Starting phenix.real_space_refine on Thu Sep 18 00:37:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8znj_60273/09_2025/8znj_60273.cif Found real_map, /net/cci-nas-00/data/ceres_data/8znj_60273/09_2025/8znj_60273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8znj_60273/09_2025/8znj_60273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8znj_60273/09_2025/8znj_60273.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8znj_60273/09_2025/8znj_60273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8znj_60273/09_2025/8znj_60273.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.085 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: 7 Type Number sf(0) Gaussians P 43 5.49 5 Mg 1 5.21 5 S 14 5.16 5 C 4023 2.51 5 N 1112 2.21 5 O 1316 1.98 5 H 6190 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12699 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 7310 Classifications: {'peptide': 444} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 422} Chain breaks: 2 Chain: "B" Number of atoms: 4038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 4038 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 3, 'TRANS': 233} Chain: "D" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 663 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 9} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "E" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 687 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.36, per 1000 atoms: 0.19 Number of scatterers: 12699 At special positions: 0 Unit cell: (75.97, 77.04, 110.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 14 16.00 P 43 15.00 Mg 1 11.99 O 1316 8.00 N 1112 7.00 C 4023 6.00 H 6190 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 85 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 345.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1306 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 7 sheets defined 35.2% alpha, 18.9% beta 20 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 28 through 33 Processing helix chain 'A' and resid 50 through 62 Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 107 through 117 removed outlier: 3.661A pdb=" N SER A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 145 removed outlier: 4.125A pdb=" N GLU A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LYS A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 172 through 184 Processing helix chain 'A' and resid 194 through 201 removed outlier: 4.192A pdb=" N ASP A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER A 200 " --> pdb=" O TYR A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 279 Processing helix chain 'A' and resid 295 through 306 Processing helix chain 'A' and resid 402 through 416 removed outlier: 3.529A pdb=" N ALA A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 441 Processing helix chain 'A' and resid 442 through 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 454 through 459 Processing helix chain 'B' and resid 26 through 38 removed outlier: 3.809A pdb=" N LYS B 32 " --> pdb=" O LYS B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 74 removed outlier: 3.510A pdb=" N TYR B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 114 removed outlier: 3.691A pdb=" N PHE B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B 114 " --> pdb=" O TYR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 194 removed outlier: 4.015A pdb=" N ARG B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 213 removed outlier: 3.655A pdb=" N ILE B 211 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.858A pdb=" N THR A 339 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU A 356 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N SER A 397 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 286 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE A 315 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE A 288 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ALA A 317 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS A 290 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N MET A 208 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE A 289 " --> pdb=" O MET A 208 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N MET A 210 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 213 " --> pdb=" O SER A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA3, first strand: chain 'A' and resid 40 through 41 removed outlier: 6.248A pdb=" N ILE A 40 " --> pdb=" O ASN A 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 100 Processing sheet with id=AA5, first strand: chain 'A' and resid 368 through 370 removed outlier: 3.738A pdb=" N LYS A 370 " --> pdb=" O GLU A 380 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 127 through 128 removed outlier: 4.125A pdb=" N VAL B 135 " --> pdb=" O PHE B 155 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL B 151 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG B 141 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE B 149 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP B 143 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 42 through 47 removed outlier: 6.727A pdb=" N THR B 55 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 10.134A pdb=" N ILE B 18 " --> pdb=" O THR B 55 " (cutoff:3.500A) 223 hydrogen bonds defined for protein. 