Starting phenix.real_space_refine on Thu Jul 24 06:47:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e6v_27927/07_2025/8e6v_27927.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e6v_27927/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8e6v_27927/07_2025/8e6v_27927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e6v_27927/07_2025/8e6v_27927.map" model { file = "/net/cci-nas-00/data/ceres_data/8e6v_27927/07_2025/8e6v_27927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e6v_27927/07_2025/8e6v_27927.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.042 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 6, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 10, 'HIS: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: 4.00, per 1000 atoms: 0.73 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: 1.30 Conformation dependent library (CDL) restraints added in 725.9 milliseconds 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: 0.69 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: 1.66 Time building geometry restraints manager: 1.52 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: 0.010 Normalize map: mean=0, sd=1: 3.830 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.260 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.790 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.015 0.001 TRP A 113 HIS 0.005 0.001 HIS A 118 PHE 0.022 0.002 PHE A 260 TYR 0.015 0.001 TYR A1428 ARG 0.008 0.000 ARG A 192 Details of bonding type rmsd hydrogen bonds : bond 0.22235 ( 137) hydrogen bonds : angle 6.40283 ( 399) metal coordination : bond 0.28586 ( 4) metal coordination : angle 39.64859 ( 3) covalent geometry : bond 0.00450 ( 5613) covalent geometry : angle 0.89969 ( 7647) *********************** 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 : 0.541 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: 0.1919 time to fit residues: 21.2103 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 : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 54 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 40 optimal weight: 0.2980 chunk 63 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.124669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.108631 restraints weight = 9135.170| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.44 r_work: 0.3284 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1060 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= 0.134 Angle : 0.729 12.285 7650 Z= 0.358 Chirality : 0.046 0.235 853 Planarity : 0.008 0.154 976 Dihedral : 10.390 84.109 827 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 1.00 % Allowed : 10.41 % Favored : 88.59 % Rotamer: Outliers : 0.90 % Allowed : 9.75 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.32), residues: 701 helix: 0.01 (0.39), residues: 192 sheet: -0.93 (0.53), residues: 105 loop : -2.61 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1411 HIS 0.004 0.001 HIS A 98 PHE 0.011 0.001 PHE A 132 TYR 0.015 0.001 TYR A1428 ARG 0.009 0.001 ARG A1407 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 137) hydrogen bonds : angle 4.39323 ( 399) metal coordination : bond 0.01934 ( 4) metal coordination : angle 6.38303 ( 3) covalent geometry : bond 0.00304 ( 5613) covalent geometry : angle 0.71829 ( 7647) *********************** 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 83 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.638 Fit side-chains REVERT: A 408 ASP cc_start: 0.8725 (m-30) cc_final: 0.8431 (m-30) REVERT: A 444 GLN cc_start: 0.8166 (tt0) cc_final: 0.7928 (tt0) REVERT: A 501 LYS cc_start: 0.8355 (ttpt) cc_final: 0.8116 (mtpp) REVERT: A 1317 TYR cc_start: 0.8628 (p90) cc_final: 0.8406 (p90) outliers start: 5 outliers final: 4 residues processed: 81 average time/residue: 0.2047 time to fit residues: 21.3793 Evaluate side-chains 72 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 37 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 40 optimal weight: 0.0970 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.123506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.108892 restraints weight = 8888.239| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.05 r_work: 0.3286 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5617 Z= 0.149 Angle : 0.703 10.658 7650 Z= 0.353 Chirality : 0.046 0.222 853 Planarity : 0.008 0.152 976 Dihedral : 8.133 73.822 827 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 1.00 % Allowed : 10.56 % Favored : 88.45 % Rotamer: Outliers : 1.08 % Allowed : 13.90 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.32), residues: 701 helix: 0.23 (0.39), residues: 193 sheet: -0.93 (0.51), residues: 110 loop : -2.56 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1411 HIS 0.004 0.001 HIS A 95 PHE 0.017 0.002 PHE A1414 TYR 0.014 0.001 TYR A1428 ARG 0.008 0.001 ARG A1407 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 137) hydrogen bonds : angle 4.23564 ( 399) metal coordination : bond 0.01331 ( 4) metal coordination : angle 5.27017 ( 3) covalent geometry : bond 0.00344 ( 5613) covalent geometry : angle 0.69500 ( 7647) *********************** 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 77 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.600 Fit side-chains REVERT: A 408 ASP cc_start: 