Starting phenix.real_space_refine on Fri Aug 22 16:00:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e6v_27927/08_2025/8e6v_27927.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e6v_27927/08_2025/8e6v_27927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e6v_27927/08_2025/8e6v_27927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e6v_27927/08_2025/8e6v_27927.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e6v_27927/08_2025/8e6v_27927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e6v_27927/08_2025/8e6v_27927.map" } resolution = 3.3 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= 0.042 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 Zn 1 6.06 5 P 4 5.49 5 S 22 5.16 5 C 3468 2.51 5 N 982 2.21 5 O 999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5476 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 5414 Classifications: {'peptide': 707} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 37, 'TRANS': 669} Chain breaks: 2 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 276 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 10, 'HIS:plan': 2, 'GLN:plan1': 6, 'TYR:plan': 1, 'ASP:plan': 8, 'ASN:plan1': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 142 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {' ZN': 1, 'APR': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 108 SG CYS A 72 33.531 73.163 59.457 1.00 81.67 S ATOM 225 SG CYS A 89 38.047 75.383 58.425 1.00 83.89 S ATOM 240 SG CYS A 91 36.674 72.454 57.633 1.00 77.93 S Time building chain proxies: 1.66, per 1000 atoms: 0.30 Number of scatterers: 5476 At special positions: 0 Unit cell: (74.52, 95.04, 95.04, 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) Zn 1 29.99 S 22 16.00 P 4 15.00 O 999 8.00 N 982 7.00 C 3468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 211.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1603 " pdb="ZN ZN A1603 " - pdb=" NE2 HIS A 98 " pdb="ZN ZN A1603 " - pdb=" SG CYS A 89 " pdb="ZN ZN A1603 " - pdb=" SG CYS A 91 " pdb="ZN ZN A1603 " - pdb=" SG CYS A 72 " Number of angles added : 3 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1308 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 5 sheets defined 30.7% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.813A pdb=" N HIS A 98 " --> pdb=" O HIS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 160 removed outlier: 3.561A pdb=" N HIS A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 200 removed outlier: 3.590A pdb=" N SER A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 228 removed outlier: 4.097A pdb=" N GLY A 219 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 312 removed outlier: 4.639A pdb=" N LEU A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 347 removed outlier: 3.502A pdb=" N LEU A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 375 through 383 Processing helix chain 'A' and resid 395 through 412 removed outlier: 4.134A pdb=" N GLU A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 406 " --> pdb=" O TRP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 443 removed outlier: 3.509A pdb=" N ARG A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 462 removed outlier: 4.128A pdb=" N GLN A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 456 " --> pdb=" O TRP A 452 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS A 457 " --> pdb=" O ASP A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 473 removed outlier: 4.004A pdb=" N ALA A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 483 Processing helix chain 'A' and resid 484 through 494 removed outlier: 3.903A pdb=" N ALA A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 506 removed outlier: 3.733A pdb=" N VAL A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1262 removed outlier: 3.783A pdb=" N VAL A1262 " --> pdb=" O ASN A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1419 removed outlier: 3.620A pdb=" N LYS A1419 " --> pdb=" O GLU A1415 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1465 removed outlier: 4.014A pdb=" N ARG A1459 " --> pdb=" O VAL A1455 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN A1461 " --> pdb=" O LEU A1457 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1496 removed outlier: 3.654A pdb=" N LEU A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1497 through 1499 No H-bonds generated for 'chain 'A' and resid 1497 through 1499' Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 