615 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6188 1.03 - 1.23: 27 1.23 - 1.42: 2858 1.42 - 1.62: 3815 1.62 - 1.81: 24 Bond restraints: 12912 Sorted by residual: bond pdb=" N VAL B 2 " pdb=" CA VAL B 2 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.58e+00 bond pdb=" N VAL B 2 " pdb=" H VAL B 2 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" C3' DT E 3 " pdb=" O3' DT E 3 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.74e+00 bond pdb=" CB ARG A 166 " pdb=" CG ARG A 166 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.39e+00 bond pdb=" N GLY A 49 " pdb=" CA GLY A 49 " ideal model delta sigma weight residual 1.458 1.448 0.010 9.20e-03 1.18e+04 1.17e+00 ... (remaining 12907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 22443 1.31 - 2.63: 835 2.63 - 3.94: 99 3.94 - 5.26: 8 5.26 - 6.57: 4 Bond angle restraints: 23389 Sorted by residual: angle pdb=" N ARG A 166 " pdb=" CA ARG A 166 " pdb=" CB ARG A 166 " ideal model delta sigma weight residual 114.17 110.12 4.05 1.14e+00 7.69e-01 1.26e+01 angle pdb=" CA ARG A 166 " pdb=" CB ARG A 166 " pdb=" CG ARG A 166 " ideal model delta sigma weight residual 114.10 120.21 -6.11 2.00e+00 2.50e-01 9.34e+00 angle pdb=" C GLY A 327 " pdb=" N ASN A 328 " pdb=" CA ASN A 328 " ideal model delta sigma weight residual 121.54 127.02 -5.48 1.91e+00 2.74e-01 8.22e+00 angle pdb=" CB ARG A 166 " pdb=" CG ARG A 166 " pdb=" CD ARG A 166 " ideal model delta sigma weight residual 111.30 117.87 -6.57 2.30e+00 1.89e-01 8.17e+00 angle pdb=" C LEU A 232 " pdb=" N ASN A 233 " pdb=" CA ASN A 233 " ideal model delta sigma weight residual 121.54 126.18 -4.64 1.91e+00 2.74e-01 5.90e+00 ... (remaining 23384 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 5453 25.94 - 51.88: 411 51.88 - 77.81: 86 77.81 - 103.75: 8 103.75 - 129.69: 2 Dihedral angle restraints: 5960 sinusoidal: 3574 harmonic: 2386 Sorted by residual: dihedral pdb=" CA ALA A 416 " pdb=" C ALA A 416 " pdb=" N ASP A 417 " pdb=" CA ASP A 417 " ideal model delta harmonic sigma weight residual 180.00 153.06 26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA ARG A 216 " pdb=" C ARG A 216 " pdb=" N THR A 217 " pdb=" CA THR A 217 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CB CYS B 21 " pdb=" SG CYS B 21 " pdb=" SG CYS B 85 " pdb=" CB CYS B 85 " ideal model delta sinusoidal sigma weight residual 93.00 52.28 40.72 1 1.00e+01 1.00e-02 2.32e+01 ... (remaining 5957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 674 0.031 - 0.063: 221 0.063 - 0.094: 87 0.094 - 0.125: 66 0.125 - 0.157: 8 Chirality restraints: 1056 Sorted by residual: chirality pdb=" CA ILE A 341 " pdb=" N ILE A 341 " pdb=" C ILE A 341 " pdb=" CB ILE A 341 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA ILE B 89 " pdb=" N ILE B 89 " pdb=" C ILE B 89 " pdb=" CB ILE B 89 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA ILE B 51 " pdb=" N ILE B 51 " pdb=" C ILE B 51 " pdb=" CB ILE B 51 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 1053 not shown) Planarity restraints: 1699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 94 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO A 95 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 166 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C ARG A 166 " -0.032 2.00e-02 2.50e+03 pdb=" O ARG A 166 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS A 167 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C D 7 " 0.021 2.00e-02 2.50e+03 9.86e-03 2.67e+00 pdb=" N1 C D 7 " -0.024 2.00e-02 2.50e+03 pdb=" C2 C D 7 " 0.001 2.00e-02 2.50e+03 pdb=" O2 C D 7 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C D 7 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C D 7 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C D 7 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C D 7 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C D 7 " -0.002 2.00e-02 2.50e+03 pdb=" H5 C D 7 " 0.004 2.00e-02 2.50e+03 pdb=" H6 C D 7 " -0.004 2.00e-02 2.50e+03 ... (remaining 1696 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 885 2.20 - 2.80: 26200 2.80 - 3.40: 34765 3.40 - 4.00: 48829 4.00 - 4.60: 73458 Nonbonded interactions: 184137 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 183 " pdb="MG MG A 501 " model vdw 1.601 1.700 nonbonded pdb="HH12 ARG A 216 " pdb=" H22 G D 11 " model vdw 1.804 2.100 nonbonded pdb=" OP2 U D 1 " pdb="MG MG A 501 " model vdw 1.861 2.050 nonbonded pdb=" H GLY B 44 " pdb="HD21 ASN B 103 " model vdw 1.864 2.100 nonbonded pdb=" O ASN A 165 " pdb="HD21 ASN A 165 " model vdw 1.869 2.450 ... (remaining 184132 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.130 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: 0.070 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.640 Find NCS groups from input model: 0.040 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:8.