Starting phenix.real_space_refine on Wed Mar 4 00:40:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7och_12807/03_2026/7och_12807.cif Found real_map, /net/cci-nas-00/data/ceres_data/7och_12807/03_2026/7och_12807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7och_12807/03_2026/7och_12807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7och_12807/03_2026/7och_12807.map" model { file = "/net/cci-nas-00/data/ceres_data/7och_12807/03_2026/7och_12807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7och_12807/03_2026/7och_12807.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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 Mg 1 5.21 5 S 57 5.16 5 C 6084 2.51 5 N 1600 2.21 5 O 1773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9516 Number of models: 1 Model: "" Number of chains: 2 Chain: "L" Number of atoms: 9514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1181, 9514 Classifications: {'peptide': 1181} Link IDs: {'PTRANS': 39, 'TRANS': 1141} Chain breaks: 10 Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1010 SG CYS L 321 40.543 105.212 68.291 1.00 87.95 S ATOM 1331 SG CYS L 366 39.729 105.981 71.333 1.00 95.02 S Time building chain proxies: 2.53, per 1000 atoms: 0.27 Number of scatterers: 9516 At special positions: 0 Unit cell: (96.57, 134.85, 107.01, 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 57 16.00 Mg 1 11.99 O 1773 8.00 N 1600 7.00 C 6084 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: 0.69 Conformation dependent library (CDL) restraints added in 507.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L2301 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L 316 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L 364 " pdb="ZN ZN L2301 " - pdb=" SG CYS L 366 " pdb="ZN ZN L2301 " - pdb=" SG CYS L 321 " Number of angles added : 2 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2258 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 8 sheets defined 53.5% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'L' and resid 199 through 206 removed outlier: 3.650A pdb=" N LEU L 203 " --> pdb=" O VAL L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 212 through 222 removed outlier: 4.183A pdb=" N GLU L 216 " --> pdb=" O SER L 212 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE L 217 " --> pdb=" O HIS L 213 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE L 218 " --> pdb=" O TYR L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 252 removed outlier: 4.340A pdb=" N LEU L 236 " --> pdb=" O HIS L 232 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN L 237 " --> pdb=" O GLU L 233 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS L 251 " --> pdb=" O ASN L 247 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY L 252 " --> pdb=" O ARG L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 272 removed outlier: 4.014A pdb=" N ASN L 272 " --> pdb=" O ASN L 268 " (cutoff:3.500A) Processing helix chain 'L' and resid 284 through 293 removed outlier: 4.010A pdb=" N LYS L 293 " --> pdb=" O ILE L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 302 Processing helix chain 'L' and resid 311 through 316 Processing helix chain 'L' and resid 317 through 319 No H-bonds generated for 'chain 'L' and resid 317 through 319' Processing helix chain 'L' and resid 321 through 335 removed outlier: 3.864A pdb=" N TYR L 325 " --> pdb=" O CYS L 321 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER L 335 " --> pdb=" O ASN L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 345 through 365 removed outlier: 3.527A pdb=" N PHE L 349 " --> pdb=" O LEU L 345 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG L 363 " --> pdb=" O HIS L 359 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS L 364 " --> pdb=" O ASP L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 405 removed outlier: 4.110A pdb=" N SER L 405 " --> pdb=" O GLN L 401 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 433 removed outlier: 3.707A pdb=" N ILE L 416 " --> pdb=" O ASP L 412 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU L 417 " --> pdb=" O LYS L 413 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE L 418 " --> pdb=" O ASN L 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 445 through 449 removed outlier: 3.748A pdb=" N VAL L 448 " --> pdb=" O ASN L 445 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE L 449 " --> pdb=" O MET L 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 445 through 449' Processing helix chain 'L' and resid 453 through 458 Processing helix chain 'L' and resid 491 through 507 removed outlier: 4.320A pdb=" N GLU L 495 " --> pdb=" O SER L 491 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG L 496 " --> pdb=" O THR L 492 " (cutoff:3.500A) Processing helix chain 'L' and resid 587 through 599 removed outlier: 3.984A pdb=" N GLN L 591 " --> pdb=" O ALA L 587 " (cutoff:3.500A) Processing helix chain 'L' and resid 612 through 628 removed outlier: 3.785A pdb=" N SER L 616 " --> pdb=" O CYS L 612 " (cutoff:3.500A) Processing helix chain 'L' and resid 630 through 639 removed outlier: 3.918A pdb=" N GLN L 634 " --> pdb=" O SER L 630 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS L 635 " --> pdb=" O LYS L 631 " (cutoff:3.500A) Processing helix chain 'L' and resid 639 through 647 removed outlier: 3.825A pdb=" N PHE L 643 " --> pdb=" O ASN L 639 " (cutoff:3.500A) Processing helix chain 'L' and resid 666 through 684 removed outlier: 4.228A pdb=" N PHE L 670 " --> pdb=" O THR L 666 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU L 671 " --> pdb=" O ASP L 667 " (cutoff:3.500A) Processing helix chain 'L' and resid 691 through 703 removed outlier: 3.763A pdb=" N ARG L 695 " --> pdb=" O MET L 691 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER L 703 " --> pdb=" O ILE L 699 " (cutoff:3.500A) Processing helix chain 'L' and resid 705 through 709 removed outlier: 3.538A pdb=" N PHE L 708 " --> pdb=" O MET L 705 " (cutoff:3.500A) Processing helix chain 'L' and resid 715 through 729 removed outlier: 4.074A pdb=" N ASP L 719 " --> pdb=" O ASP L 715 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN L 720 " --> pdb=" O ARG L 716 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE L 721 " --> pdb=" O LEU L 717 " (cutoff:3.500A) Processing helix chain 'L' and resid 729 through 735 removed outlier: 4.153A pdb=" N GLU L 733 " --> pdb=" O GLU L 729 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE L 734 " --> pdb=" O PRO L 730 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY L 735 " --> pdb=" O LYS L 731 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 729 through 735' Processing helix chain 'L' and resid 746 through 761 removed outlier: 3.853A pdb=" N LEU L 750 " --> pdb=" O THR L 746 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU L 761 " --> pdb=" O ALA L 757 " (cutoff:3.500A) Processing helix chain 'L' and resid 780 through 794 removed outlier: 3.559A pdb=" N GLY L 794 " --> pdb=" O SER L 790 " (cutoff:3.500A) Processing helix chain 'L' and resid 1137 through 1158 removed outlier: 3.626A pdb=" N ARG L1145 " --> pdb=" O LYS L1141 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU L1146 " --> pdb=" O MET L1142 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE L1147 " --> pdb=" O PHE L1143 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU L1158 " --> pdb=" O LEU L1154 " (cutoff:3.500A) Processing helix chain 'L' and resid 1166 through 1183 removed outlier: 3.920A pdb=" N GLU L1170 " --> pdb=" O GLU L1166 " (cutoff:3.500A) Processing helix chain 'L' and resid 1194 through 1198 removed outlier: 3.719A pdb=" N MET L1197 " --> pdb=" O TRP L1194 " (cutoff:3.500A) Processing helix chain 'L' and resid 1199 through 1208 removed outlier: 3.734A pdb=" N PHE L1203 " --> pdb=" O CYS L1199 " (cutoff:3.500A) Processing helix chain 'L' and resid 1220 through 1236 removed outlier: 3.586A pdb=" N HIS L1236 " --> pdb=" O THR L1232 " (cutoff:3.500A) Processing helix chain 'L' and resid 1242 through 1258 removed outlier: 3.855A pdb=" N VAL L1246 " --> pdb=" O PRO L1242 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU L1258 " --> pdb=" O ILE L1254 " (cutoff:3.500A) Processing helix chain 'L' and resid 1267 through 1278 removed outlier: 3.687A pdb=" N PHE L1272 " --> pdb=" O ILE L1268 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE L1273 " --> pdb=" O THR L1269 " (cutoff:3.500A) Processing helix chain 'L' and resid 1297 through 1320 removed outlier: 3.757A pdb=" N SER L1301 " --> pdb=" O LEU L1297 " (cutoff:3.500A) Processing helix chain 'L' and resid 1338 through 1348 removed outlier: 3.983A pdb=" N GLN L1346 " --> pdb=" O THR L1342 " (cutoff:3.500A) Processing helix chain 'L' and resid 1348 through 1365 Processing helix chain 'L' and resid 1396 through 1406 removed outlier: 3.843A pdb=" N HIS L1406 " --> pdb=" O ALA L1402 " (cutoff:3.500A) Processing helix chain 'L' and resid 1415 through 1429 removed outlier: 3.736A pdb=" N ALA L1429 " --> pdb=" O ASP L1425 " (cutoff:3.500A) Processing helix chain 'L' and resid 1433 through 1435 No H-bonds generated for 'chain 'L' and resid 1433 through 1435' Processing helix chain 'L' and resid 1436 through 1451 removed outlier: 3.703A pdb=" N ILE L1440 " --> pdb=" O LEU L1436 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA L1451 " --> pdb=" O LEU L1447 " (cutoff:3.500A) Processing helix chain 'L' and resid 1466 through 1471 Processing helix chain 'L' and resid 1473 through 1486 Processing helix chain 'L' and resid 1490 through 1505 Processing helix chain 'L' and resid 1510 through 1515 removed outlier: 4.152A pdb=" N THR L1514 " --> pdb=" O HIS L1510 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR L1515 " --> pdb=" O GLU L1511 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1510 through 1515' Processing helix chain 'L' and resid 1522 through 1533 removed outlier: 4.190A pdb=" N LEU L1526 " --> pdb=" O HIS L1522 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER L1527 " --> pdb=" O LEU L1523 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASN L1528 " --> pdb=" O SER L1524 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU L1533 " --> pdb=" O LEU L1529 " (cutoff:3.500A) Processing helix chain 'L' and resid 1612 through 1624 Processing helix chain 'L' and resid 1638 through 1648 removed outlier: 3.922A pdb=" N ILE L1642 " --> pdb=" O TYR L1638 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN L1643 " --> pdb=" O ILE L1639 " (cutoff:3.500A) Processing helix chain 'L' and resid 1684 through 1699 Processing helix chain 'L' and resid 1779 through 1789 removed outlier: 3.677A pdb=" N VAL L1788 " --> pdb=" O VAL L1784 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN L1789 " --> pdb=" O ALA L1785 " (cutoff:3.500A) Processing helix chain 'L' and resid 1796 through 1800 Processing sheet with id=AA1, first strand: chain 'L' and resid 258 through 260 removed outlier: 3.673A pdb=" N ILE L1376 " --> pdb=" O TYR L 651 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN L1333 " --> pdb=" O MET L1189 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE L1334 " --> pdb=" O TYR L1327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 370 through 371 removed outlier: 3.694A pdb=" N CYS L 374 " --> pdb=" O LEU L 371 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 535 through 540 removed outlier: 3.738A pdb=" N CYS L 571 " --> pdb=" O ILE L 562 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 1107 through 1108 removed outlier: 3.698A pdb=" N GLY L1111 " --> pdb=" O SER L1108 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 1130 through 1136 removed outlier: 3.648A pdb=" N ARG L1131 " --> pdb=" O LYS L1124 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N PHE L1119 " --> pdb=" O GLU L1240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 1381 through 1382 Processing sheet with id=AA7, first strand: chain 'L' and resid 1653 through 1656 removed outlier: 9.046A pdb=" N GLN L1662 " --> pdb=" O LEU L1548 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU L1548 " --> pdb=" O GLN L1662 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 1723 through 1726 416 hydrogen bonds defined for protein. 