Starting phenix.real_space_refine on Wed Sep 17 09:27:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jqa_61725/09_2025/9jqa_61725.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jqa_61725/09_2025/9jqa_61725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jqa_61725/09_2025/9jqa_61725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jqa_61725/09_2025/9jqa_61725.map" model { file = "/net/cci-nas-00/data/ceres_data/9jqa_61725/09_2025/9jqa_61725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jqa_61725/09_2025/9jqa_61725.cif" } resolution = 2.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.050 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: 6 Type Number sf(0) Gaussians Fe 5 7.16 5 P 2 5.49 5 S 41 5.16 5 C 4655 2.51 5 N 1297 2.21 5 O 1431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 7431 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4173 Classifications: {'peptide': 541} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 504} Chain: "B" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1088 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 7, 'TRANS': 129} Chain: "C" Number of atoms: 2024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2024 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 13, 'TRANS': 254} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1773 SG CYS A 226 39.958 57.361 52.874 1.00 62.70 S ATOM 1744 SG CYS A 222 36.595 62.721 54.233 1.00 64.17 S ATOM 1704 SG CYS A 216 35.472 58.004 57.757 1.00 58.11 S Time building chain proxies: 1.93, per 1000 atoms: 0.26 Number of scatterers: 7431 At special positions: 0 Unit cell: (88.74, 103.53, 91.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 5 26.01 S 41 16.00 P 2 15.00 O 1431 8.00 N 1297 7.00 C 4655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 276.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE4 F3S A 602 " - pdb=" SG CYS A 216 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " Number of angles added : 9 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1750 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 41.9% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 16 through 29 Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.566A pdb=" N LYS A 97 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.660A pdb=" N THR A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 138 through 154 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.964A pdb=" N LYS A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 244 removed outlier: 3.519A pdb=" N ALA A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 301 removed outlier: 3.879A pdb=" N GLU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Proline residue: A 295 - end of helix Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 387 through 401 removed outlier: 3.531A pdb=" N LEU A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 462 removed outlier: 3.963A pdb=" N VAL A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 Processing helix chain 'A' and resid 522 through 542 Processing helix chain 'B' and resid 48 through 63 Processing helix chain 'B' and resid 68 through 83 Processing helix chain 'B' and resid 85 through 101 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.575A pdb=" N VAL B 171 " --> pdb=" O ASN B 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 197 Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 245 through 256 Processing helix chain 'C' and resid 265 through 274 Processing helix chain 'C' and resid 275 through 278 Processing helix chain 'C' and resid 279 through 291 Processing helix chain 'C' and resid 317 through 324 removed outlier: 3.783A pdb=" N SER C 322 " --> pdb=" O ASN C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 332 removed outlier: 4.482A pdb=" N LYS C 331 " --> pdb=" O THR C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 344 removed outlier: 3.509A pdb=" N ALA C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 408 through 424 Processing helix chain 'C' and resid 431 through 440 Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.746A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP A 9 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA A 282 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N THR A 266 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE A 265 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR A 259 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA A 267 " --> pdb=" O MET A 257 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N MET A 257 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N SER A 269 " --> pdb=" O TYR A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.746A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP A 9 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N PHE A 507 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE A 285 " --> pdb=" O PHE A 507 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.482A pdb=" N ILE A 87 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N HIS A 433 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 157 Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 200 removed outlier: 5.420A pdb=" N SER A 347 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR A 368 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP A 404 " --> pdb=" O ASN A 369 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N GLN A 332 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLU A 466 " --> pdb=" O GLN A 332 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 223 through 225 Processing sheet with id=AA7, first strand: chain 'C' and resid 384 through 388 296 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.04 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.76: 7548 1.76 - 2.30: 78 2.30 - 2.85: 0 2.85 - 3.40: 0 3.40 - 3.94: 3 Bond restraints: 7629 Sorted by residual: bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.941 -1.641 2.00e-02 2.50e+03 6.73e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 3.790 -1.557 2.00e-02 2.50e+03 6.06e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.778 -1.520 2.00e-02 2.50e+03 5.78e+03 bond pdb=" C2D HEC C 502 " pdb=" C3D HEC C 502 " ideal model delta sigma weight residual 1.544 1.329 0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C2D HEC C 501 " pdb=" C3D HEC C 501 " ideal model delta sigma weight residual 1.544 1.338 0.206 2.00e-02 2.50e+03 1.06e+02 ... (remaining 7624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.41: 10415 9.41 - 18.82: 1 18.82 - 28.24: 0 28.24 - 37.65: 8 37.65 - 47.06: 2 Bond angle restraints: 10426 Sorted by residual: angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 67.69 47.06 3.00e+00 1.11e-01 2.46e+02 angle pdb=" S3 F3S A 602 " pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 112.59 68.20 44.39 3.00e+00 1.11e-01 2.19e+02 angle pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 103.26 68.69 34.57 3.00e+00 1.11e-01 1.33e+02 angle pdb=" S1 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S2 F3S A 602 " ideal model delta sigma weight residual 103.25 69.16 34.09 3.00e+00 1.11e-01 1.29e+02 angle pdb="FE3 F3S A 602 " pdb=" S2 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 71.75 38.80 32.95 3.00e+00 1.11e-01 1.21e+02 ... (remaining 10421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 3944 17.56 - 35.12: 426 35.12 - 52.68: 113 52.68 - 70.23: 32 70.23 - 87.79: 10 Dihedral angle restraints: 4525 sinusoidal: 1787 harmonic: 2738 Sorted by residual: dihedral pdb=" CA PHE A 80 " pdb=" C PHE A 80 " pdb=" N PRO A 81 " pdb=" CA PRO A 81 " ideal model delta harmonic sigma weight residual 180.00 143.38 36.62 0 5.00e+00 4.00e-02 5.36e+01 dihedral pdb=" CA ILE B 159 " pdb=" C ILE B 159 " pdb=" N PRO B 160 " pdb=" CA PRO B 160 " ideal model delta harmonic sigma weight residual 180.00 -155.16 -24.84 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA VAL C 342 " pdb=" C VAL C 342 " pdb=" N CYS C 343 " pdb=" CA CYS C 343 " ideal model delta harmonic sigma weight residual -180.00 -156.27 -23.73 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 4522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.400: 1110 3.400 - 6.800: 0 6.800 - 10.200: 0 10.200 - 13.600: 0 13.600 - 16.999: 1 Chirality restraints: 1111 Sorted by residual: chirality pdb=" S2 F3S A 602 " pdb="FE1 F3S A 602 " pdb="FE3 F3S A 602 " pdb="FE4 F3S A 602 " both_signs ideal model delta sigma weight residual False 10.77 -6.23 17.00 2.00e-01 2.50e+01 7.22e+03 chirality pdb=" CA PRO B 160 " pdb=" N PRO B 160 " pdb=" C PRO B 160 " pdb=" CB PRO B 160 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA PRO B 167 " pdb=" N PRO B 167 " pdb=" C PRO B 167 " pdb=" CB PRO B 167 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.79e-01 ... (remaining 1108 not shown) Planarity restraints: 1359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CBD HEC C 501 " -0.023 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" CGD HEC C 501 " 0.085 2.00e-02 2.50e+03 pdb=" O1D HEC C 501 " -0.030 2.00e-02 2.50e+03 pdb=" O2D HEC C 501 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBD HEC C 502 " -0.019 2.00e-02 2.50e+03 4.15e-02 1.73e+01 pdb=" CGD HEC C 502 " 0.072 2.00e-02 2.50e+03 pdb=" O1D HEC C 502 " -0.026 2.00e-02 2.50e+03 pdb=" O2D HEC C 502 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBA HEC C 501 " 0.016 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" CGA HEC C 501 " -0.059 2.00e-02 2.50e+03 pdb=" O1A HEC C 501 " 0.022 2.00e-02 2.50e+03 pdb=" O2A HEC C 501 " 0.022 2.00e-02 2.50e+03 ... (remaining 1356 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1267 2.76 - 3.29: 7317 3.29 - 3.83: 14353 3.83 - 4.36: 17373 4.36 - 4.90: 27930 Nonbonded interactions: 68240 Sorted by model distance: nonbonded pdb=" NH2 ARG C 386 " pdb=" O1D HEC C 501 " model vdw 2.221 3.120 nonbonded pdb=" OG SER A 330 " pdb=" OD1 ASP A 404 " model vdw 2.247 3.040 nonbonded pdb=" O ARG A 358 " pdb=" OH TYR A 443 " model vdw 2.250 3.040 nonbonded pdb=" S3 F3S A 602 " pdb="FE3 F3S A 602 " model vdw 2.255 2.688 nonbonded pdb=" S4 F3S A 602 " pdb="FE4 F3S A 602 " model vdw 2.257 2.688 ... (remaining 68235 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: 2.980 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.120 Find NCS groups from input model: 0.030 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:7.