0.8590 (m-30) cc_final: 0.8323 (m-30) REVERT: A 501 LYS cc_start: 0.8262 (ttpt) cc_final: 0.8058 (mtpp) REVERT: A 1317 TYR cc_start: 0.8601 (p90) cc_final: 0.8373 (p90) outliers start: 6 outliers final: 5 residues processed: 74 average time/residue: 0.1928 time to fit residues: 18.6792 Evaluate side-chains 74 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 1477 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 51 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.0030 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.124632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.109685 restraints weight = 9059.023| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.10 r_work: 0.3304 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 5617 Z= 0.126 Angle : 0.660 10.090 7650 Z= 0.332 Chirality : 0.045 0.216 853 Planarity : 0.008 0.152 976 Dihedral : 7.602 71.688 827 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 1.00 % Allowed : 10.13 % Favored : 88.87 % Rotamer: Outliers : 3.07 % Allowed : 13.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.32), residues: 701 helix: 0.53 (0.39), residues: 192 sheet: -0.89 (0.51), residues: 111 loop : -2.54 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1411 HIS 0.003 0.001 HIS A 283 PHE 0.013 0.001 PHE A 387 TYR 0.013 0.001 TYR A1428 ARG 0.007 0.001 ARG A1407 Details of bonding type rmsd hydrogen bonds : bond 0.03321 ( 137) hydrogen bonds : angle 4.08019 ( 399) metal coordination : bond 0.01290 ( 4) metal coordination : angle 4.19358 ( 3) covalent geometry : bond 0.00296 ( 5613) covalent geometry : angle 0.65480 ( 7647) *********************** 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 93 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.634 Fit side-chains REVERT: A 118 HIS cc_start: 0.6312 (p-80) cc_final: 0.5766 (p-80) REVERT: A 408 ASP cc_start: 0.8579 (m-30) cc_final: 0.8272 (m-30) REVERT: A 501 LYS cc_start: 0.8248 (ttpt) cc_final: 0.8021 (mtpp) outliers start: 17 outliers final: 11 residues processed: 88 average time/residue: 0.1844 time to fit residues: 21.1985 Evaluate side-chains 79 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 1353 THR Chi-restraints excluded: chain A residue 1372 LEU 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 34 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 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 = 0.3556 r_free = 0.3556 target = 0.122291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.107730 restraints weight = 8917.205| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.05 r_work: 0.3277 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5617 Z= 0.153 Angle : 0.729 23.220 7650 Z= 0.350 Chirality : 0.046 0.291 853 Planarity : 0.009 0.192 976 Dihedral : 7.613 72.029 827 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.86 % Allowed : 11.41 % Favored : 87.73 % Rotamer: Outliers : 3.07 % Allowed : 14.26 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.32), residues: 701 helix: 0.66 (0.39), residues: 193 sheet: -0.99 (0.51), residues: 109 loop : -2.48 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1411 HIS 0.004 0.001 HIS A 95 PHE 0.013 0.001 PHE A 387 TYR 0.019 0.001 TYR A1317 ARG 0.007 0.001 ARG A 192 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 137) hydrogen bonds : angle 4.11519 ( 399) metal coordination : bond 0.01744 ( 4) metal coordination : angle 5.62839 ( 3) covalent geometry : bond 0.00348 ( 5613) covalent geometry : angle 0.72050 ( 7647) *********************** 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 90 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.584 Fit side-chains REVERT: A 118 HIS cc_start: 0.6265 (p-80) cc_final: 0.5668 (p-80) REVERT: A 408 ASP cc_start: 0.8618 (m-30) cc_final: 0.8339 (m-30) REVERT: A 501 LYS cc_start: 0.8237 (ttpt) cc_final: 0.8012 (mtpp) REVERT: A 1317 TYR cc_start: 0.8596 (p90) cc_final: 0.8363 (p90) outliers start: 17 outliers final: 14 residues processed: 83 average time/residue: 0.1738 time to fit residues: 19.2853 Evaluate side-chains 85 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 504 LEU 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 1372 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 60 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.122759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.107966 restraints weight = 8942.063| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.09 r_work: 0.3270 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5617 Z= 0.146 Angle : 0.704 15.989 7650 Z= 0.345 Chirality : 0.045 0.243 853 Planarity : 0.008 0.171 976 Dihedral : 7.620 72.963 827 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.86 % Allowed : 10.84 % Favored : 88.30 % Rotamer: Outliers : 3.07 % Allowed : 15.