72 Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 264 removed outlier: 7.398A pdb=" N TYR A 264 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL A 131 " --> pdb=" O TYR A 264 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS A 141 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU A 286 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL A 143 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ASP A 288 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL A 145 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE A 171 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL A 328 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER A 172 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU A 330 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR A 174 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N CYS A 327 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL A 353 " --> pdb=" O CYS A 327 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL A 329 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N CYS A 350 " --> pdb=" O THR A 417 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N PHE A 419 " --> pdb=" O CYS A 350 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 352 " --> pdb=" O PHE A 419 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1319 through 1320 Processing sheet with id=AA4, first strand: chain 'A' and resid 1343 through 1347 removed outlier: 6.066A pdb=" N GLY A1343 " --> pdb=" O TRP A1439 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLU A1441 " --> pdb=" O GLY A1343 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ASN A1345 " --> pdb=" O GLU A1441 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL A1443 " --> pdb=" O ASN A1345 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR A1347 " --> pdb=" O VAL A1443 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N VAL A1445 " --> pdb=" O THR A1347 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N MET A1351 " --> pdb=" O VAL A1447 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N PHE A1449 " --> pdb=" O MET A1351 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A1353 " --> pdb=" O PHE A1449 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N VAL A1352 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A1375 " --> pdb=" O VAL A1352 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1385 through 1386 removed outlier: 3.666A pdb=" N LEU A1375 " --> pdb=" O VAL A1352 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N VAL A1352 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N MET A1351 " --> pdb=" O VAL A1447 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N PHE A1449 " --> pdb=" O MET A1351 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A1353 " --> pdb=" O PHE A1449 " (cutoff:3.500A) 139 hydrogen bonds defined for protein. 399 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.58 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1801 1.34 - 1.46: 1108 1.46 - 1.57: 2661 1.57 - 1.69: 8 1.69 - 1.81: 35 Bond restraints: 5613 Sorted by residual: bond pdb=" O5D APR A1602 " pdb=" PB APR A1602 " ideal model delta sigma weight residual 1.641 1.492 0.149 2.00e-02 2.50e+03 5.53e+01 bond pdb=" O1B APR A1602 " pdb=" PB APR A1602 " ideal model delta sigma weight residual 1.497 1.604 -0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" O3A APR A1601 " pdb=" PA APR A1601 " ideal model delta sigma weight residual 1.648 1.603 0.045 2.00e-02 2.50e+03 5.11e+00 bond pdb=" O3A APR A1602 " pdb=" PA APR A1602 " ideal model delta sigma weight residual 1.648 1.604 0.044 2.00e-02 2.50e+03 4.94e+00 bond pdb=" C5' APR A1602 " pdb=" O5' APR A1602 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.85e+00 ... (remaining 5608 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.35: 7626 5.35 - 10.70: 19 10.70 - 16.06: 1 16.06 - 21.41: 0 21.41 - 26.76: 1 Bond angle restraints: 7647 Sorted by residual: angle pdb=" C ILE A 63 " pdb=" N PRO A 64 " pdb=" CD PRO A 64 " ideal model delta sigma weight residual 125.00 98.24 26.76 4.10e+00 5.95e-02 4.26e+01 angle pdb=" C THR A 201 " pdb=" CA THR A 201 " pdb=" CB THR A 201 " ideal model delta sigma weight residual 115.89 109.85 6.04 1.32e+00 5.74e-01 2.09e+01 angle pdb=" O1B APR A1602 " pdb=" PB APR A1602 " pdb=" O2B APR A1602 " ideal model delta sigma weight residual 122.24 109.32 12.92 3.00e+00 1.11e-01 1.86e+01 angle pdb=" C