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 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 : 0.032 1.641 7638 Z= 1.594 Angle : 1.313 47.059 10435 Z= 0.495 Chirality : 0.512 16.999 1111 Planarity : 0.005 0.050 1359 Dihedral : 16.540 87.793 2775 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.03 % Allowed : 15.50 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.40 (0.27), residues: 940 helix: 1.00 (0.28), residues: 345 sheet: 0.46 (0.57), residues: 78 loop : -0.21 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 305 TYR 0.014 0.002 TYR A 96 PHE 0.024 0.002 PHE C 210 TRP 0.013 0.002 TRP B 170 HIS 0.006 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.03207 ( 7629) covalent geometry : angle 1.29964 (10426) hydrogen bonds : bond 0.12888 ( 289) hydrogen bonds : angle 7.14130 ( 810) metal coordination : bond 0.00148 ( 3) metal coordination : angle 6.50487 ( 9) Misc. bond : bond 0.06873 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.210 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 97 average time/residue: 0.7012 time to fit residues: 71.1192 Evaluate side-chains 97 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.0470 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.082343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.063280 restraints weight = 10566.149| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 1.86 r_work: 0.2629 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 7638 Z= 0.231 Angle : 1.612 59.291 10435 Z= 0.515 Chirality : 0.086 2.441 1111 Planarity : 0.004 0.050 1359 Dihedral : 9.648 87.234 1108 Min Nonbonded Distance : 1.433 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.71 % Allowed : 14.08 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.83 (0.27), residues: 940 helix: 1.65 (0.29), residues: 332 sheet: 0.47 (0.60), residues: 78 loop : -0.10 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 213 TYR 0.012 0.001 TYR A 443 PHE 0.031 0.002 PHE C 210 TRP 0.010 0.002 TRP A 51 HIS 0.005 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 7629) covalent geometry : angle 1.37836 (10426) hydrogen bonds : bond 0.04034 ( 289) hydrogen bonds : angle 5.53184 ( 810) metal coordination : bond 0.03249 ( 3) metal coordination : angle 28.47342 ( 9) Misc. bond : bond 0.07828 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 163 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7954 (mm) REVERT: B 49 ASP cc_start: 0.7262 (m-30) cc_final: 0.7022 (m-30) REVERT: B 91 LYS cc_start: 0.9122 (mttp) cc_final: 0.8736 (mtpp) REVERT: B 154 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8502 (mtt180) outliers start: 21 outliers final: 5 residues processed: 115 average time/residue: 0.6608 time to fit residues: 79.6754 Evaluate side-chains 103 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 302 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 57 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 0.0570 chunk 75 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 83 optimal weight: 0.2980 chunk 77 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.081997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.063194 restraints weight = 10794.125| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 1.87 r_work: 0.2628 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 7638 Z= 0.167 Angle : 1.488 84.539 10435 Z= 0.432 Chirality : 0.061 1.383 1111 Planarity : 0.004 0.053 1359 Dihedral : 9.179 86.095 1099 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.81 % Allowed : 14.60 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.92 (0.28), residues: 940 helix: 1.80 (0.30), residues: 333 sheet: 0.50 (0.59), residues: 80 loop : -0.09 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 208 TYR 0.012 0.001 TYR A 443 PHE 0.051 0.002 PHE C 210 TRP 0.009 0.002 TRP A 51 HIS 0.004 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 7629) covalent geometry : angle 1.09776 (10426) hydrogen bonds : bond 0.03742 ( 289) hydrogen bonds : angle 5.35057 ( 810) metal coordination : bond 0.00278 ( 3) metal coordination : angle 34.23807 ( 9) Misc. bond : bond 0.07398 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 290 ASN