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 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 0.040 6723 Z= 0.138 Angle : 0.594 6.572 9266 Z= 0.333 Chirality : 0.044 0.157 1056 Planarity : 0.005 0.056 1015 Dihedral : 19.149 129.689 2745 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 1.75 % Allowed : 24.64 % Favored : 73.61 % 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 aren not related in a simple way. whole: -1.72 (0.32), residues: 673 helix: 0.78 (0.38), residues: 212 sheet: -1.63 (0.42), residues: 136 loop : -2.29 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 125 TYR 0.010 0.001 TYR B 175 PHE 0.022 0.001 PHE A 109 TRP 0.009 0.001 TRP A 274 HIS 0.002 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6722) covalent geometry : angle 0.59353 ( 9264) SS BOND : bond 0.00082 ( 1) SS BOND : angle 0.81177 ( 2) hydrogen bonds : bond 0.11039 ( 272) hydrogen bonds : angle 6.41859 ( 713) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7938 (p) REVERT: A 210 MET cc_start: 0.8381 (ttm) cc_final: 0.8066 (ttp) REVERT: B 130 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7559 (mp0) outliers start: 11 outliers final: 9 residues processed: 92 average time/residue: 0.9656 time to fit residues: 94.1546 Evaluate side-chains 90 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 0.0670 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.184220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.156893 restraints weight = 20937.045| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.92 r_work: 0.3845 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.0620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6723 Z= 0.172 Angle : 0.579 5.360 9266 Z= 0.322 Chirality : 0.045 0.150 1056 Planarity : 0.004 0.047 1015 Dihedral : 17.885 129.427 1321 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 2.54 % Allowed : 24.01 % Favored : 73.45 % 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 aren not related in a simple way. whole: -1.56 (0.33), residues: 673 helix: 0.92 (0.38), residues: 212 sheet: -1.54 (0.42), residues: 135 loop : -2.19 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 125 TYR 0.010 0.001 TYR B 175 PHE 0.014 0.001 PHE A 109 TRP 0.008 0.001 TRP A 274 HIS 0.002 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 6722) covalent geometry : angle 0.57883 ( 9264) SS BOND : bond 0.00013 ( 1) SS BOND : angle 0.52930 ( 2) hydrogen bonds : bond 0.03971 ( 272) hydrogen bonds : angle 4.98804 ( 713) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8411 (ttm) cc_final: 0.8087 (ttp) outliers start: 16 outliers final: 10 residues processed: 99 average time/residue: 0.8671 time to fit residues: 91.2995 Evaluate side-chains 88 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 228 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 0.0670 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.186845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.158998 restraints weight = 20854.781| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.01 r_work: 0.3865 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.0707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6723 Z= 0.124 Angle : 0.548 5.992 9266 Z= 0.304 Chirality : 0.043 0.150 1056 Planarity : 0.004 0.045 1015 Dihedral : 17.703 128.909 1309 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 2.07 % Allowed : 25.12 % Favored : 72.81 % 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 aren not related in a simple way. whole: -1.46 (0.33), residues: 673 helix: 0.93 (0.37), residues: 218 sheet: -1.39 (0.43), residues: 135 loop : -2.18 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 125 TYR 0.008 0.001 TYR A 396 PHE 0.008 0.001 PHE A 17 TRP 0.008 0.001 TRP A 274 HIS 0.002 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 6722) covalent geometry : angle 0.54825 ( 9264) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.62266 ( 2) hydrogen bonds : bond 0.03586 ( 272) hydrogen bonds : angle 4.73269 ( 713) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8405 (ttm) cc_final: 0.8099 (ttp) REVERT: B 130 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7740 (mp0) outliers start: 13 outliers final: 12 residues processed: 97 average time/residue: 0.8678 time to fit residues: 89.8360 Evaluate side-chains 91 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 228 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 41 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.186513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.158566 restraints weight = 20634.508| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.00 r_work: 0.3859 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6723 Z= 0.133 Angle : 0.546 6.680 9266 Z= 0.303 Chirality : 0.043 0.150 1056 Planarity : 0.004 0.042 1015 Dihedral : 17.685 128.597 1309 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer: Outliers : 2.70 % Allowed : 24.80 % Favored : 72.50 % 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 aren not related in a simple way. whole: -1.43 (0.33), residues: 673 helix: 1.00 (0.37), residues: 219 sheet: -1.47 (0.39), residues: 158 loop : -2.17 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 125 TYR 0.008 0.001 TYR A 54 PHE 0.016 0.001 PHE A 109 TRP 0.008 0.001 TRP A 274 HIS 0.002 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6722) covalent geometry : angle 0.54579 ( 9264) SS BOND : bond 0.00006 ( 1) SS BOND : angle 0.54656 ( 2) hydrogen bonds : bond 0.03443 ( 272) hydrogen bonds : angle 4.57395 ( 713) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8398 (ttm) cc_final: 0.8084 (ttp) REVERT: B 130 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7665 (mp0) outliers start: 17 outliers final: 13 residues processed: 94 average time/residue: 0.8839 time to fit residues: 87.9791 Evaluate side-chains 93 