LYS A 86 " pdb=" N VAL A 87 " pdb=" CA VAL A 87 " ideal model delta sigma weight residual 121.97 128.93 -6.96 1.80e+00 3.09e-01 1.49e+01 angle pdb=" C LEU A1293 " pdb=" N GLU A1294 " pdb=" CA GLU A1294 " ideal model delta sigma weight residual 121.80 131.04 -9.24 2.44e+00 1.68e-01 1.43e+01 ... (remaining 7642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 3007 17.92 - 35.85: 256 35.85 - 53.77: 52 53.77 - 71.69: 15 71.69 - 89.61: 25 Dihedral angle restraints: 3355 sinusoidal: 1326 harmonic: 2029 Sorted by residual: dihedral pdb=" CA PHE A 260 " pdb=" C PHE A 260 " pdb=" N PRO A 261 " pdb=" CA PRO A 261 " ideal model delta harmonic sigma weight residual 180.00 136.35 43.65 0 5.00e+00 4.00e-02 7.62e+01 dihedral pdb=" CA ILE A 63 " pdb=" C ILE A 63 " pdb=" N PRO A 64 " pdb=" CA PRO A 64 " ideal model delta harmonic sigma weight residual -180.00 -140.21 -39.79 0 5.00e+00 4.00e-02 6.33e+01 dihedral pdb=" CA GLN A 160 " pdb=" C GLN A 160 " pdb=" N HIS A 161 " pdb=" CA HIS A 161 " ideal model delta harmonic sigma weight residual 180.00 144.11 35.89 0 5.00e+00 4.00e-02 5.15e+01 ... (remaining 3352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 705 0.058 - 0.116: 121 0.116 - 0.173: 20 0.173 - 0.231: 5 0.231 - 0.289: 2 Chirality restraints: 853 Sorted by residual: chirality pdb=" CA PRO A 64 " pdb=" N PRO A 64 " pdb=" C PRO A 64 " pdb=" CB PRO A 64 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB VAL A 87 " pdb=" CA VAL A 87 " pdb=" CG1 VAL A 87 " pdb=" CG2 VAL A 87 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C3' APR A1602 " pdb=" C2' APR A1602 " pdb=" C4' APR A1602 " pdb=" O3' APR A1602 " both_signs ideal model delta sigma weight residual False -2.54 -2.74 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 850 not shown) Planarity restraints: 976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 63 " -0.124 5.00e-02 4.00e+02 1.96e-01 6.13e+01 pdb=" N PRO A 64 " 0.338 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " -0.123 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " -0.091 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 260 " -0.080 5.00e-02 4.00e+02 1.24e-01 2.45e+01 pdb=" N PRO A 261 " 0.214 5.00e-02 4.00e+02 pdb=" CA PRO A 261 " -0.067 5.00e-02 4.00e+02 pdb=" CD PRO A 261 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1294 " 0.046 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO A1295 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A1295 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A1295 " 0.039 5.00e-02 4.00e+02 ... (remaining 973 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 999 2.77 - 3.30: 5182 3.30 - 3.84: 8558 3.84 - 4.37: 10281 4.37 - 4.90: 17518 Nonbonded interactions: 42538 Sorted by model distance: nonbonded pdb=" NE2 HIS A1239 " pdb=" O ARG A1330 " model vdw 2.240 3.120 nonbonded pdb=" OG1 THR A1331 " pdb=" OD1 ASP A1436 " model vdw 2.259 3.040 nonbonded pdb=" NH2 ARG A1243 " pdb=" OD1 ASN A1259 " model vdw 2.278 3.120 nonbonded pdb=" OH TYR A1271 " pdb=" OD2 ASP A1436 " model vdw 2.287 3.040 nonbonded pdb=" O ASN A 273 " pdb=" OH TYR A 295 " model vdw 2.317 3.040 ... (remaining 42533 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.220 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 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 : 0.009 0.525 5617 Z= 0.349 Angle : 1.194 62.565 7650 Z= 0.496 Chirality : 0.049 0.289 853 Planarity : 0.009 0.196 976 Dihedral : 16.784 89.611 2047 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 1.00 % Allowed : 9.84 % Favored : 89.16 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.15 % 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: -2.50 (0.32), residues: 701 helix: -0.22 (0.40), residues: 185 sheet: -1.16 (0.54), residues: 102 loop : -2.62 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 192 TYR 0.015 0.001 TYR A1428 PHE 0.022 0.002 PHE A 260 TRP 0.015 0.001 TRP A 113 HIS 0.005 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 5613) covalent geometry : angle 0.89969 ( 7647) hydrogen bonds : bond 0.22235 ( 137) hydrogen bonds : angle 6.40283 ( 399) metal coordination : bond 0.28586 ( 4) metal coordination : angle 39.64859 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.168 Fit side-chains REVERT: A 408 ASP cc_start: 0.8213 (m-30) cc_final: 0.7868 (m-30) REVERT: A 1317 TYR cc_start: 0.8490 (p90) cc_final: 0.8203 (p90) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0804 