cc_start: 0.8974 (OUTLIER) cc_final: 0.8675 (p0) REVERT: B 91 LYS cc_start: 0.9120 (mttp) cc_final: 0.8732 (mtpp) REVERT: B 154 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8479 (mtt180) REVERT: C 192 ARG cc_start: 0.8545 (tmm-80) cc_final: 0.8289 (tmm-80) outliers start: 14 outliers final: 4 residues processed: 107 average time/residue: 0.7541 time to fit residues: 84.4960 Evaluate side-chains 102 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 302 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 chunk 85 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN B 56 GLN B 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.080324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.061406 restraints weight = 10951.440| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 1.87 r_work: 0.2594 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.177 7638 Z= 0.200 Angle : 1.543 82.932 10435 Z= 0.438 Chirality : 0.063 1.466 1111 Planarity : 0.005 0.054 1359 Dihedral : 9.094 87.961 1098 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.42 % Allowed : 14.47 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.90 (0.27), residues: 940 helix: 1.74 (0.29), residues: 334 sheet: 0.57 (0.59), residues: 80 loop : -0.10 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 311 TYR 0.012 0.002 TYR A 443 PHE 0.035 0.002 PHE C 210 TRP 0.009 0.002 TRP A 338 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 7629) covalent geometry : angle 1.10039 (10426) hydrogen bonds : bond 0.03925 ( 289) hydrogen bonds : angle 5.35019 ( 810) metal coordination : bond 0.00420 ( 3) metal coordination : angle 36.84596 ( 9) Misc. bond : bond 0.08440 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 290 ASN cc_start: 0.8945 (OUTLIER) cc_final: 0.8644 (p0) REVERT: A 505 ASN cc_start: 0.8411 (t0) cc_final: 0.8198 (t0) REVERT: B 91 LYS cc_start: 0.9113 (mttp) cc_final: 0.8726 (mtpp) REVERT: B 136 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7182 (pt0) REVERT: B 154 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8511 (mtt180) outliers start: 11 outliers final: 5 residues processed: 103 average time/residue: 0.7344 time to fit residues: 79.3393 Evaluate side-chains 100 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 302 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 65 optimal weight: 0.0270 chunk 76 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.081474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.062648 restraints weight = 10811.566| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 1.89 r_work: 0.2620 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.170 7638 Z= 0.173 Angle : 1.527 83.006 10435 Z= 0.429 Chirality : 0.062 1.447 1111 Planarity : 0.004 0.054 1359 Dihedral : 8.760 89.807 1098 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.81 % Allowed : 13.70 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.92 (0.27), residues: 940 helix: 1.78 (0.29), residues: 335 sheet: 0.60 (0.60), residues: 80 loop : -0.11 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 311 TYR 0.014 0.001 TYR A 443 PHE 0.026 0.002 PHE C 210 TRP 0.010 0.002 TRP A 51 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 7629) covalent geometry : angle 1.08847 (10426) hydrogen bonds : bond 0.03617 ( 289) hydrogen bonds : angle 5.22181 ( 810) metal coordination : bond 0.00304 ( 3) metal coordination : angle 36.48149 ( 9) Misc. bond : bond 0.08207 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.7299 (OUTLIER) cc_final: 0.6667 (t) REVERT: B 91 LYS cc_start: 0.9111 (mttp) cc_final: 0.8723 (mtpp) REVERT: B 136 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7233 (pt0) REVERT: B 154 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8489 (mtt180) REVERT: C 254 LYS cc_start: 0.8963 (tptp) cc_final: 0.8751 (tptt) outliers start: 14 outliers final: 5 residues processed: 102 average time/residue: 0.7246 time to fit residues: 77.6293 Evaluate side-chains 100 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 302 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 90 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 60 optimal weight: 0.0670 chunk 20 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.083242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.064601 restraints weight = 10713.913| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 1.88 r_work: 0.2660 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 7638 Z= 0.151 Angle : 1.508 83.059 10435 Z= 0.422 Chirality : 0.061 1.450 1111 Planarity : 0.004 0.054 1359 Dihedral : 8.371 89.994 1098 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.29 % Allowed : 14.34 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 1.03 (0.28), residues: 940 helix: 1.88 (0.30), residues: 334 sheet: 0.74 (0.61), residues: 78 loop : -0.06 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 