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.32), residues: 701 helix: 0.80 (0.39), residues: 193 sheet: -1.00 (0.51), residues: 109 loop : -2.48 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1411 HIS 0.003 0.001 HIS A 292 PHE 0.013 0.001 PHE A 387 TYR 0.014 0.001 TYR A1428 ARG 0.013 0.001 ARG A 192 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 137) hydrogen bonds : angle 4.08301 ( 399) metal coordination : bond 0.02332 ( 4) metal coordination : angle 5.14726 ( 3) covalent geometry : bond 0.00336 ( 5613) covalent geometry : angle 0.69661 ( 7647) *********************** 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 92 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.650 Fit side-chains REVERT: A 118 HIS cc_start: 0.6153 (p-80) cc_final: 0.5862 (p-80) REVERT: A 408 ASP cc_start: 0.8629 (m-30) cc_final: 0.8367 (m-30) REVERT: A 1317 TYR cc_start: 0.8560 (p90) cc_final: 0.8293 (p90) outliers start: 17 outliers final: 15 residues processed: 83 average time/residue: 0.1864 time to fit residues: 20.3446 Evaluate side-chains 87 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 500 VAL Chi-restraints excluded: chain A residue 504 LEU 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 1372 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 62 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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** A1410 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.124304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.109484 restraints weight = 8993.363| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.10 r_work: 0.3306 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5617 Z= 0.122 Angle : 0.671 12.724 7650 Z= 0.332 Chirality : 0.044 0.223 853 Planarity : 0.008 0.161 976 Dihedral : 7.459 72.192 827 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.86 % Allowed : 10.56 % Favored : 88.59 % Rotamer: Outliers : 3.25 % Allowed : 15.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.33), residues: 701 helix: 0.95 (0.39), residues: 193 sheet: -0.94 (0.51), residues: 109 loop : -2.47 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1411 HIS 0.003 0.001 HIS A 283 PHE 0.013 0.001 PHE A 260 TYR 0.014 0.001 TYR A1428 ARG 0.012 0.001 ARG A 192 Details of bonding type rmsd hydrogen bonds : bond 0.03005 ( 137) hydrogen bonds : angle 3.98426 ( 399) metal coordination : bond 0.02669 ( 4) metal coordination : angle 4.54040 ( 3) covalent geometry : bond 0.00281 ( 5613) covalent geometry : angle 0.66552 ( 7647) *********************** 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 93 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.631 Fit side-chains REVERT: A 118 HIS cc_start: 0.6229 (OUTLIER) cc_final: 0.5882 (p-80) REVERT: A 408 ASP cc_start: 0.8637 (m-30) cc_final: 0.8372 (m-30) REVERT: A 501 LYS cc_start: 0.8206 (ttpt) cc_final: 0.8002 (mtpp) REVERT: A 1317 TYR cc_start: 0.8536 (p90) cc_final: 0.8283 (p90) outliers start: 18 outliers final: 14 residues processed: 84 average time/residue: 0.1810 time to fit residues: 20.2164 Evaluate side-chains 85 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 500 VAL Chi-restraints excluded: chain A residue 504 LEU 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 1402 LEU 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 19 optimal weight: 0.0040 chunk 36 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- 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 156 HIS ** 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 = 0.3514 r_free = 0.3514 target = 0.119067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.104810 restraints weight = 8918.574| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.02 r_work: 0.3231 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2302 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= 0.206 Angle : 0.746 12.713 7650 Z= 0.376 Chirality : 0.047 0.199 853 Planarity : 0.008 0.160 976 Dihedral : 7.878 74.100 827 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.86 % Allowed : 11.84 % Favored : 87.30 % Rotamer: Outliers : 3.07 % Allowed : 16.25 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.33), residues: 701 helix: 0.59 (0.39), residues: 200 sheet: -1.06 (0.51), residues: 109 loop : -2.43 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1411 HIS 0.006 0.001 HIS A 95 PHE 0.015 0.002 PHE A 387 TYR 0.025 0.002 TYR A1428 ARG 0.014 0.001 ARG A 192 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 137) hydrogen bonds : angle 4.25043 ( 399) metal coordination : bond 0.02345 ( 4) metal coordination : angle 6.10432 ( 3) covalent geometry : bond 0.00473 ( 5613) covalent geometry : angle 0.73649 ( 7647) *********************** 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 92 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.577 Fit side-chains REVERT: A 408 ASP cc_start: 0.8615 (m-30) cc_final: 0.8339 (m-30) REVERT: A 474 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.6758 (ttm) REVERT: A 1317 TYR cc_start: 0.8592 (p90) cc_final: 0.8312 (p90) REVERT: A 1413 SER cc_start: 0.7479 (t) cc_final: 0.7197 (m) REVERT: A 1419 LYS cc_start: 0.7652 (mttt) cc_final: 0.6377 (tppt) outliers start: 17 outliers final: 13 residues processed: 84 average time/residue: 0.1821 time to fit residues: 19.9904 Evaluate side-chains 84 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 241 VAL 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 474 MET Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 504 LEU 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 35 optimal weight: 0.0870 chunk 62 optimal weight: 0.0050 chunk 6 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 0.0980 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 0.0670 chunk 34 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.1710 ------------------------------------------------------------------------------- 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 156 HIS ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1434 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 = 0.3606 r_free = 0.3606 target = 0.125925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.111271 restraints weight = 8928.661| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.08 r_work: 0.3326 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2302 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= 0.110 Angle : 0.680 11.032 7650 Z= 0.339 Chirality : 0.044 0.217 853 Planarity : 0.008 0.155 976 Dihedral : 7.424 72.823 827 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.86 % Allowed : 9.27 % Favored : 89.87 % Rotamer: Outliers : 2.17 % Allowed : 17.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.33), residues: 701 helix: 1.11 (0.40), residues: 192 sheet: -0.90 (0.52), residues: 109 loop : -2.49 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 462 HIS 0.005 0.001 HIS A 118 PHE 0.013 0.001 PHE A 260 TYR 0.020 0.001 TYR A1428 ARG 0.014 0.001 ARG A 192 Details of bonding type rmsd hydrogen bonds : bond 0.02744 ( 137) hydrogen bonds : angle 3.97755 ( 399) metal coordination : bond 0.02865 ( 4) metal coordination : angle 4.05904 ( 3) covalent geometry : bond 0.00251 ( 5613) covalent geometry : angle 0.67527 ( 7647) *********************** 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 89 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.607 Fit side-chains REVERT: A 408 ASP cc_start: 0.8669 (m-30) cc_final: 0.8412 (m-30) REVERT: A 501 LYS cc_start: 0.8219 (ttpt) cc_final: 0.7991 (mtpp) REVERT: A 1419 LYS cc_start: 0.7458 (mttt) cc_final: 0.6231 (tppt) outliers start: 12 outliers final: 9 residues processed: 84 average time/residue: 0.1913 time to fit residues: 20.9930 Evaluate side-chains 81 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 1270 ILE 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 47 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.0020 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.125147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.110786 restraints weight = 8933.629| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.05 r_work: 0.3308 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 5617 Z= 0.127 Angle : 0.758 31.591 7650 Z= 0.350 Chirality : 0.046 0.312 853 Planarity : 0.009 0.213 976 Dihedral : 7.370 70.825 827 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.86 % Allowed : 10.13 % Favored : 89.02 % Rotamer: Outliers : 2.17 % Allowed : 18.05 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.33), residues: 701 helix: 1.19 (0.40), residues: 192 sheet: -0.86 (0.52), residues: 107 loop : -2.52 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1411 HIS 0.004 0.001 HIS A 161 PHE 0.013 0.001 PHE A 260 TYR 0.013 0.001 TYR A1428 ARG 0.015 0.001 ARG A 192 Details of bonding type rmsd hydrogen bonds : bond 0.02954 ( 137) hydrogen bonds : angle 3.99092 ( 399) metal coordination : bond 0.02540 ( 4) metal coordination : angle 4.30132 ( 3) covalent geometry : bond 0.00297 ( 5613) covalent geometry : angle 0.75355 ( 7647) ********************** 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 84 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.589 Fit side-chains REVERT: A 408 ASP cc_start: 0.8650 (m-30) cc_final: 0.8405 (m-30) REVERT: A 474 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.6792 (ttm) REVERT: A 501 LYS cc_start: 0.8227 (ttpt) cc_final: 0.8000 (mtpp) REVERT: A 1413 SER cc_start: 0.7337 (t) cc_final: 0.7077 (m) REVERT: A 1419 LYS cc_start: 0.7517 (mttt) cc_final: 0.6305 (tppt) outliers start: 12 outliers final: 10 residues processed: 79 average time/residue: 0.1847 time to fit residues: 19.3396 Evaluate side-chains 83 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 1270 ILE 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 4 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** A1241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.120623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106134 restraints weight = 9041.679| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.07 r_work: 0.3251 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5617 Z= 0.185 Angle : 0.773 28.505 7650 Z= 0.368 Chirality : 0.047 0.277 853 Planarity : 0.009 0.201 976 Dihedral : 7.771 73.825 827 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.86 % Allowed : 11.27 % Favored : 87.87 % Rotamer: Outliers : 2.17 % Allowed : 18.05 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.33), residues: 701 helix: 0.81 (0.39), residues: 200 sheet: -1.10 (0.52), residues: 111 loop : -2.38 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1411 HIS 0.005 0.001 HIS A 95 PHE 0.014 0.001 PHE A 387 TYR 0.010 0.001 TYR A1428 ARG 0.015 0.001 ARG A 192 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 137) hydrogen bonds : angle 4.15855 ( 399) metal coordination : bond 0.02374 ( 4) metal coordination : angle 5.19260 ( 3) covalent geometry : bond 0.00427 ( 5613) covalent geometry : angle 0.76668 ( 7647) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3008.08 seconds wall clock time: 52 minutes 22.42 seconds (3142.42 seconds total)