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 52 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 10 optimal weight: 0.0980 chunk 67 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.183321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.155040 restraints weight = 20832.142| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.01 r_work: 0.3822 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6723 Z= 0.184 Angle : 0.578 7.134 9266 Z= 0.321 Chirality : 0.045 0.150 1056 Planarity : 0.004 0.041 1015 Dihedral : 17.785 128.737 1308 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 3.18 % Allowed : 23.85 % Favored : 72.97 % 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 aren not related in a simple way. whole: -1.57 (0.33), residues: 673 helix: 0.82 (0.37), residues: 219 sheet: -1.54 (0.39), residues: 158 loop : -2.19 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 125 TYR 0.010 0.001 TYR A 396 PHE 0.010 0.001 PHE A 17 TRP 0.007 0.001 TRP A 274 HIS 0.001 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 6722) covalent geometry : angle 0.57777 ( 9264) SS BOND : bond 0.00047 ( 1) SS BOND : angle 0.46778 ( 2) hydrogen bonds : bond 0.03756 ( 272) hydrogen bonds : angle 4.62324 ( 713) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8433 (ttm) cc_final: 0.8106 (ttp) REVERT: B 130 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7645 (mp0) outliers start: 20 outliers final: 15 residues processed: 100 average time/residue: 1.0018 time to fit residues: 106.4534 Evaluate side-chains 95 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 228 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 39 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 0.0570 chunk 51 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.187756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.160542 restraints weight = 20203.854| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.92 r_work: 0.3895 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6723 Z= 0.121 Angle : 0.548 7.315 9266 Z= 0.303 Chirality : 0.043 0.149 1056 Planarity : 0.004 0.041 1015 Dihedral : 17.703 128.814 1306 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 2.54 % Allowed : 24.96 % Favored : 72.50 % 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 aren not related in a simple way. whole: -1.41 (0.33), residues: 673 helix: 1.03 (0.37), residues: 219 sheet: -1.41 (0.40), residues: 158 loop : -2.20 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 125 TYR 0.009 0.001 TYR A 54 PHE 0.019 0.001 PHE A 109 TRP 0.007 0.001 TRP A 274 HIS 0.002 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6722) covalent geometry : angle 0.54759 ( 9264) SS BOND : bond 0.00002 ( 1) SS BOND : angle 0.56141 ( 2) hydrogen bonds : bond 0.03296 ( 272) hydrogen bonds : angle 4.46861 ( 713) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8342 (ttm) cc_final: 0.8015 (ttp) REVERT: B 130 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7593 (mp0) outliers start: 16 outliers final: 12 residues processed: 95 average time/residue: 0.9308 time to fit residues: 94.0637 Evaluate side-chains 90 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 228 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.181525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.154104 restraints weight = 20644.008| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 1.93 r_work: 0.3818 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 6723 Z= 0.260 Angle : 0.637 7.596 9266 Z= 0.353 Chirality : 0.047 0.163 1056 Planarity : 0.005 0.039 1015 Dihedral : 17.839 129.087 1306 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.59 % Favored : 88.26 % Rotamer: Outliers : 3.34 % Allowed : 25.76 % Favored : 70.91 % 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 aren not related in a simple way. whole: -1.72 (0.32), residues: 673 helix: 0.62 (0.36), residues: 219 sheet: -1.58 (0.39), residues: 158 loop : -2.24 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 125 TYR 0.012 0.002 TYR A 433 PHE 0.013 0.002 PHE B 8 TRP 0.006 0.002 TRP A 418 HIS 0.002 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00593 ( 6722) covalent geometry : angle 0.63682 ( 9264) SS BOND : bond 0.00056 ( 1) SS BOND : angle 0.41747 ( 2) hydrogen bonds : bond 0.04174 ( 272) hydrogen bonds : angle 4.74030 ( 713) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8445 (ttm) cc_final: 0.8161 (ttp) REVERT: B 130 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7535 (mp0) outliers start: 21 outliers final: 15 residues processed: 96 average time/residue: 0.9384 time to fit residues: 95.7930 Evaluate side-chains 95 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 228 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 28 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.184995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.157493 restraints weight = 20228.340| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 1.97 r_work: 0.3859 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 0.041 6723 Z= 0.152 Angle : 0.586 7.718 9266 Z= 0.324 Chirality : 0.044 0.150 1056 Planarity : 0.004 0.043 1015 Dihedral : 17.712 129.758 1306 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 2.54 % Allowed : 26.39 % Favored : 71.07 % 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 aren not related in a simple way. whole: -1.57 (0.33), residues: 673 helix: 0.80 (0.37), residues: 219 sheet: -1.48 (0.40), residues: 158 loop : -2.23 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 125 TYR 0.012 0.001 TYR A 54 PHE 0.022 0.001 PHE A 109 TRP 0.007 0.001 TRP A 274 HIS 0.002 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6722) covalent geometry : angle 0.58614 ( 9264) SS BOND : bond 0.00014 ( 1) SS BOND : angle 0.55983 ( 2) hydrogen bonds : bond 0.03518 ( 272) hydrogen bonds : angle 4.57204 ( 713) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8418 (ttm) cc_final: 0.8072 (ttp) REVERT: B 130 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7530 (mp0) outliers start: 16 outliers final: 13 residues processed: 94 average time/residue: 0.9465 time to fit residues: 94.8795 Evaluate side-chains 93 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 228 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.186177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.159247 restraints weight = 20451.053| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.91 r_work: 0.3877 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6723 Z= 0.134 Angle : 0.577 7.906 9266 Z= 0.318 Chirality : 0.044 0.148 1056 Planarity : 0.004 0.043 1015 Dihedral : 17.641 129.362 1306 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.14 % Favored : 88.86 % Rotamer: Outliers : 2.23 % Allowed : 26.39 % Favored : 71.38 % 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 aren not related in a simple way. whole: -1.42 (0.33), residues: 673 helix: 1.08 (0.37), residues: 213 sheet: -1.42 (0.40), residues: 158 loop : -2.19 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 125 TYR 0.021 0.001 TYR B 175 PHE 0.010 0.001 PHE A 137 TRP 0.008 0.001 TRP A 274 HIS 0.002 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6722) covalent geometry : angle 0.57693 ( 9264) SS BOND : bond 0.00006 ( 1) SS BOND : angle 0.57690 ( 2) hydrogen bonds : bond 0.03377 ( 272) hydrogen bonds : angle 4.48091 ( 713) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8373 (ttm) cc_final: 0.8066 (ttp) REVERT: B 130 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7561 (mp0) outliers start: 14 outliers final: 10 residues processed: 92 average time/residue: 0.8724 time to fit residues: 85.9144 Evaluate side-chains 90 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 228 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 69 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.0670 chunk 32 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.188022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.161149 restraints weight = 20329.793| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 1.92 r_work: 0.3902 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6723 Z= 0.121 Angle : 0.570 8.073 9266 Z= 0.313 Chirality : 0.043 0.148 1056 Planarity : 0.004 0.045 1015 Dihedral : 17.553 128.624 1305 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer: Outliers : 2.07 % Allowed : 26.87 % Favored : 71.07 % 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 aren not related in a simple way. whole: -1.32 (0.33), residues: 673 helix: 1.24 (0.38), residues: 213 sheet: -1.42 (0.40), residues: 158 loop : -2.16 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 125 TYR 0.020 0.001 TYR B 175 PHE 0.026 0.001 PHE A 109 TRP 0.010 0.001 TRP A 274 HIS 0.002 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6722) covalent geometry : angle 0.57018 ( 9264) SS BOND : bond 0.00017 ( 1) SS BOND : angle 0.66527 ( 2) hydrogen bonds : bond 0.03226 ( 272) hydrogen bonds : angle 4.37858 ( 713) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8381 (ttm) cc_final: 0.8064 (ttp) REVERT: B 130 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7614 (mp0) outliers start: 13 outliers final: 12 residues processed: 92 average time/residue: 0.9195 time to fit residues: 90.5092 Evaluate side-chains 90 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 228 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 442 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.182102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.154849 restraints weight = 20548.902| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 1.94 r_work: 0.3845 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3699 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6723 Z= 0.228 Angle : 0.631 7.899 9266 Z= 0.348 Chirality : 0.047 0.156 1056 Planarity : 0.005 0.044 1015 Dihedral : 17.619 129.347 1305 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.14 % Favored : 88.86 % Rotamer: Outliers : 2.54 % Allowed : 26.55 % Favored : 70.91 % 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 aren not related in a simple way. whole: -1.67 (0.32), residues: 673 helix: 0.79 (0.36), residues: 213 sheet: -1.63 (0.39), residues: 158 loop : -2.22 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 125 TYR 0.023 0.002 TYR B 175 PHE 0.013 0.002 PHE B 8 TRP 0.006 0.001 TRP A 418 HIS 0.002 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 6722) covalent geometry : angle 0.63106 ( 9264) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.40897 ( 2) hydrogen bonds : bond 0.03996 ( 272) hydrogen bonds : angle 4.59353 ( 713) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4280.27 seconds wall clock time: 73 minutes 11.22 seconds (4391.22 seconds total)