planarity : 0.003 0.031 610 Dihedral : 10.418 86.860 488 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.96 % Allowed : 10.34 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.15 (0.40), residues: 420 helix: 0.69 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -1.91 (0.60), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 146 HIS 0.001 0.000 HIS A 276 PHE 0.009 0.001 PHE B 277 TYR 0.010 0.001 TYR B 87 ARG 0.001 0.000 ARG A 84 *********************** 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: 12 poor density : 41 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7898 (pttm) cc_final: 0.7169 (tmtm) REVERT: A 74 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7264 (tm-30) REVERT: A 81 GLN cc_start: 0.8227 (mt0) cc_final: 0.7964 (mp10) REVERT: A 94 ASN cc_start: 0.7564 (OUTLIER) cc_final: 0.7318 (t0) REVERT: A 141 PHE cc_start: 0.8410 (m-80) cc_final: 0.8156 (m-80) REVERT: A 142 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7669 (mptm) REVERT: B 111 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8137 (mt-10) REVERT: B 131 ASP cc_start: 0.7666 (t0) cc_final: 0.7410 (t0) REVERT: B 173 MET cc_start: 0.8641 (mmm) cc_final: 0.8180 (tpp) REVERT: B 252 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7801 (mm-30) outliers start: 12 outliers final: 3 residues processed: 51 average time/residue: 1.2943 time to fit residues: 68.1192 Evaluate side-chains 47 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 143 VAL 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 22 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 3 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.125174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.110208 restraints weight = 4503.058| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.72 r_work: 0.3286 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3616 Z= 0.157 Angle : 0.441 6.415 4888 Z= 0.239 Chirality : 0.039 0.189 568 Planarity : 0.002 0.031 610 Dihedral : 9.836 86.363 482 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % 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 (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: 0.62 (0.41), residues: 420 helix: 0.96 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -1.45 (0.62), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 146 HIS 0.001 0.000 HIS A 276 PHE 0.009 0.001 PHE B 277 TYR 0.010 0.001 TYR B 87 ARG 0.001 0.000 ARG A 188 *********************** 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 50 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7855 (pttm) cc_final: 0.7053 (tmtm) REVERT: A 74 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7194 (tp30) REVERT: A 81 GLN cc_start: 0.8252 (mt0) cc_final: 0.8025 (mp10) REVERT: A 94 ASN cc_start: 0.7502 (OUTLIER) cc_final: 0.7191 (t160) REVERT: A 141 PHE cc_start: 0.8373 (m-80) cc_final: 0.8094 (m-80) REVERT: A 142 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7642 (mptm) REVERT: B 111 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8132 (mt-10) REVERT: B 131 ASP cc_start: 0.7590 (t0) cc_final: 0.7389 (t0) REVERT: B 252 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7850 (mm-30) outliers start: 10 outliers final: 3 residues processed: 48 average time/residue: 1.3814 time to fit residues: 68.3660 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 : 0.420 ------------------------------------------------------------------------------- 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 19 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.0670 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 30 optimal weight: 0.0570 chunk 10 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 overall best weight: 0.2836 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.130530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.116025 restraints weight = 4505.359| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.70 r_work: 0.3319 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2000 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= 0.110 Angle : 0.417 8.902 4888 Z= 0.221 Chirality : 0.037 0.172 568 Planarity : 0.002 0.031 610 Dihedral : 9.661 85.734 481 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.71 % Allowed : 11.08 % 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 (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: 1.23 (0.42), residues: 420 helix: 1.34 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.92 (0.65), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 146 HIS 0.001 0.000 HIS A 120 PHE 0.009 0.001 PHE B 277 TYR 0.008 0.001 TYR B 87 ARG 0.001 0.000 ARG A 84 *********************** 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 52 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7829 (pttm) cc_final: 0.7003 (tmtm) REVERT: A 74 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7228 (tp30) REVERT: A 94 ASN cc_start: 0.7540 (OUTLIER) cc_final: 0.7126 (t160) REVERT: A 141 PHE cc_start: 0.8317 (m-80) cc_final: 0.8065 (m-80) REVERT: A 142 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7647 (mptm) REVERT: A 189 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7951 (tt) REVERT: B 252 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7861 (mm-30) outliers start: 11 outliers final: 1 residues processed: 48 average time/residue: 1.2367 time to fit residues: 61.4127 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 : 0.430 ------------------------------------------------------------------------------- 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 15 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 0.0070 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.125188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110389 restraints weight = 4466.250| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.72 r_work: 0.3274 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 3616 Z= 0.192 Angle : 0.433 4.909 4888 Z= 0.237 Chirality : 0.038 0.148 568 Planarity : 0.003 0.029 610 Dihedral : 9.055 86.762 477 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.46 % Allowed : 11.82 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.29 (0.41), residues: 420 helix: 1.40 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.96 (0.63), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 146 HIS 0.001 0.000 HIS A 276 PHE 0.008 0.001 PHE B 277 TYR 0.009 0.001 TYR B 87 ARG 0.001 0.000 ARG A 188 *********************** 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 49 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7842 (pttm) cc_final: 0.7070 (tmtm) REVERT: A 74 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7239 (tp30) REVERT: A 94 ASN cc_start: 0.7504 (OUTLIER) cc_final: 0.7160 (t0) REVERT: A 141 PHE cc_start: 0.8403 (m-80) cc_final: 0.8167 (m-80) REVERT: A 142 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7668 (mptm) REVERT: A 189 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7961 (tt) REVERT: B 252 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7828 (mm-30) outliers start: 10 outliers final: 2 residues processed: 46 average time/residue: 1.3430 time to fit residues: 63.7771 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 : 0.386 ------------------------------------------------------------------------------- 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 248 THR 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 10 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 0.0980 chunk 30 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.124817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.107908 restraints weight = 4398.839| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.05 r_work: 0.3181 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2102 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= 0.132 Angle : 0.405 4.528 4888 Z= 0.223 Chirality : 0.037 0.142 568 Planarity : 0.002 0.030 610 Dihedral : 8.926 85.922 477 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.71 % Allowed : 11.82 % 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 (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: 1.49 (0.42), residues: 420 helix: 1.54 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.89 (0.62), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 146 HIS 0.001 0.000 HIS A 276 PHE 0.009 0.001 PHE B 277 TYR 0.008 0.001 TYR B 87 ARG 0.001 0.000 ARG A 188 *********************** 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 50 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7814 (pttm) cc_final: 0.6975 (tmtm) REVERT: A 74 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7176 (tp30) REVERT: A 94 ASN cc_start: 0.7500 (OUTLIER) cc_final: 0.7062 (t0) REVERT: A 141 PHE cc_start: 0.8375 (m-80) cc_final: 0.8081 (m-80) REVERT: A 142 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7382 (mptm) REVERT: A 189 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7695 (tt) REVERT: B 252 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7749 (mm-30) outliers start: 11 outliers final: 2 residues processed: 47 average time/residue: 1.3060 time to fit residues: 63.2948 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 : 0.377 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 0.0070 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.0670 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 overall best weight: 0.5336 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.123753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.106916 restraints weight = 4363.400| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.01 r_work: 0.3173 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3616 Z= 0.157 Angle : 0.423 4.384 4888 Z= 0.232 Chirality : 0.038 0.139 568 Planarity : 0.002 0.030 610 Dihedral : 8.933 86.001 477 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.97 % Allowed : 12.56 % 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 (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: 1.59 (0.41), residues: 420 helix: 1.61 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.84 (0.62), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 146 HIS 0.001 0.000 HIS A 276 PHE 0.009 0.001 PHE B 277 TYR 0.008 0.001 TYR B 87 ARG 0.001 0.000 ARG A 244 *********************** 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: 8 poor density : 38 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7813 (pttm) cc_final: 0.6976 (tmtm) REVERT: A 74 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7161 (tp30) REVERT: A 94 ASN cc_start: 0.7461 (OUTLIER) cc_final: 0.7015 (t0) REVERT: A 141 PHE cc_start: 0.8411 (m-80) cc_final: 0.8134 (m-80) REVERT: A 142 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7421 (mptm) REVERT: A 189 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7715 (tt) REVERT: B 252 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7697 (mm-30) outliers start: 8 outliers final: 2 residues processed: 43 average time/residue: 1.2504 time to fit residues: 55.5810 Evaluate side-chains 44 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 0.0020 chunk 15 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 14 optimal weight: 0.0970 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.125403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.108538 restraints weight = 4331.682| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.03 r_work: 0.3194 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 3616 Z= 0.141 Angle : 0.408 4.272 4888 Z= 0.226 Chirality : 0.037 0.135 568 Planarity : 0.002 0.030 610 Dihedral : 8.826 85.257 477 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.97 % Allowed : 12.81 % 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 (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: 1.73 (0.42), residues: 420 helix: 1.69 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.73 (0.63), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 245 HIS 0.001 0.000 HIS A 120 PHE 0.009 0.001 PHE B 277 TYR 0.007 0.001 TYR B 87 ARG 0.001 0.000 ARG A 188 ********************** 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: 8 poor density : 38 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7811 (pttm) cc_final: 0.6952 (tmtm) REVERT: A 74 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7076 (tp30) REVERT: A 94 ASN cc_start: 0.7437 (OUTLIER) cc_final: 0.7030 (t0) REVERT: A 142 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7370 (mptm) REVERT: A 189 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7690 (tt) REVERT: B 252 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7683 (mm-30) outliers start: 8 outliers final: 1 residues processed: 44 average time/residue: 1.2665 time to fit residues: 57.5787 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 : 0.375 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 0.0020 chunk 37 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3475 r_free = 0.3475 target = 0.123241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.106350 restraints weight = 4357.117| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.00 r_work: 0.3163 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 3616 Z= 0.180 Angle : 0.436 4.328 4888 Z= 0.240 Chirality : 0.038 0.140 568 Planarity : 0.002 0.030 610 Dihedral : 8.928 86.702 477 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.97 % Allowed : 12.56 % 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 (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: 1.65 (0.41), residues: 420 helix: 1.64 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.76 (0.62), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 146 HIS 0.001 0.000 HIS A 276 PHE 0.008 0.001 PHE B 277 TYR 0.008 0.001 TYR A 87 ARG 0.001 0.000 ARG A 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2576.39 seconds wall clock time: 44 minutes 47.38 seconds (2687.38 seconds total)