1197 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: 1.73 Time building geometry restraints manager: 0.99 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: 3063 1.34 - 1.46: 2034 1.46 - 1.58: 4523 1.58 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 9705 Sorted by residual: bond pdb=" N ILE L 376 " pdb=" CA ILE L 376 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.17e-02 7.31e+03 8.59e+00 bond pdb=" N CYS L 374 " pdb=" CA CYS L 374 " ideal model delta sigma weight residual 1.453 1.488 -0.034 1.22e-02 6.72e+03 7.95e+00 bond pdb=" N TRP L 370 " pdb=" CA TRP L 370 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.23e-02 6.61e+03 7.27e+00 bond pdb=" N TYR L 704 " pdb=" CA TYR L 704 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.18e-02 7.18e+03 7.12e+00 bond pdb=" N ILE L 702 " pdb=" CA ILE L 702 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.31e-02 5.83e+03 6.84e+00 ... (remaining 9700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 12861 1.70 - 3.40: 209 3.40 - 5.10: 23 5.10 - 6.80: 4 6.80 - 8.50: 1 Bond angle restraints: 13098 Sorted by residual: angle pdb=" C SER L1329 " pdb=" N SER L1330 " pdb=" CA SER L1330 " ideal model delta sigma weight residual 121.54 130.04 -8.50 1.91e+00 2.74e-01 1.98e+01 angle pdb=" N SER L 373 " pdb=" CA SER L 373 " pdb=" C SER L 373 " ideal model delta sigma weight residual 114.56 109.25 5.31 1.27e+00 6.20e-01 1.75e+01 angle pdb=" N HIS L 707 " pdb=" CA HIS L 707 " pdb=" C HIS L 707 " ideal model delta sigma weight residual 113.01 108.96 4.05 1.20e+00 6.94e-01 1.14e+01 angle pdb=" N MET L 705 " pdb=" CA MET L 705 " pdb=" C MET L 705 " ideal model delta sigma weight residual 113.16 109.06 4.10 1.24e+00 6.50e-01 1.09e+01 angle pdb=" N ILE L 702 " pdb=" CA ILE L 702 " pdb=" C ILE L 702 " ideal model delta sigma weight residual 113.07 108.72 4.35 1.37e+00 5.33e-01 1.01e+01 ... (remaining 13093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 5104 17.49 - 34.97: 592 34.97 - 52.45: 143 52.45 - 69.94: 30 69.94 - 87.42: 10 Dihedral angle restraints: 5879 sinusoidal: 2406 harmonic: 3473 Sorted by residual: dihedral pdb=" CA VAL L 275 " pdb=" C VAL L 275 " pdb=" N ASP L 276 " pdb=" CA ASP L 276 " ideal model delta harmonic sigma weight residual 180.00 155.69 24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA SER L1330 " pdb=" C SER L1330 " pdb=" N ASP L1331 " pdb=" CA ASP L1331 " ideal model delta harmonic sigma weight residual 180.00 162.04 17.96 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ILE L1289 " pdb=" C ILE L1289 " pdb=" N LEU L1290 " pdb=" CA LEU L1290 " ideal model delta harmonic sigma weight residual -180.00 -162.88 -17.12 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 5876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1130 0.042 - 0.084: 270 0.084 - 0.127: 68 0.127 - 0.169: 8 0.169 - 0.211: 2 Chirality restraints: 1478 Sorted by residual: chirality pdb=" CA ILE L 376 " pdb=" N ILE L 376 " pdb=" C ILE L 376 " pdb=" CB ILE L 376 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE L 702 " pdb=" N ILE L 702 " pdb=" C ILE L 702 " pdb=" CB ILE L 702 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" CB ILE L1279 " pdb=" CA ILE L1279 " pdb=" CG1 ILE L1279 " pdb=" CG2 ILE L1279 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.11e-01 ... (remaining 1475 not shown) Planarity restraints: 1653 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L1371 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.15e+00 pdb=" N PRO L1372 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO L1372 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO L1372 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN L 740 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO L 741 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO L 741 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 741 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE L 479 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO L 480 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO L 480 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 480 " 0.022 5.00e-02 4.00e+02 ... (remaining 1650 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 88 2.64 - 3.20: 7939 3.20 - 3.77: 12734 3.77 - 4.33: 17514 4.33 - 4.90: 30666 Nonbonded interactions: 68941 Sorted by model distance: nonbonded pdb=" OD1 ASP L1332 " pdb="MG MG L2302 " model vdw 2.072 2.170 nonbonded pdb=" OG SER L 498 " pdb=" O ILE L 584 " model vdw 2.203 3.040 nonbonded pdb=" O ILE L 709 " pdb=" OG1 THR L 710 " model vdw 2.249 3.040 nonbonded pdb=" O GLY L 199 " pdb=" OG SER L 202 " model vdw 2.305 3.040 nonbonded pdb=" O SER L 367 " pdb=" OG SER L 367 " model vdw 2.308 3.040 ... (remaining 68936 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: 2.350 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: 0.180 Check model and map are aligned: 0.070 Set scattering table: 0.020 Process input