time to fit residues: 8.8923 Evaluate side-chains 71 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.0070 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.0000 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.125079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.108898 restraints weight = 9290.490| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.48 r_work: 0.3290 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5617 Z= 0.130 Angle : 0.724 11.581 7650 Z= 0.356 Chirality : 0.046 0.243 853 Planarity : 0.008 0.151 976 Dihedral : 10.024 82.660 827 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 1.00 % Allowed : 10.13 % Favored : 88.87 % Rotamer: Outliers : 0.90 % Allowed : 9.57 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.15 % 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: -2.28 (0.32), residues: 701 helix: 0.04 (0.39), residues: 191 sheet: -0.86 (0.53), residues: 107 loop : -2.62 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1407 TYR 0.015 0.001 TYR A1428 PHE 0.010 0.001 PHE A 132 TRP 0.010 0.001 TRP A1411 HIS 0.004 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5613) covalent geometry : angle 0.71245 ( 7647) hydrogen bonds : bond 0.04197 ( 137) hydrogen bonds : angle 4.35184 ( 399) metal coordination : bond 0.02132 ( 4) metal coordination : angle 6.40574 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.162 Fit side-chains REVERT: A 408 ASP cc_start: 0.8498 (m-30) cc_final: 0.8182 (m-30) REVERT: A 501 LYS cc_start: 0.8133 (ttpt) cc_final: 0.7914 (mtpp) REVERT: A 1317 TYR cc_start: 0.8584 (p90) cc_final: 0.8356 (p90) outliers start: 5 outliers final: 4 residues processed: 80 average time/residue: 0.0882 time to fit residues: 8.9576 Evaluate side-chains 74 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 1318 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.119563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.103328 restraints weight = 9098.944| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.49 r_work: 0.3200 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5617 Z= 0.218 Angle : 0.761 11.620 7650 Z= 0.382 Chirality : 0.048 0.207 853 Planarity : 0.008 0.154 976 Dihedral : 8.486 75.371 827 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 1.00 % Allowed : 11.55 % Favored : 87.45 % Rotamer: Outliers : 1.99 % Allowed : 13.72 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.15 % 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: -2.28 (0.32), residues: 701 helix: -0.10 (0.38), residues: 200 sheet: -1.06 (0.50), residues: 111 loop : -2.53 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1407 TYR 0.012 0.001 TYR A1428 PHE 0.015 0.002 PHE A 132 TRP 0.013 0.002 TRP A1411 HIS 0.006 0.002 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 5613) covalent geometry : angle 0.74945 ( 7647) hydrogen bonds : bond 0.04450 ( 137) hydrogen bonds : angle 4.38079 ( 399) metal coordination : bond 0.01048 ( 4) metal coordination : angle 6.63102 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.214 Fit side-chains REVERT: A 408 ASP cc_start: 0.8449 (m-30) cc_final: 0.8168 (m-30) REVERT: A 1317 TYR cc_start: 0.8609 (p90) cc_final: 0.8365 (p90) outliers start: 11 outliers final: 10 residues processed: 77 average time/residue: 0.0877 time to fit residues: 8.6747 Evaluate side-chains 81 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1405 ILE Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain A residue 1490 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.0770 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1410 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.123092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.107081 restraints weight = 9026.262| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.49 r_work: 0.3244 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 5617 Z= 0.134 Angle : 0.679 10.532 7650 Z= 0.342 Chirality : 0.045 0.212 853 Planarity : 0.008 0.153 976 Dihedral : 7.864 74.269 827 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 1.00 % Allowed : 9.99 % Favored : 89.02 % Rotamer: Outliers : 2.89 % Allowed : 13.90 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.15 % 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: -2.07 (0.32), residues: 701 helix: 0.43 (0.39), residues: 192 sheet: -1.07 (0.51), residues: 109 loop : -2.51 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1407 TYR 0.015 0.001 