305 TYR 0.015 0.001 TYR A 443 PHE 0.023 0.001 PHE C 210 TRP 0.009 0.001 TRP A 51 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7629) covalent geometry : angle 1.08162 (10426) hydrogen bonds : bond 0.03311 ( 289) hydrogen bonds : angle 5.07868 ( 810) metal coordination : bond 0.00240 ( 3) metal coordination : angle 35.77987 ( 9) Misc. bond : bond 0.08579 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: B 91 LYS cc_start: 0.9095 (mttp) cc_final: 0.8699 (mtpp) REVERT: B 134 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8255 (mm-30) REVERT: B 136 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7346 (pt0) REVERT: B 154 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8465 (mtt180) REVERT: C 254 LYS cc_start: 0.8940 (tptp) cc_final: 0.8736 (tptt) outliers start: 10 outliers final: 4 residues processed: 105 average time/residue: 0.6938 time to fit residues: 76.6334 Evaluate side-chains 100 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 302 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 84 optimal weight: 0.0370 chunk 92 optimal weight: 3.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 ASN B 82 GLN C 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.080845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.061955 restraints weight = 10812.398| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 1.88 r_work: 0.2603 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.217 7638 Z= 0.205 Angle : 1.548 82.918 10435 Z= 0.437 Chirality : 0.063 1.449 1111 Planarity : 0.004 0.054 1359 Dihedral : 8.660 89.293 1096 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.55 % Allowed : 14.47 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.91 (0.27), residues: 940 helix: 1.76 (0.29), residues: 334 sheet: 0.54 (0.60), residues: 80 loop : -0.09 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 94 TYR 0.012 0.002 TYR A 443 PHE 0.023 0.002 PHE A 80 TRP 0.010 0.002 TRP B 128 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 7629) covalent geometry : angle 1.10142 (10426) hydrogen bonds : bond 0.03800 ( 289) hydrogen bonds : angle 5.23656 ( 810) metal coordination : bond 0.00344 ( 3) metal coordination : angle 37.07832 ( 9) Misc. bond : bond 0.10234 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 505 ASN cc_start: 0.8366 (t0) cc_final: 0.8137 (t0) REVERT: B 91 LYS cc_start: 0.9111 (mttp) cc_final: 0.8717 (mtpp) REVERT: B 136 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7314 (pt0) REVERT: B 154 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8521 (mtt180) REVERT: C 254 LYS cc_start: 0.8976 (tptp) cc_final: 0.8750 (tptt) outliers start: 12 outliers final: 4 residues processed: 101 average time/residue: 0.7227 time to fit residues: 76.6937 Evaluate side-chains 98 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 302 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 70 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 47 optimal weight: 0.0970 chunk 69 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN C 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.082594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.063865 restraints weight = 10789.120| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 1.88 r_work: 0.2643 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.207 7638 Z= 0.162 Angle : 1.525 83.073 10435 Z= 0.426 Chirality : 0.062 1.444 1111 Planarity : 0.004 0.053 1359 Dihedral : 8.302 89.708 1096 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.29 % Allowed : 14.73 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.95 (0.28), residues: 940 helix: 1.80 (0.30), residues: 334 sheet: 0.53 (0.61), residues: 80 loop : -0.07 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 94 TYR 0.015 0.001 TYR A 443 PHE 0.018 0.001 PHE C 210 TRP 0.009 0.001 TRP A 51 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 7629) covalent geometry : angle 1.08654 (10426) hydrogen bonds : bond 0.03416 ( 289) hydrogen bonds : angle 5.09094 ( 810) metal coordination : bond 0.00242 ( 3) metal coordination : angle 36.44516 ( 9) Misc. bond : bond 0.10096 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: B 91 LYS cc_start: 0.9106 (mttp) cc_final: 0.8707 (mtpp) REVERT: B 136 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7469 (pt0) REVERT: B 154 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8479 (mtt180) REVERT: C 187 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8463 (t0) REVERT: C 254 LYS cc_start: 0.8955 (tptp) cc_final: 0.8733 (tptt) outliers start: 10 outliers final: 4 residues processed: 97 average time/residue: 0.6999 time to fit residues: 71.1426 Evaluate side-chains 99 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 302 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 15 optimal weight: 0.0020 chunk 83 optimal weight: 0.9980 