model: 11.840 Find NCS groups from input model: 0.040 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 9709 Z= 0.167 Angle : 0.589 27.390 13100 Z= 0.323 Chirality : 0.040 0.211 1478 Planarity : 0.004 0.044 1653 Dihedral : 15.967 87.425 3621 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.80 % Allowed : 17.70 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.21), residues: 1159 helix: -0.50 (0.20), residues: 574 sheet: -1.46 (0.55), residues: 72 loop : -3.78 (0.19), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L1116 TYR 0.010 0.001 TYR L1107 PHE 0.010 0.001 PHE L 539 TRP 0.009 0.001 TRP L1547 HIS 0.004 0.001 HIS L 652 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9705) covalent geometry : angle 0.53703 (13098) hydrogen bonds : bond 0.13557 ( 416) hydrogen bonds : angle 4.69999 ( 1197) metal coordination : bond 0.06003 ( 4) metal coordination : angle 19.64097 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 81 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 1406 HIS cc_start: 0.8207 (OUTLIER) cc_final: 0.7338 (p-80) outliers start: 41 outliers final: 20 residues processed: 120 average time/residue: 0.1029 time to fit residues: 17.4355 Evaluate side-chains 83 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 230 THR Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 264 SER Chi-restraints excluded: chain L residue 362 THR Chi-restraints excluded: chain L residue 376 ILE Chi-restraints excluded: chain L residue 425 ILE Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 625 ILE Chi-restraints excluded: chain L residue 702 ILE Chi-restraints excluded: chain L residue 710 THR Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1318 CYS Chi-restraints excluded: chain L residue 1374 SER Chi-restraints excluded: chain L residue 1406 HIS Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1492 ARG Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1718 HIS Chi-restraints excluded: chain L residue 1786 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.0010 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 0.0040 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 315 HIS ** L 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 707 HIS L1553 HIS L1643 GLN L1798 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.074163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.055974 restraints weight = 26829.872| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.90 r_work: 0.2769 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9709 Z= 0.133 Angle : 0.511 6.000 13100 Z= 0.270 Chirality : 0.039 0.138 1478 Planarity : 0.004 0.046 1653 Dihedral : 5.907 57.190 1305 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.24 % Allowed : 17.52 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.24), residues: 1159 helix: 0.93 (0.23), residues: 567 sheet: -1.13 (0.53), residues: 74 loop : -3.27 (0.22), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L1630 TYR 0.011 0.001 TYR L1107 PHE 0.015 0.001 PHE L1513 TRP 0.008 0.001 TRP L1547 HIS 0.010 0.001 HIS L 441 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9705) covalent geometry : angle 0.50901 (13098) hydrogen bonds : bond 0.04597 ( 416) hydrogen bonds : angle 3.62016 ( 1197) metal coordination : bond 0.00953 ( 4) metal coordination : angle 3.49961 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 64 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 318 ILE cc_start: 0.9443 (mm) cc_final: 0.9169 (mp) REVERT: L 1213 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6925 (tt) REVERT: L 1406 HIS cc_start: 0.8613 (OUTLIER) cc_final: 0.7749 (p-80) outliers start: 35 outliers final: 20 residues processed: 97 average time/residue: 0.0810 time to fit residues: 11.7036 Evaluate side-chains 81 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 230 THR Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 376 ILE Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 584 ILE Chi-restraints excluded: chain L residue 608 GLU Chi-restraints excluded: chain L residue 710 THR Chi-restraints excluded: chain L residue 1213 LEU Chi-restraints excluded: chain L residue 1221 ILE Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1292 MET Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1394 VAL Chi-restraints excluded: chain L residue 1406 HIS Chi-restraints excluded: chain L residue 1492 ARG Chi-restraints excluded: chain L residue 1531 GLU Chi-restraints excluded: chain L residue 1536 GLU Chi-restraints excluded: chain L residue 1718 HIS Chi-restraints excluded: chain L residue 1807 HIS Chi-restraints excluded: chain L residue 1820 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 31 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 23 optimal weight: 0.0980 chunk 65 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 87 optimal weight: 0.4980 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.3333 r_free = 0.3333 target = 0.073747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.055662 restraints weight = 27126.746| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.90 r_work: 0.2773 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9709 Z= 0.124 Angle : 0.493 7.724 13100 Z= 0.258 Chirality : 0.038 0.136 1478 Planarity : 0.004 0.044 1653 Dihedral : 5.083 49.594 1286 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.80 % Allowed : 17.61 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.25), residues: 1159 helix: 1.55 (0.23), residues: 567 sheet: -0.87 (0.53), residues: 74 loop : -2.99 (0.23), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L1557 TYR 0.011 0.001 TYR L1150 PHE 0.010 0.001 PHE L 539 TRP 0.007 0.001 TRP L1547 HIS 0.006 0.001 HIS L 441 