TYR A1428 PHE 0.013 0.001 PHE A 260 TRP 0.008 0.001 TRP A1411 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 5613) covalent geometry : angle 0.67370 ( 7647) hydrogen bonds : bond 0.03476 ( 137) hydrogen bonds : angle 4.14780 ( 399) metal coordination : bond 0.01168 ( 4) metal coordination : angle 4.17363 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.200 Fit side-chains REVERT: A 118 HIS cc_start: 0.6262 (p-80) cc_final: 0.5388 (p-80) REVERT: A 408 ASP cc_start: 0.8419 (m-30) cc_final: 0.8123 (m-30) REVERT: A 501 LYS cc_start: 0.8099 (ttpt) cc_final: 0.7868 (mtpp) outliers start: 16 outliers final: 11 residues processed: 84 average time/residue: 0.0766 time to fit residues: 8.3750 Evaluate side-chains 80 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1405 ILE Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1477 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 67 optimal weight: 0.0050 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 21 optimal weight: 0.0670 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.3932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.123971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.109437 restraints weight = 9031.165| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.07 r_work: 0.3298 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5617 Z= 0.116 Angle : 0.708 23.203 7650 Z= 0.339 Chirality : 0.045 0.282 853 Planarity : 0.008 0.192 976 Dihedral : 7.568 72.113 827 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.86 % Allowed : 10.56 % Favored : 88.59 % Rotamer: Outliers : 2.89 % Allowed : 14.98 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.15 % 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: -1.90 (0.32), residues: 701 helix: 0.66 (0.39), residues: 194 sheet: -0.97 (0.51), residues: 109 loop : -2.47 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 192 TYR 0.015 0.001 TYR A1428 PHE 0.012 0.001 PHE A 260 TRP 0.007 0.001 TRP A1411 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 5613) covalent geometry : angle 0.70312 ( 7647) hydrogen bonds : bond 0.03085 ( 137) hydrogen bonds : angle 4.02706 ( 399) metal coordination : bond 0.01011 ( 4) metal coordination : angle 4.16108 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.218 Fit side-chains REVERT: A 118 HIS cc_start: 0.6269 (p-80) cc_final: 0.5837 (p-80) REVERT: A 408 ASP cc_start: 0.8611 (m-30) cc_final: 0.8354 (m-30) REVERT: A 1317 TYR cc_start: 0.8547 (p90) cc_final: 0.8300 (p90) outliers start: 16 outliers final: 10 residues processed: 87 average time/residue: 0.0731 time to fit residues: 8.4703 Evaluate side-chains 81 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1405 ILE Chi-restraints excluded: chain A residue 1477 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 0.0870 chunk 37 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN ** A 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.122783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.108127 restraints weight = 9043.046| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.10 r_work: 0.3266 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5617 Z= 0.149 Angle : 0.707 15.950 7650 Z= 0.349 Chirality : 0.045 0.244 853 Planarity : 0.008 0.170 976 Dihedral : 7.604 72.366 827 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.86 % Allowed : 11.13 % Favored : 88.02 % Rotamer: Outliers : 2.89 % Allowed : 15.34 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.15 % 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: -1.84 (0.33), residues: 701 helix: 0.79 (0.39), residues: 194 sheet: -0.98 (0.51), residues: 109 loop : -2.47 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 192 TYR 0.014 0.001 TYR A1428 PHE 0.011 0.001 PHE A 260 TRP 0.008 0.001 TRP A1411 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5613) covalent geometry : angle 0.70226 ( 7647) hydrogen bonds : bond 0.03379 ( 137) hydrogen bonds : angle 4.06486 ( 399) metal coordination : bond 0.01365 ( 4) metal coordination : angle 4.16223 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.181 Fit side-chains REVERT: A 118 HIS cc_start: 0.6245 (OUTLIER) cc_final: 0.5886 (p-80) REVERT: A 408 ASP cc_start: 0.8641 (m-30) cc_final: 0.8415 (m-30) REVERT: A 1317 TYR cc_start: 0.8605 (p90) cc_final: 0.8328 (p90) outliers start: 16 outliers final: 11 residues processed: 81 average time/residue: 0.0625 time to fit residues: 6.6098 Evaluate