Starting phenix.real_space_refine on Thu May 15 03:23:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8znj_60273/05_2025/8znj_60273.cif Found real_map, /net/cci-nas-00/data/ceres_data/8znj_60273/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8znj_60273/05_2025/8znj_60273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8znj_60273/05_2025/8znj_60273.map" model { file = "/net/cci-nas-00/data/ceres_data/8znj_60273/05_2025/8znj_60273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8znj_60273/05_2025/8znj_60273.cif" } resolution = 3.0 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= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.57, per 1000 atoms: 0.52 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: 3.51 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 6.23 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: 5.05 Time building geometry restraints manager: 4.18 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: 0.590 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: 0.190 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 36.070 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.730 ------------------------------------------------------------------------------- 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 (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: -1.72 (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 TRP 0.009 0.001 TRP A 274 HIS 0.002 0.001 HIS A 24 PHE 0.022 0.001 PHE A 109 TYR 0.010 0.001 TYR B 175 ARG 0.007 0.000 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.11039 ( 272) hydrogen bonds : angle 6.41859 ( 713) SS BOND : bond 0.00082 ( 1) SS BOND : angle 0.81177 ( 2) covalent geometry : bond 0.00297 ( 6722) covalent geometry : angle 0.59353 ( 9264) *********************** 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 : 0.918 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: 2.0161 time to fit residues: 197.5475 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 : 1.033 ------------------------------------------------------------------------------- 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 59 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4260 r_free = 0.4260 target = 0.184591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.157105 restraints weight = 20744.252| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 1.91 r_work: 0.3845 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.0599 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= 0.167 Angle : 0.575 5.345 9266 Z= 0.320 Chirality : 0.045 0.150 1056 Planarity : 0.004 0.047 1015 Dihedral : 17.873 129.476 1321 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 2.54 % Allowed : 24.17 % Favored : 73.29 % 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: -1.54 (0.33), residues: 673 helix: 0.94 (0.38), residues: 212 sheet: -1.54 (0.42), residues: 135 loop : -2.18 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 274 HIS 0.002 0.001 HIS A 138 PHE 0.015 0.001 PHE A 109 TYR 0.011 0.001 TYR B 175 ARG 0.004 0.000 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 272) hydrogen bonds : angle 4.98112 ( 713) SS BOND : bond 0.00004 ( 1) SS BOND : angle 0.51319 ( 2) covalent geometry : bond 0.00377 ( 6722) covalent geometry : angle 0.57535 ( 9264) *********************** 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 : 1.023 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: 0.8409 (ttm) cc_final: 0.8083 (ttp) REVERT: A 391 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7985 (mt) outliers start: 16 outliers final: 8 residues processed: 99 average time/residue: 1.9029 time to fit residues: 201.6687 Evaluate side-chains 87 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 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 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4257 r_free = 0.4257 target = 0.184352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.156080 restraints weight = 20924.929| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.03 r_work: 0.3835 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.0730 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= 0.162 Angle : 0.569 5.923 9266 Z= 0.316 Chirality : 0.044 0.151 1056 Planarity : 0.004 0.044 1015 Dihedral : 17.787 129.262 1309 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 2.23 % Allowed : 24.64 % Favored : 73.13 % 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 (0.33), residues: 673 helix: 0.78 (0.37), residues: 218 sheet: -1.54 (0.41), residues: 148 loop : -2.19 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 274 HIS 0.002 0.001 HIS A 138 PHE 0.009 0.001 PHE A 17 TYR 0.010 0.001 TYR A 396 ARG 0.004 0.000 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 272) hydrogen bonds : angle 4.79861 ( 713) SS BOND : bond 0.00007 ( 1) SS BOND : angle 0.58971 ( 2) covalent geometry : bond 0.00367 ( 6722) covalent geometry : angle 0.56882 ( 9264) *********************** 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 97 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 1.039 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 210 MET cc_start: 0.8429 (ttm) cc_final: 0.8097 (ttp) REVERT: B 130 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7647 (mp0) outliers start: 14 outliers final: 13 residues processed: 96 average time/residue: 2.0112 time to fit residues: 205.9990 Evaluate side-chains 92 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG 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 22 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.4272 r_free = 0.4272 target = 0.184118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.156583 restraints weight = 20363.352| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 1.93 r_work: 0.3852 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.0979 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= 0.186 Angle : 0.582 6.520 9266 Z= 0.323 Chirality : 0.045 0.152 1056 Planarity : 0.004 0.041 1015 Dihedral : 17.828 129.244 1309 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 3.50 % Allowed : 24.48 % Favored : 72.02 % 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 (0.33), residues: 673 helix: 0.71 (0.37), residues: 219 sheet: -1.60 (0.39), residues: 158 loop : -2.21 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 274 HIS 0.002 0.001 HIS A 138 PHE 0.016 0.002 PHE A 109 TYR 0.010 0.001 TYR A 396 ARG 0.005 0.000 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 