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9705) covalent geometry : angle 0.49207 (13098) hydrogen bonds : bond 0.04407 ( 416) hydrogen bonds : angle 3.43862 ( 1197) metal coordination : bond 0.00438 ( 4) metal coordination : angle 2.26512 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 61 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 318 ILE cc_start: 0.9483 (mm) cc_final: 0.9216 (mp) REVERT: L 1125 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8264 (mm-30) REVERT: L 1213 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6938 (tt) REVERT: L 1406 HIS cc_start: 0.8622 (OUTLIER) cc_final: 0.7588 (p-80) outliers start: 41 outliers final: 25 residues processed: 96 average time/residue: 0.0744 time to fit residues: 11.0503 Evaluate side-chains 86 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 221 CYS Chi-restraints excluded: chain L residue 230 THR Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 277 GLU Chi-restraints excluded: chain L residue 376 ILE Chi-restraints excluded: chain L residue 439 VAL Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain L residue 557 SER Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 584 ILE Chi-restraints excluded: chain L residue 737 VAL Chi-restraints excluded: chain L residue 1125 GLU Chi-restraints excluded: chain L residue 1213 LEU Chi-restraints excluded: chain L residue 1221 ILE Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1292 MET Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1406 HIS Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1462 CYS Chi-restraints excluded: chain L residue 1492 ARG Chi-restraints excluded: chain L residue 1531 GLU Chi-restraints excluded: chain L residue 1536 GLU Chi-restraints excluded: chain L residue 1623 THR Chi-restraints excluded: chain L residue 1718 HIS Chi-restraints excluded: chain L residue 1807 HIS Chi-restraints excluded: chain L residue 1820 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 82 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 72 optimal weight: 0.0970 chunk 17 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 109 optimal weight: 0.0980 chunk 56 optimal weight: 0.2980 chunk 8 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 291 GLN ** L 441 HIS ** 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 = 0.3377 r_free = 0.3377 target = 0.075958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.058060 restraints weight = 27220.885| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.90 r_work: 0.2854 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9709 Z= 0.079 Angle : 0.439 5.952 13100 Z= 0.228 Chirality : 0.037 0.131 1478 Planarity : 0.003 0.041 1653 Dihedral : 4.512 50.646 1285 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.95 % Allowed : 19.18 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.25), residues: 1159 helix: 1.85 (0.23), residues: 571 sheet: -0.57 (0.54), residues: 74 loop : -2.73 (0.24), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L1557 TYR 0.007 0.001 TYR L 442 PHE 0.017 0.001 PHE L1513 TRP 0.007 0.001 TRP L1547 HIS 0.004 0.001 HIS L 441 Details of bonding type rmsd covalent geometry : bond 0.00171 ( 9705) covalent geometry : angle 0.43868 (13098) hydrogen bonds : bond 0.02840 ( 416) hydrogen bonds : angle 3.15957 ( 1197) metal coordination : bond 0.00608 ( 4) metal coordination : angle 1.53745 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 330 LEU cc_start: 0.9045 (mt) cc_final: 0.8829 (mt) REVERT: L 1213 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6885 (tt) REVERT: L 1406 HIS cc_start: 0.8447 (OUTLIER) cc_final: 0.7612 (p-80) outliers start: 21 outliers final: 15 residues processed: 87 average time/residue: 0.0879 time to fit residues: 11.5061 Evaluate side-chains 75 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 376 ILE Chi-restraints excluded: chain L residue 439 VAL Chi-restraints excluded: chain L residue 557 SER Chi-restraints excluded: chain L residue 608 GLU Chi-restraints excluded: chain L residue 1138 LEU Chi-restraints excluded: chain L residue 1213 LEU Chi-restraints excluded: chain L residue 1221 ILE Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1292 MET Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1406 HIS Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1462 CYS Chi-restraints excluded: chain L residue 1492 ARG Chi-restraints excluded: chain L residue 1640 LYS Chi-restraints excluded: chain L residue 1807 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 58 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 291 GLN L 315 HIS ** L 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1415 GLN L1789 ASN L1819 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.070456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.052452 restraints weight = 27530.910| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.86 r_work: 0.2726 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9709 Z= 0.258 Angle : 0.606 6.068 13100 Z= 0.317 Chirality : 0.042 0.141 1478 Planarity : 0.004 0.039 1653 Dihedral : 4.978 48.431 1281 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.71 % Allowed : 19.28 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.25), residues: 1159 helix: 1.61 (0.22), residues: 574 sheet: -0.88 (0.53), residues: 76 loop : -2.77 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 641 TYR 0.021 0.002 TYR L1107 PHE 0.013 0.002 PHE L 539 TRP 0.008 0.001 TRP L 395 HIS 0.005 0.001 HIS L 652 Details of bonding type rmsd covalent geometry : bond 0.00616 ( 9705) covalent geometry : angle 0.60467 (13098) hydrogen bonds : bond 0.06455 ( 416) hydrogen bonds : angle 3.71048 ( 1197) metal coordination : bond 0.00747 ( 