side-chains 83 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1405 ILE Chi-restraints excluded: chain A residue 1477 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 45 optimal weight: 0.2980 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 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.121816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.107055 restraints weight = 9120.912| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.08 r_work: 0.3269 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5617 Z= 0.150 Angle : 0.700 13.459 7650 Z= 0.348 Chirality : 0.045 0.221 853 Planarity : 0.008 0.164 976 Dihedral : 7.642 73.228 827 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.86 % Allowed : 11.13 % Favored : 88.02 % Rotamer: Outliers : 2.89 % Allowed : 15.34 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.15 % 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: -1.79 (0.33), residues: 701 helix: 0.88 (0.39), residues: 193 sheet: -0.94 (0.51), residues: 111 loop : -2.46 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 192 TYR 0.016 0.001 TYR A1428 PHE 0.012 0.001 PHE A 260 TRP 0.008 0.001 TRP A1411 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 5613) covalent geometry : angle 0.69311 ( 7647) hydrogen bonds : bond 0.03363 ( 137) hydrogen bonds : angle 4.07718 ( 399) metal coordination : bond 0.02196 ( 4) metal coordination : angle 4.96614 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.181 Fit side-chains REVERT: A 408 ASP cc_start: 0.8619 (m-30) cc_final: 0.8404 (m-30) REVERT: A 474 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.6742 (ttm) REVERT: A 1317 TYR cc_start: 0.8565 (p90) cc_final: 0.8275 (p90) outliers start: 16 outliers final: 11 residues processed: 79 average time/residue: 0.0690 time to fit residues: 7.0253 Evaluate side-chains 82 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1405 ILE Chi-restraints excluded: chain A residue 1477 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 21 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 0.0040 chunk 42 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.123094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.108340 restraints weight = 9027.084| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.07 r_work: 0.3288 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 5617 Z= 0.128 Angle : 0.679 12.138 7650 Z= 0.339 Chirality : 0.045 0.214 853 Planarity : 0.008 0.159 976 Dihedral : 7.543 72.919 827 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.86 % Allowed : 10.27 % Favored : 88.87 % Rotamer: Outliers : 2.53 % Allowed : 16.06 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.15 % 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: -1.78 (0.33), residues: 701 helix: 0.95 (0.39), residues: 194 sheet: -1.00 (0.51), residues: 109 loop : -2.47 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 192 TYR 0.016 0.001 TYR A1428 PHE 0.012 0.001 PHE A 260 TRP 0.008 0.001 TRP A 113 HIS 0.008 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 5613) covalent geometry : angle 0.67250 ( 7647) hydrogen bonds : bond 0.03118 ( 137) hydrogen bonds : angle 4.02107 ( 399) metal coordination : bond 0.02421 ( 4) metal coordination : angle 4.65961 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.174 Fit side-chains REVERT: A 408 ASP cc_start: 0.8605 (m-30) cc_final: 0.8395 (m-30) REVERT: A 474 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6799 (ttm) REVERT: A 1317 TYR cc_start: 0.8537 (p90) cc_final: 0.8311 (p90) outliers start: 14 outliers final: 11 residues processed: 81 average time/residue: 0.0709 time to fit residues: 7.4442 Evaluate side-chains 83 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1405 ILE Chi-restraints excluded: chain A residue 1477 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 33 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 49 optimal weight: 0.0020 chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 0.1980 chunk 66 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.122905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.108084 restraints weight = 9085.650| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.12 r_work: 0.3275 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 5617 Z= 0.142 Angle : 0.688 11.745 7650 Z= 0.347 Chirality : 0.045 0.203 853 Planarity : 0.008 0.158 976 Dihedral : 7.556 72.783 827 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.86 % Allowed : 11.13 % Favored : 88.02 % Rotamer: Outliers : 2.35 % Allowed : 16.79 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.15 % 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: -1.78 (0.33), residues: 701 helix: 0.77 (0.39), residues: 200 sheet: -1.02 (0.51), residues: 109 loop : -2.40 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 192 TYR 0.030 0.001 TYR A1428 PHE 0.012 0.001 PHE A 260 TRP 0.008 0.001 TRP A1411 HIS 0.005 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 5613) covalent geometry : angle 0.68253 ( 7647) hydrogen bonds : bond 0.03262 ( 137) hydrogen bonds : angle 4.03992 ( 399) metal coordination : bond 0.02382 ( 4) metal coordination : angle 4.57490 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.209 Fit side-chains REVERT: A 408 ASP cc_start: 0.8638 (m-30) cc_final: 0.8429 (m-30) REVERT: A 474 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6757 (ttm) REVERT: A 1317 TYR cc_start: 0.8526 (p90) cc_final: 0.8229 (p90) REVERT: A 1413 SER cc_start: 0.7453 (t) cc_final: 0.7203 (m) outliers start: 13 outliers final: 11 residues processed: 80 average time/residue: 0.0766 time to fit residues: 8.0903 Evaluate side-chains 85 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1405 ILE Chi-restraints excluded: chain A residue 1477 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 67 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.107341 restraints weight = 9057.347| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.21 r_work: 0.3265 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5617 Z= 0.141 Angle : 0.684 11.323 7650 Z= 0.345 Chirality : 0.045 0.202 853 Planarity : 0.008 0.156 976 Dihedral : 7.563 73.051 827 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.86 % Allowed : 10.70 % Favored : 88.45 % Rotamer: Outliers : 2.35 % Allowed : 17.15 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.15 % 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: -1.76 (0.33), residues: 701 helix: 0.82 (0.39), residues: 200 sheet: -1.10 (0.51), residues: 109 loop : -2.38 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 192 TYR 0.023 0.001 TYR A1428 PHE 0.012 0.001 PHE A 260 TRP 0.008 0.001 TRP A1411 HIS 0.005 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 5613) covalent geometry : angle 0.67877 ( 7647) hydrogen bonds : bond 0.03205 ( 137) hydrogen bonds : angle 4.01975 ( 399) metal coordination : bond 0.02355 ( 4) metal coordination : angle 4.38700 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.160 Fit side-chains REVERT: A 408 ASP cc_start: 0.8645 (m-30) cc_final: 0.8432 (m-30) REVERT: A 474 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.6869 (ttm) REVERT: A 1317 TYR cc_start: 0.8540 (p90) cc_final: 0.8243 (p90) outliers start: 13 outliers final: 11 residues processed: 81 average time/residue: 0.0656 time to fit residues: 6.9736 Evaluate side-chains 82 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1405 ILE Chi-restraints excluded: chain A residue 1477 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 12 optimal weight: 0.0770 chunk 4 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.123578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.109131 restraints weight = 9031.764| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.06 r_work: 0.3299 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 5617 Z= 0.124 Angle : 0.775 31.990 7650 Z= 0.353 Chirality : 0.045 0.309 853 Planarity : 0.009 0.213 976 Dihedral : 7.480 72.183 827 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.86 % Allowed : 10.41 % Favored : 88.73 % Rotamer: Outliers : 2.35 % Allowed : 17.33 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.15 % 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: -1.68 (0.33), residues: 701 helix: 0.97 (0.39), residues: 198 sheet: -0.95 (0.52), residues: 107 loop : -2.39 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 192 TYR 0.023 0.001 TYR A1428 PHE 0.012 0.001 PHE A 260 TRP 0.006 0.001 TRP A 477 HIS 0.006 0.001 HIS A1410 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 5613) covalent geometry : angle 0.77072 ( 7647) hydrogen bonds : bond 0.03009 ( 137) hydrogen bonds : angle 3.95830 ( 399) metal coordination : bond 0.02585 ( 4) metal coordination : angle 4.17909 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1202.36 seconds wall clock time: 21 minutes 12.89 seconds (1272.89 seconds total)