Starting phenix.real_space_refine on Fri Mar 14 05:30:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7och_12807/03_2025/7och_12807.cif Found real_map, /net/cci-nas-00/data/ceres_data/7och_12807/03_2025/7och_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_2025/7och_12807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7och_12807/03_2025/7och_12807.map" model { file = "/net/cci-nas-00/data/ceres_data/7och_12807/03_2025/7och_12807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7och_12807/03_2025/7och_12807.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.97, per 1000 atoms: 0.63 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: 2.57 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.01 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: 3.09 Time building geometry restraints manager: 3.01 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: 1.910 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.740 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.480 ------------------------------------------------------------------------------- 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 0.034 9705 Z= 0.197 Angle : 0.537 8.502 13098 Z= 0.319 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 : 3.99 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 (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: -2.88 (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 TRP 0.009 0.001 TRP L1547 HIS 0.004 0.001 HIS L 652 PHE 0.010 0.001 PHE L 539 TYR 0.010 0.001 TYR L1107 ARG 0.002 0.000 ARG L1116 *********************** 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 : 1.135 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: 0.2337 time to fit residues: 39.5726 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 : 1.177 ------------------------------------------------------------------------------- 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 99 optimal weight: 9.9990 chunk 89 optimal weight: 0.0570 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 0.1980 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.076066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.058141 restraints weight = 26756.236| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.89 r_work: 0.2820 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9705 Z= 0.137 Angle : 0.470 5.965 13098 Z= 0.249 Chirality : 0.038 0.137 1478 Planarity : 0.004 0.045 1653 Dihedral : 5.679 56.286 1305 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.97 % Allowed : 17.61 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.24), residues: 1159 helix: 0.89 (0.23), residues: 573 sheet: -1.08 (0.53), residues: 74 loop : -3.22 (0.22), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L1547 HIS 0.010 0.001 HIS L 441 PHE 0.015 0.001 PHE L1513 TYR 0.008 0.001 TYR L1150 ARG 0.006 0.000 ARG L1630 *********************** 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: 32 poor density : 67 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 318 ILE cc_start: 0.9401 (mm) cc_final: 0.9138 (mp) REVERT: L 1213 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6894 (tt) REVERT: L 1406 HIS cc_start: 0.8457 (OUTLIER) cc_final: 0.7644 (p-80) outliers start: 32 outliers final: 18 residues processed: 97 average time/residue: 0.2541 time to fit residues: 38.1084 Evaluate side-chains 78 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 567 VAL 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 101 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 63 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1789 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.073372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.055572 restraints weight = 27308.838| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.87 r_work: 0.2774 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9705 Z= 0.220 Angle : 0.510 7.854 13098 Z= 0.268 Chirality : 0.039 0.137 1478 Planarity : 0.004 0.042 1653 Dihedral : 5.124 52.576 1286 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.34 % Allowed : 18.44 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.25), residues: 1159 helix: 1.42 (0.23), residues: 568 sheet: -0.82 (0.54), residues: 74 loop : -2.97 (0.23), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L1547 HIS 0.006 0.001 HIS L 441 PHE 0.012 0.001 PHE L 539 TYR 0.013 0.001 TYR L1150 ARG 0.003 0.000 ARG L1557 *********************** 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 94 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 58 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 318 ILE cc_start: 0.9470 (mm) cc_final: 0.9199 (mp) REVERT: L 1213 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6947 (tt) REVERT: L 1406 HIS cc_start: 0.8631 (OUTLIER) cc_final: 0.7672 (p-80) outliers start: 36 outliers final: 21 residues processed: 89 average time/residue: 0.1832 time to fit residues: 25.1448 Evaluate side-chains 80 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 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 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 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 1718 HIS Chi-restraints excluded: chain L residue 1787 ASP 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 108 optimal weight: 0.0050 chunk 63 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 97 optimal weight: 0.0570 chunk 64 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.073080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.055128 restraints weight = 26935.647| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.87 r_work: 0.2793 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9705 Z= 0.194 Angle : 0.485 5.999 13098 Z= 0.255 Chirality : 0.038 0.135 1478 Planarity : 0.003 0.042 1653 Dihedral : 4.824 49.117 1285 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.52 % Allowed : 18.35 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.25), residues: 1159 helix: 1.70 (0.23), residues: 567 sheet: -0.74 (0.54), residues: 74 loop : -2.83 (0.23), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L1547 HIS 0.004 0.001 HIS L 652 PHE 0.011 0.001 PHE L 539 TYR 0.011 0.001 TYR L1107 ARG 0.002 0.000 ARG L 390 *********************** 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 97 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 59 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 318 ILE cc_start: 0.9508 (mm) cc_final: 0.9249 (mp) REVERT: L 1125 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8233 (mm-30) REVERT: L 1213 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6974 (tt) REVERT: L 1406 HIS cc_start: 0.8604 (OUTLIER) cc_final: 0.7548 (p-80) outliers start: 38 outliers final: 30 residues processed: 92 average time/residue: 0.1977 time to fit residues: 27.2313 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 : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 368 LYS 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 598 ILE Chi-restraints excluded: chain L residue 608 GLU 