4) metal coordination : angle 2.82394 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 57 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1125 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8237 (mm-30) REVERT: L 1406 HIS cc_start: 0.8807 (OUTLIER) cc_final: 0.7640 (p-80) outliers start: 40 outliers final: 31 residues processed: 91 average time/residue: 0.0813 time to fit residues: 11.1870 Evaluate side-chains 89 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 56 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 221 CYS Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 368 LYS Chi-restraints excluded: chain L residue 376 ILE Chi-restraints excluded: chain L residue 439 VAL Chi-restraints excluded: chain L residue 557 SER Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 598 ILE Chi-restraints excluded: chain L residue 612 CYS Chi-restraints excluded: chain L residue 737 VAL Chi-restraints excluded: chain L residue 1125 GLU Chi-restraints excluded: chain L residue 1138 LEU Chi-restraints excluded: chain L residue 1221 ILE Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1317 SER Chi-restraints excluded: chain L residue 1323 THR Chi-restraints excluded: chain L residue 1394 VAL Chi-restraints excluded: chain L residue 1406 HIS Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1456 ASP Chi-restraints excluded: chain L residue 1462 CYS Chi-restraints excluded: chain L residue 1492 ARG Chi-restraints excluded: chain L residue 1531 GLU Chi-restraints excluded: chain L residue 1536 GLU Chi-restraints excluded: chain L residue 1559 VAL Chi-restraints excluded: chain L residue 1623 THR Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1718 HIS Chi-restraints excluded: chain L residue 1807 HIS Chi-restraints excluded: chain L residue 1820 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 10 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 99 optimal weight: 0.3980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.073364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.055407 restraints weight = 27250.092| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.89 r_work: 0.2802 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9709 Z= 0.104 Angle : 0.469 5.978 13100 Z= 0.247 Chirality : 0.038 0.138 1478 Planarity : 0.003 0.041 1653 Dihedral : 4.631 51.293 1281 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.87 % Allowed : 19.65 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.25), residues: 1159 helix: 2.03 (0.22), residues: 569 sheet: -0.68 (0.54), residues: 76 loop : -2.63 (0.24), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 390 TYR 0.008 0.001 TYR L 242 PHE 0.010 0.001 PHE L1151 TRP 0.008 0.001 TRP L1547 HIS 0.004 0.001 HIS L 652 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9705) covalent geometry : angle 0.46841 (13098) hydrogen bonds : bond 0.03811 ( 416) hydrogen bonds : angle 3.29906 ( 1197) metal coordination : bond 0.00478 ( 4) metal coordination : angle 1.78140 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 58 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 547 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.7933 (mm-40) REVERT: L 1125 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8221 (mm-30) REVERT: L 1213 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.6983 (tt) REVERT: L 1406 HIS cc_start: 0.8512 (OUTLIER) cc_final: 0.7484 (p-80) outliers start: 31 outliers final: 21 residues processed: 86 average time/residue: 0.0781 time to fit residues: 10.4318 Evaluate side-chains 80 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 221 CYS Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 376 ILE Chi-restraints excluded: chain L residue 439 VAL Chi-restraints excluded: chain L residue 513 THR Chi-restraints excluded: chain L residue 547 GLN Chi-restraints excluded: chain L residue 557 SER Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 608 GLU Chi-restraints excluded: chain L residue 1125 GLU Chi-restraints excluded: chain L residue 1138 LEU Chi-restraints excluded: chain L residue 1213 LEU Chi-restraints excluded: chain L residue 1221 ILE Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1406 HIS Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1462 CYS Chi-restraints excluded: chain L residue 1492 ARG Chi-restraints excluded: chain L residue 1559 VAL Chi-restraints excluded: chain L residue 1633 ASN Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1807 HIS Chi-restraints excluded: chain L residue 1820 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 72 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 112 optimal weight: 0.0670 chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 291 GLN L 441 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.074563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.056825 restraints weight = 27204.821| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.89 r_work: 0.2838 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9709 Z= 0.084 Angle : 0.445 6.242 13100 Z= 0.233 Chirality : 0.037 0.133 1478 Planarity : 0.003 0.039 1653 Dihedral : 4.307 52.177 1281 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.87 % Allowed : 20.02 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.25), residues: 1159 helix: 2.16 (0.22), residues: 578 sheet: -0.43 (0.54), residues: 74 loop : -2.45 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L1139 TYR 0.008 0.001 TYR L 242 PHE 0.010 0.001 PHE L1151 TRP 0.006 0.001 TRP L1686 HIS 0.004 0.000 HIS L 364 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 9705) covalent geometry : angle 0.44460 (13098) hydrogen bonds : bond 0.03153 ( 416) hydrogen bonds : angle 3.13278 ( 