272) hydrogen bonds : angle 4.72399 ( 713) SS BOND : bond 0.00009 ( 1) SS BOND : angle 0.55422 ( 2) covalent geometry : bond 0.00422 ( 6722) covalent geometry : angle 0.58179 ( 9264) *********************** 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 105 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.969 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 210 MET cc_start: 0.8405 (ttm) cc_final: 0.8083 (ttp) REVERT: B 130 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7523 (mp0) outliers start: 22 outliers final: 14 residues processed: 100 average time/residue: 2.0230 time to fit residues: 215.4589 Evaluate side-chains 96 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 77 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 0.0040 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- 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 = 0.4268 r_free = 0.4268 target = 0.183823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.157147 restraints weight = 20513.218| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.88 r_work: 0.3855 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1115 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= 0.193 Angle : 0.590 7.058 9266 Z= 0.328 Chirality : 0.045 0.152 1056 Planarity : 0.004 0.041 1015 Dihedral : 17.847 129.287 1309 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.14 % Favored : 88.86 % Rotamer: Outliers : 3.18 % Allowed : 25.28 % Favored : 71.54 % 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 (0.32), residues: 673 helix: 0.64 (0.36), residues: 219 sheet: -1.62 (0.39), residues: 158 loop : -2.25 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 274 HIS 0.002 0.001 HIS A 138 PHE 0.010 0.001 PHE A 17 TYR 0.010 0.001 TYR A 433 ARG 0.005 0.000 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 272) hydrogen bonds : angle 4.70792 ( 713) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.51928 ( 2) covalent geometry : bond 0.00436 ( 6722) covalent geometry : angle 0.59025 ( 9264) *********************** 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 107 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 1.011 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 210 MET cc_start: 0.8351 (ttm) cc_final: 0.8048 (ttp) REVERT: B 130 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7499 (mp0) outliers start: 20 outliers final: 16 residues processed: 102 average time/residue: 1.9850 time to fit residues: 216.5048 Evaluate side-chains 98 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 77 THR 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 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 66 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4277 r_free = 0.4277 target = 0.184798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.157858 restraints weight = 20603.050| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 1.92 r_work: 0.3875 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1227 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= 0.146 Angle : 0.573 7.268 9266 Z= 0.317 Chirality : 0.044 0.151 1056 Planarity : 0.004 0.040 1015 Dihedral : 17.794 129.454 1307 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.85 % Favored : 89.00 % Rotamer: Outliers : 3.02 % Allowed : 25.44 % Favored : 71.54 % 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: -1.58 (0.33), residues: 673 helix: 0.81 (0.37), residues: 219 sheet: -1.52 (0.39), residues: 158 loop : -2.23 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 274 HIS 0.002 0.001 HIS A 138 PHE 0.019 0.001 PHE A 109 TYR 0.009 0.001 TYR A 54 ARG 0.005 0.000 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 272) hydrogen bonds : angle 4.59784 ( 713) SS BOND : bond 0.00013 ( 1) SS BOND : angle 0.51907 ( 2) covalent geometry : bond 0.00330 ( 6722) covalent geometry : angle 0.57261 ( 9264) *********************** 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 101 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.916 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: 0.8355 (ttm) cc_final: 0.8023 (ttp) REVERT: B 130 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7507 (mp0) outliers start: 19 outliers final: 11 residues processed: 97 average time/residue: 1.9383 time to fit residues: 200.9514 Evaluate side-chains 92 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 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 228 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 58 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.4273 r_free = 0.4273 target = 0.184227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.156851 restraints weight = 20457.633| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 1.94 r_work: 0.3858 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6723 Z= 0.169 Angle : 0.587 7.512 9266 Z= 0.324 Chirality : 0.045 0.150 1056 Planarity : 0.004 0.040 1015 Dihedral : 17.777 129.428 1307 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 3.18 % Allowed : 25.60 % Favored : 71.22 % 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: -1.61 (0.33), residues: 673 helix: 0.74 (0.37), residues: 219 sheet: -1.50 (0.39), residues: 158 loop : -2.23 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 274 HIS 0.002 0.001 HIS A 138 PHE 0.010 0.001 PHE A 137 TYR 0.012 0.001 TYR A 54 ARG 0.006 0.000 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 272) hydrogen bonds : angle 4.60155 ( 713) SS BOND : bond 0.00015 ( 1) SS BOND : angle 0.52513 ( 2) covalent geometry : bond 0.00383 ( 6722) covalent geometry : angle 0.58694 ( 9264) *********************** 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 105 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.941 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 70 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.7978 (p) REVERT: A 210 MET cc_start: 0.8372 (ttm) cc_final: 0.8054 (ttp) REVERT: B 130 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7546 (mp0) outliers start: 20 outliers final: 13 residues processed: 101 average time/residue: 1.9806 time to fit residues: 214.7733 Evaluate side-chains 98 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 221 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4274 r_free = 0.4274 target = 0.184473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.157025 restraints weight = 20504.681| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 1.94 r_work: 0.3857 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6723 