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 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 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 1640 LYS Chi-restraints excluded: chain L residue 1787 ASP Chi-restraints excluded: chain L residue 1807 HIS Chi-restraints excluded: chain L residue 1820 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 62 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 78 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 114 optimal weight: 0.4980 chunk 24 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1415 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.074885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.057141 restraints weight = 26997.480| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.88 r_work: 0.2844 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9705 Z= 0.122 Angle : 0.450 5.972 13098 Z= 0.236 Chirality : 0.037 0.130 1478 Planarity : 0.003 0.041 1653 Dihedral : 4.461 51.128 1283 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.69 % Allowed : 19.65 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.25), residues: 1159 helix: 1.95 (0.23), residues: 572 sheet: -0.49 (0.54), residues: 74 loop : -2.60 (0.24), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L1547 HIS 0.004 0.001 HIS L 364 PHE 0.009 0.001 PHE L1151 TYR 0.007 0.001 TYR L 442 ARG 0.001 0.000 ARG L1557 *********************** 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 92 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 63 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 330 LEU cc_start: 0.8986 (mt) cc_final: 0.8671 (mt) REVERT: L 1213 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6943 (tt) REVERT: L 1406 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.7578 (p-80) outliers start: 29 outliers final: 22 residues processed: 89 average time/residue: 0.1994 time to fit residues: 26.6040 Evaluate side-chains 82 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 567 VAL Chi-restraints excluded: chain L residue 608 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 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 1531 GLU Chi-restraints excluded: chain L residue 1536 GLU Chi-restraints excluded: chain L residue 1559 VAL Chi-restraints excluded: chain L residue 1640 LYS Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1718 HIS Chi-restraints excluded: chain L residue 1787 ASP Chi-restraints excluded: chain L residue 1807 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 49 optimal weight: 0.2980 chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.073861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.055905 restraints weight = 27282.535| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.90 r_work: 0.2816 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9705 Z= 0.155 Angle : 0.472 9.093 13098 Z= 0.245 Chirality : 0.037 0.136 1478 Planarity : 0.003 0.038 1653 Dihedral : 4.400 51.042 1282 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.06 % Allowed : 19.74 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1159 helix: 2.11 (0.23), residues: 571 sheet: -0.40 (0.54), residues: 74 loop : -2.43 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L1390 HIS 0.004 0.001 HIS L 652 PHE 0.010 0.001 PHE L 539 TYR 0.008 0.001 TYR L 242 ARG 0.002 0.000 ARG L 390 *********************** 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 91 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 58 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 547 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8695 (mm-40) REVERT: L 1213 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6933 (tt) REVERT: L 1406 HIS cc_start: 0.8580 (OUTLIER) cc_final: 0.7643 (p-80) outliers start: 33 outliers final: 25 residues processed: 87 average time/residue: 0.1694 time to fit residues: 23.3152 Evaluate side-chains 84 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 56 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 504 LEU 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 598 ILE 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 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 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 1640 LYS Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1718 HIS Chi-restraints excluded: chain L residue 1787 ASP 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 31 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 80 optimal weight: 0.0980 chunk 106 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.074649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.056780 restraints weight = 27192.605| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.88 r_work: 0.2839 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9705 Z= 0.129 Angle : 0.462 8.771 13098 Z= 0.238 Chirality : 0.037 0.133 1478 Planarity : 0.003 0.037 1653 Dihedral : 4.324 52.569 1282 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % 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 (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: 0.22 (0.25), residues: 1159 helix: 2.23 (0.23), residues: 572 sheet: -0.32 (0.54), residues: 74 loop : -2.39 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L1547 HIS 0.004 0.000 HIS L 364 PHE 0.008 0.001 PHE L1151 TYR 0.008 0.001 TYR L 242 ARG 0.001 0.000 ARG L 390 *********************** 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 : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 547 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8682 (mm-40) REVERT: L 1213 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6926 (tt) REVERT: L 1406 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.7556 (p-80) outliers start: 31 outliers final: 26 residues processed: 90 average time/residue: 0.1813 time to fit residues: 25.0237 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 : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1189 MET 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 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 1640 LYS Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1718 HIS Chi-restraints excluded: chain L residue 1787 ASP 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 54 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 116 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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** 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 = 0.073300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.055342 restraints weight = 27498.619| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.90 r_work: 0.2801 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9705 Z= 0.183 Angle : 0.491 7.977 13098 Z= 0.254 Chirality : 0.038 0.137 1478 Planarity : 0.003 0.036 1653 Dihedral : 4.421 51.418 1282 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.34 % Allowed : 19.18 % 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 (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: 0.21 (0.25), residues: 1159 