1197) metal coordination : bond 0.00758 ( 4) metal coordination : angle 1.56169 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 62 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 330 LEU cc_start: 0.9082 (mt) cc_final: 0.8871 (mt) REVERT: L 547 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8686 (mm-40) REVERT: L 1125 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8254 (mm-30) REVERT: L 1213 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6859 (tt) REVERT: L 1406 HIS cc_start: 0.8509 (OUTLIER) cc_final: 0.7589 (p-80) outliers start: 31 outliers final: 24 residues processed: 90 average time/residue: 0.0778 time to fit residues: 10.7094 Evaluate side-chains 89 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 221 CYS Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 376 ILE Chi-restraints excluded: chain L residue 439 VAL Chi-restraints excluded: chain L residue 513 THR Chi-restraints excluded: chain L residue 547 GLN Chi-restraints excluded: chain L residue 557 SER Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 608 GLU Chi-restraints excluded: chain L residue 612 CYS Chi-restraints excluded: chain L residue 1125 GLU Chi-restraints excluded: chain L residue 1138 LEU Chi-restraints excluded: chain L residue 1213 LEU Chi-restraints excluded: chain L residue 1221 ILE Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1394 VAL Chi-restraints excluded: chain L residue 1406 HIS Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1462 CYS Chi-restraints excluded: chain L residue 1463 GLU Chi-restraints excluded: chain L residue 1492 ARG Chi-restraints excluded: chain L residue 1559 VAL Chi-restraints excluded: chain L residue 1633 ASN Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1807 HIS Chi-restraints excluded: chain L residue 1820 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 8 optimal weight: 0.0030 chunk 82 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 chunk 99 optimal weight: 0.0050 chunk 94 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 overall best weight: 0.3806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.075684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.057822 restraints weight = 27191.139| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.89 r_work: 0.2848 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9709 Z= 0.077 Angle : 0.446 7.405 13100 Z= 0.229 Chirality : 0.037 0.140 1478 Planarity : 0.003 0.038 1653 Dihedral : 4.149 52.210 1281 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.50 % Allowed : 20.48 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.26), residues: 1159 helix: 2.27 (0.22), residues: 580 sheet: -0.25 (0.55), residues: 74 loop : -2.35 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 390 TYR 0.008 0.001 TYR L 242 PHE 0.009 0.001 PHE L1151 TRP 0.006 0.000 TRP L1547 HIS 0.004 0.000 HIS L 364 Details of bonding type rmsd covalent geometry : bond 0.00169 ( 9705) covalent geometry : angle 0.44547 (13098) hydrogen bonds : bond 0.02718 ( 416) hydrogen bonds : angle 3.04610 ( 1197) metal coordination : bond 0.00685 ( 4) metal coordination : angle 0.98931 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 547 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8691 (mm-40) REVERT: L 1125 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8255 (mm-30) REVERT: L 1213 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6784 (tt) REVERT: L 1406 HIS cc_start: 0.8437 (OUTLIER) cc_final: 0.7580 (p-80) outliers start: 27 outliers final: 20 residues processed: 91 average time/residue: 0.0825 time to fit residues: 11.5787 Evaluate side-chains 83 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 221 CYS Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 376 ILE Chi-restraints excluded: chain L residue 439 VAL Chi-restraints excluded: chain L residue 513 THR Chi-restraints excluded: chain L residue 547 GLN Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 608 GLU Chi-restraints excluded: chain L residue 612 CYS Chi-restraints excluded: chain L residue 1125 GLU Chi-restraints excluded: chain L residue 1213 LEU Chi-restraints excluded: chain L residue 1221 ILE Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1317 SER Chi-restraints excluded: chain L residue 1394 VAL Chi-restraints excluded: chain L residue 1406 HIS Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1462 CYS Chi-restraints excluded: chain L residue 1492 ARG Chi-restraints excluded: chain L residue 1559 VAL Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1807 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 8 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 14 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.074860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.057182 restraints weight = 27172.655| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.88 r_work: 0.2841 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9709 Z= 0.089 Angle : 0.484 10.258 13100 Z= 0.244 Chirality : 0.037 0.146 1478 Planarity : 0.003 0.034 1653 Dihedral : 4.130 51.369 1281 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.78 % Allowed : 20.11 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.26), residues: 1159 helix: 2.25 (0.22), residues: 585 sheet: -0.21 (0.54), residues: 74 loop : -2.30 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 390 TYR 0.007 0.001 TYR L1150 PHE 0.009 0.001 PHE L 539 TRP 0.005 0.000 TRP L1547 HIS 0.004 0.001 HIS L 364 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 9705) covalent geometry : angle 0.48416 (13098) hydrogen bonds : bond 0.03190 ( 416) hydrogen bonds : angle 3.07299 ( 1197) metal coordination : bond 0.00520 ( 4) metal coordination : angle 