Z= 0.165 Angle : 0.590 7.902 9266 Z= 0.326 Chirality : 0.045 0.150 1056 Planarity : 0.004 0.041 1015 Dihedral : 17.724 129.602 1307 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.14 % Favored : 88.86 % Rotamer: Outliers : 2.86 % Allowed : 26.39 % Favored : 70.75 % 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: -1.56 (0.33), residues: 673 helix: 0.92 (0.37), residues: 213 sheet: -1.52 (0.39), residues: 158 loop : -2.22 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 274 HIS 0.002 0.001 HIS A 138 PHE 0.022 0.002 PHE A 109 TYR 0.012 0.001 TYR A 54 ARG 0.006 0.000 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 272) hydrogen bonds : angle 4.56779 ( 713) SS BOND : bond 0.00002 ( 1) SS BOND : angle 0.53805 ( 2) covalent geometry : bond 0.00375 ( 6722) covalent geometry : angle 0.58986 ( 9264) *********************** 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 101 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.889 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 70 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.7999 (p) REVERT: A 210 MET cc_start: 0.8353 (ttm) cc_final: 0.8038 (ttp) REVERT: B 130 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7532 (mp0) outliers start: 18 outliers final: 14 residues processed: 97 average time/residue: 1.8675 time to fit residues: 194.1332 Evaluate side-chains 96 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 221 LYS 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 50 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4293 r_free = 0.4293 target = 0.186509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.159551 restraints weight = 20335.469| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.92 r_work: 0.3885 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1409 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= 0.132 Angle : 0.572 8.022 9266 Z= 0.315 Chirality : 0.044 0.149 1056 Planarity : 0.004 0.044 1015 Dihedral : 17.633 129.503 1307 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 2.54 % Allowed : 26.71 % Favored : 70.75 % 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: -1.46 (0.33), residues: 673 helix: 1.05 (0.37), residues: 213 sheet: -1.48 (0.39), residues: 158 loop : -2.19 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 274 HIS 0.002 0.001 HIS B 31 PHE 0.019 0.001 PHE B 62 TYR 0.012 0.001 TYR A 54 ARG 0.005 0.000 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 272) hydrogen bonds : angle 4.44685 ( 713) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.63969 ( 2) covalent geometry : bond 0.00299 ( 6722) covalent geometry : angle 0.57190 ( 9264) *********************** 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 99 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.917 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 70 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.7983 (p) REVERT: A 210 MET cc_start: 0.8376 (ttm) cc_final: 0.8054 (ttp) REVERT: B 130 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7569 (mp0) outliers start: 16 outliers final: 12 residues processed: 96 average time/residue: 1.9217 time to fit residues: 197.1637 Evaluate side-chains 94 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 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 51 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.185457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.158365 restraints weight = 20225.133| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 1.95 r_work: 0.3871 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3729 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1464 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= 0.146 Angle : 0.583 8.058 9266 Z= 0.321 Chirality : 0.044 0.149 1056 Planarity : 0.004 0.045 1015 Dihedral : 17.584 129.248 1306 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 2.38 % Allowed : 27.19 % Favored : 70.43 % 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 (0.33), residues: 673 helix: 1.05 (0.37), residues: 213 sheet: -1.52 (0.39), residues: 158 loop : -2.21 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 274 HIS 0.002 0.001 HIS B 31 PHE 0.025 0.001 PHE A 109 TYR 0.012 0.001 TYR A 54 ARG 0.006 0.000 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 272) hydrogen bonds : angle 4.44519 ( 713) SS BOND : bond 0.00001 ( 1) SS BOND : angle 0.62576 ( 2) covalent geometry : bond 0.00332 ( 6722) covalent geometry : angle 0.58318 ( 9264) ********************** 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 96 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.923 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 70 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.7959 (p) REVERT: A 210 MET cc_start: 0.8402 (ttm) cc_final: 0.8071 (ttp) REVERT: B 130 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7565 (mp0) outliers start: 15 outliers final: 12 residues processed: 91 average time/residue: 1.9825 time to fit residues: 194.2631 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 : 1.080 ------------------------------------------------------------------------------- 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 221 LYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4287 r_free = 0.4287 target = 0.186014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.159417 restraints weight = 20399.468| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.90 r_work: 0.3890 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1482 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= 0.139 Angle : 0.578 8.067 9266 Z= 0.318 Chirality : 0.044 0.149 1056 Planarity : 0.004 0.045 1015 Dihedral : 17.525 129.191 1305 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 2.54 % Allowed : 27.03 % Favored : 70.43 % 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: -1.48 (0.33), residues: 673 helix: 1.05 (0.37), residues: 214 sheet: -1.51 (0.39), residues: 158 loop : -2.22 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 274 HIS 0.002 0.001 HIS B 31 PHE 0.011 0.001 PHE A 137 TYR 0.013 0.001 TYR A 54 ARG 0.006 0.000 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 272) hydrogen bonds : angle 4.42112 ( 713) SS BOND : bond 0.00003 ( 1) SS BOND : angle 0.63527 ( 2) covalent geometry : bond 0.00316 ( 6722) covalent geometry : angle 0.57833 ( 9264) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8679.08 seconds wall clock time: 149 minutes 21.06 seconds (8961.06 seconds total)