helix: 2.24 (0.23), residues: 570 sheet: -0.34 (0.54), residues: 74 loop : -2.40 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L1547 HIS 0.004 0.001 HIS L 652 PHE 0.010 0.001 PHE L 539 TYR 0.010 0.001 TYR L1107 ARG 0.001 0.000 ARG L 265 *********************** 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 95 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 59 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 330 LEU cc_start: 0.8893 (mp) cc_final: 0.8369 (mt) REVERT: L 547 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.7954 (mm-40) REVERT: L 1213 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6900 (tt) REVERT: L 1406 HIS cc_start: 0.8599 (OUTLIER) cc_final: 0.7584 (p-80) outliers start: 36 outliers final: 31 residues processed: 92 average time/residue: 0.1856 time to fit residues: 26.3376 Evaluate side-chains 92 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 58 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 504 LEU 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 598 ILE Chi-restraints excluded: chain L residue 612 CYS Chi-restraints excluded: chain L residue 1189 MET 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 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 1640 LYS Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1718 HIS Chi-restraints excluded: chain L residue 1787 ASP Chi-restraints excluded: chain L residue 1807 HIS Chi-restraints excluded: chain L residue 1820 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 76 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.073714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.055813 restraints weight = 27116.864| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.89 r_work: 0.2806 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9705 Z= 0.158 Angle : 0.483 8.194 13098 Z= 0.249 Chirality : 0.038 0.134 1478 Planarity : 0.003 0.036 1653 Dihedral : 4.408 52.038 1282 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.24 % Allowed : 19.37 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.26), residues: 1159 helix: 2.27 (0.23), residues: 571 sheet: -0.25 (0.54), residues: 74 loop : -2.32 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L1547 HIS 0.004 0.001 HIS L 652 PHE 0.009 0.001 PHE L 539 TYR 0.008 0.001 TYR L1663 ARG 0.009 0.000 ARG L 390 *********************** 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 94 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 59 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 330 LEU cc_start: 0.8919 (mp) cc_final: 0.8385 (mt) REVERT: L 547 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8661 (mm-40) REVERT: L 1213 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6883 (tt) REVERT: L 1406 HIS cc_start: 0.8542 (OUTLIER) cc_final: 0.7568 (p-80) REVERT: L 1650 GLN cc_start: 0.7886 (mp10) cc_final: 0.7482 (mp10) outliers start: 35 outliers final: 30 residues processed: 91 average time/residue: 0.1846 time to fit residues: 26.0699 Evaluate side-chains 90 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 57 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 612 CYS Chi-restraints excluded: chain L residue 1189 MET 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 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 1623 THR Chi-restraints excluded: chain L residue 1633 ASN Chi-restraints excluded: chain L residue 1640 LYS Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1718 HIS Chi-restraints excluded: chain L residue 1787 ASP 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 75 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 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 ** 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 = 0.3329 r_free = 0.3329 target = 0.073053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.055109 restraints weight = 27555.249| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.90 r_work: 0.2794 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9705 Z= 0.186 Angle : 0.506 8.604 13098 Z= 0.261 Chirality : 0.038 0.136 1478 Planarity : 0.003 0.036 1653 Dihedral : 4.477 51.077 1282 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.24 % Allowed : 19.56 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.26), residues: 1159 helix: 2.08 (0.23), residues: 582 sheet: -0.34 (0.54), residues: 76 loop : -2.34 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L1547 HIS 0.004 0.001 HIS L 652 PHE 0.011 0.001 PHE L 539 TYR 0.010 0.001 TYR L1107 ARG 0.002 0.000 ARG L 566 ********************** 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 92 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 57 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 330 LEU cc_start: 0.8967 (mp) cc_final: 0.8456 (mt) REVERT: L 547 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.7928 (mm-40) REVERT: L 1213 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6893 (tt) REVERT: L 1406 HIS cc_start: 0.8600 (OUTLIER) cc_final: 0.7580 (p-80) outliers start: 35 outliers final: 31 residues processed: 89 average time/residue: 0.1778 time to fit residues: 25.5866 Evaluate side-chains 91 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 57 time to evaluate : 1.329 ------------------------------------------------------------------------------- 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 504 LEU 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 612 CYS Chi-restraints excluded: chain L residue 1189 MET 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 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 1623 THR Chi-restraints excluded: chain L residue 1633 ASN Chi-restraints excluded: chain L residue 1640 LYS Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1718 HIS Chi-restraints excluded: chain L residue 1787 ASP 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 77 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 50 optimal weight: 0.0970 chunk 103 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 111 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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** 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 = 0.074502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.056723 restraints weight = 27289.081| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.90 r_work: 0.2826 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9705 Z= 0.133 Angle : 0.479 9.088 13098 Z= 0.245 Chirality : 0.037 0.131 1478 Planarity : 0.003 0.036 1653 Dihedral : 4.323 51.719 1282 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.15 % Allowed : 19.65 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1159 helix: 2.20 (0.22), residues: 583 sheet: -0.07 (0.55), residues: 74 loop : -2.27 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L1547 HIS 0.004 0.001 HIS L 652 PHE 0.008 0.001 PHE L 539 TYR 0.008 0.001 TYR L 442 ARG 0.002 0.000 ARG L 390 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4429.14 seconds wall clock time: 79 minutes 34.79 seconds (4774.79 seconds total)