1.07516 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 60 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 547 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8644 (mm-40) REVERT: L 1213 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6805 (tt) REVERT: L 1406 HIS cc_start: 0.8534 (OUTLIER) cc_final: 0.7593 (p-80) outliers start: 30 outliers final: 24 residues processed: 88 average time/residue: 0.0684 time to fit residues: 9.7362 Evaluate side-chains 85 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 58 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 221 CYS Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 376 ILE Chi-restraints excluded: chain L residue 439 VAL Chi-restraints excluded: chain L residue 513 THR Chi-restraints excluded: chain L residue 547 GLN Chi-restraints excluded: chain L residue 557 SER Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 608 GLU Chi-restraints excluded: chain L residue 612 CYS Chi-restraints excluded: chain L residue 1213 LEU Chi-restraints excluded: chain L residue 1221 ILE Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1317 SER Chi-restraints excluded: chain L residue 1394 VAL Chi-restraints excluded: chain L residue 1406 HIS Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1462 CYS Chi-restraints excluded: chain L residue 1492 ARG Chi-restraints excluded: chain L residue 1536 GLU Chi-restraints excluded: chain L residue 1559 VAL Chi-restraints excluded: chain L residue 1633 ASN Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1807 HIS Chi-restraints excluded: chain L residue 1820 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 67 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 102 optimal weight: 0.0670 chunk 53 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.074732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.056997 restraints weight = 27150.873| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.88 r_work: 0.2836 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9709 Z= 0.090 Angle : 0.481 8.660 13100 Z= 0.244 Chirality : 0.037 0.134 1478 Planarity : 0.003 0.034 1653 Dihedral : 4.147 50.825 1281 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.69 % Allowed : 20.30 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.26), residues: 1159 helix: 2.27 (0.22), residues: 586 sheet: -0.11 (0.54), residues: 74 loop : -2.26 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 390 TYR 0.007 0.001 TYR L1663 PHE 0.008 0.001 PHE L 539 TRP 0.005 0.000 TRP L1547 HIS 0.004 0.001 HIS L 364 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 9705) covalent geometry : angle 0.48065 (13098) hydrogen bonds : bond 0.03228 ( 416) hydrogen bonds : angle 3.07159 ( 1197) metal coordination : bond 0.00464 ( 4) metal coordination : angle 0.82857 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 547 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8646 (mm-40) REVERT: L 1213 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6778 (tt) REVERT: L 1406 HIS cc_start: 0.8515 (OUTLIER) cc_final: 0.7603 (p-80) outliers start: 29 outliers final: 25 residues processed: 86 average time/residue: 0.0753 time to fit residues: 10.2781 Evaluate side-chains 85 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 57 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 221 CYS Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 376 ILE Chi-restraints excluded: chain L residue 439 VAL Chi-restraints excluded: chain L residue 513 THR Chi-restraints excluded: chain L residue 547 GLN Chi-restraints excluded: chain L residue 557 SER Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 608 GLU Chi-restraints excluded: chain L residue 612 CYS Chi-restraints excluded: chain L residue 1213 LEU Chi-restraints excluded: chain L residue 1221 ILE Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1317 SER Chi-restraints excluded: chain L residue 1394 VAL Chi-restraints excluded: chain L residue 1406 HIS Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1462 CYS Chi-restraints excluded: chain L residue 1463 GLU Chi-restraints excluded: chain L residue 1492 ARG Chi-restraints excluded: chain L residue 1536 GLU Chi-restraints excluded: chain L residue 1559 VAL Chi-restraints excluded: chain L residue 1633 ASN Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1807 HIS Chi-restraints excluded: chain L residue 1820 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 95 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 315 HIS L 441 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.072973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.055084 restraints weight = 26887.961| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.87 r_work: 0.2794 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9709 Z= 0.126 Angle : 0.518 8.344 13100 Z= 0.266 Chirality : 0.038 0.137 1478 Planarity : 0.003 0.034 1653 Dihedral : 4.344 49.334 1281 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.69 % Allowed : 20.20 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.26), residues: 1159 helix: 2.19 (0.22), residues: 583 sheet: -0.25 (0.55), residues: 74 loop : -2.31 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 390 TYR 0.010 0.001 TYR L1107 PHE 0.011 0.001 PHE L 539 TRP 0.005 0.001 TRP L1547 HIS 0.004 0.001 HIS L 652 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9705) covalent geometry : angle 0.51773 (13098) hydrogen bonds : bond 0.04283 ( 416) hydrogen bonds : angle 3.23916 ( 1197) metal coordination : bond 0.00438 ( 4) metal coordination : angle 1.33261 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2058.23 seconds wall clock time: 36 minutes 1.17 seconds (2161.17 seconds total)