chunk 42 optimal weight: 0.0020 chunk 10 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.083125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.064467 restraints weight = 10605.345| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 1.86 r_work: 0.2655 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.214 7638 Z= 0.156 Angle : 1.524 83.178 10435 Z= 0.425 Chirality : 0.061 1.433 1111 Planarity : 0.004 0.053 1359 Dihedral : 8.153 89.697 1096 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.29 % Allowed : 14.86 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 1.03 (0.28), residues: 940 helix: 1.87 (0.30), residues: 335 sheet: 0.70 (0.62), residues: 78 loop : -0.05 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 94 TYR 0.015 0.001 TYR A 443 PHE 0.017 0.001 PHE C 210 TRP 0.009 0.001 TRP A 51 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 7629) covalent geometry : angle 1.08595 (10426) hydrogen bonds : bond 0.03349 ( 289) hydrogen bonds : angle 5.04472 ( 810) metal coordination : bond 0.00239 ( 3) metal coordination : angle 36.41729 ( 9) Misc. bond : bond 0.10462 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: B 91 LYS cc_start: 0.9101 (mttp) cc_final: 0.8698 (mtpp) REVERT: B 112 MET cc_start: 0.8080 (tpt) cc_final: 0.7681 (ttm) REVERT: B 136 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7494 (pt0) REVERT: B 154 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8484 (mtt180) REVERT: C 254 LYS cc_start: 0.8946 (tptp) cc_final: 0.8728 (tptt) outliers start: 10 outliers final: 5 residues processed: 97 average time/residue: 0.6732 time to fit residues: 68.6043 Evaluate side-chains 99 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 355 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 31 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 0.0370 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 0.0770 chunk 27 optimal weight: 0.9980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN C 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.083272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.064484 restraints weight = 10863.323| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 1.90 r_work: 0.2657 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.207 7638 Z= 0.157 Angle : 1.449 83.608 10435 Z= 0.423 Chirality : 0.061 1.422 1111 Planarity : 0.004 0.053 1359 Dihedral : 8.202 89.079 1096 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.16 % Allowed : 14.86 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 1.04 (0.28), residues: 940 helix: 1.87 (0.30), residues: 335 sheet: 0.68 (0.62), residues: 78 loop : -0.02 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 94 TYR 0.015 0.001 TYR A 443 PHE 0.017 0.001 PHE C 210 TRP 0.011 0.001 TRP A 51 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 7629) covalent geometry : angle 1.08606 (10426) hydrogen bonds : bond 0.03338 ( 289) hydrogen bonds : angle 5.03666 ( 810) metal coordination : bond 0.00374 ( 3) metal coordination : angle 32.66098 ( 9) Misc. bond : bond 0.09956 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: B 136 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7499 (pt0) REVERT: B 154 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8469 (mtt180) REVERT: C 254 LYS cc_start: 0.8941 (tptp) cc_final: 0.8724 (tptt) outliers start: 9 outliers final: 5 residues processed: 96 average time/residue: 0.6631 time to fit residues: 66.9065 Evaluate side-chains 99 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 355 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 50 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN C 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.081984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.063123 restraints weight = 10624.756| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 1.87 r_work: 0.2628 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.221 7638 Z= 0.179 Angle : 1.425 83.549 10435 Z= 0.429 Chirality : 0.062 1.440 1111 Planarity : 0.004 0.053 1359 Dihedral : 8.432 89.307 1096 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.16 % Allowed : 15.12 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 1.00 (0.28), residues: 940 helix: 1.79 (0.30), residues: 334 sheet: 0.71 (0.62), residues: 78 loop : -0.03 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 305 TYR 0.013 0.001 TYR A 443 PHE 0.018 0.002 PHE A 80 TRP 0.008 0.001 TRP B 128 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 7629) covalent geometry : angle 1.09358 (10426) hydrogen bonds : bond 0.03538 ( 289) hydrogen bonds : angle 5.10293 ( 810) metal coordination : bond 0.00381 ( 3) metal coordination : angle 31.12975 ( 9) Misc. bond : bond 0.10307 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3488.87 seconds wall clock time: 60 minutes 12.33 seconds (3612.33 seconds total)