Starting phenix.real_space_refine on Wed Feb 14 08:29:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw7_6847/02_2024/5yw7_6847_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw7_6847/02_2024/5yw7_6847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw7_6847/02_2024/5yw7_6847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw7_6847/02_2024/5yw7_6847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw7_6847/02_2024/5yw7_6847_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw7_6847/02_2024/5yw7_6847_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 P 3 5.49 5 S 49 5.16 5 Cl 1 4.86 5 C 5785 2.51 5 N 1524 2.21 5 O 1582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 248": "NH1" <-> "NH2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "B ARG 486": "NH1" <-> "NH2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "B ARG 521": "NH1" <-> "NH2" Residue "B ARG 527": "NH1" <-> "NH2" Residue "B ARG 534": "NH1" <-> "NH2" Residue "B ARG 598": "NH1" <-> "NH2" Residue "B ARG 702": "NH1" <-> "NH2" Residue "B ARG 705": "NH1" <-> "NH2" Residue "B ARG 826": "NH1" <-> "NH2" Residue "B ARG 835": "NH1" <-> "NH2" Residue "B ARG 878": "NH1" <-> "NH2" Residue "B ARG 882": "NH1" <-> "NH2" Residue "B ARG 919": "NH1" <-> "NH2" Residue "B ARG 999": "NH1" <-> "NH2" Residue "B ARG 1099": "NH1" <-> "NH2" Residue "B ARG 1104": "NH1" <-> "NH2" Residue "B ARG 1111": "NH1" <-> "NH2" Residue "B ARG 1145": "NH1" <-> "NH2" Residue "B TYR 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1183": "NH1" <-> "NH2" Residue "B ARG 1218": "NH1" <-> "NH2" Residue "B ARG 1274": "NH1" <-> "NH2" Residue "B ARG 1300": "NH1" <-> "NH2" Residue "B ARG 1353": "NH1" <-> "NH2" Residue "B ARG 1394": "NH1" <-> "NH2" Residue "B ARG 1402": "NH1" <-> "NH2" Residue "B ARG 1421": "NH1" <-> "NH2" Residue "B ARG 1487": "NH1" <-> "NH2" Residue "B ARG 1498": "NH1" <-> "NH2" Residue "B ARG 1531": "NH1" <-> "NH2" Residue "B ARG 1539": "NH1" <-> "NH2" Residue "B ARG 1554": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8944 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 8944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1142, 8944 Unusual residues: {'AGS': 1, 'GBM': 1} Classifications: {'peptide': 1140, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 37, 'TRANS': 1102, None: 2} Not linked: pdbres="ARG B1579 " pdbres="GBM B2001 " Not linked: pdbres="GBM B2001 " pdbres="AGS B2002 " Chain breaks: 8 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 5.43, per 1000 atoms: 0.61 Number of scatterers: 8944 At special positions: 0 Unit cell: (107.61, 78.07, 132.93, 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) Cl 1 17.00 S 49 16.00 P 3 15.00 O 1582 8.00 N 1524 7.00 C 5785 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 - 3.50 Amino acid : False - 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: 3.59 Conformation dependent library (CDL) restraints added in 1.7 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2162 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 5 sheets defined 63.3% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'B' and resid 226 through 229 No H-bonds generated for 'chain 'B' and resid 226 through 229' Processing helix chain 'B' and resid 231 through 242 removed outlier: 3.942A pdb=" N ALA B 235 " --> pdb=" O TRP B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 274 Processing helix chain 'B' and resid 284 through 328 removed outlier: 6.309A pdb=" N ARG B 297 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ARG B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) Proline residue: B 317 - end of helix Processing helix chain 'B' and resid 356 through 401 removed outlier: 3.630A pdb=" N MET B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 422 Processing helix chain 'B' and resid 424 through 500 Proline residue: B 436 - end of helix removed outlier: 3.536A pdb=" N TRP B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Proline residue: B 442 - end of helix removed outlier: 8.211A pdb=" N VAL B 458 " --> pdb=" O TYR B 454 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N SER B 459 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 461 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Proline residue: B 472 - end of helix Processing helix chain 'B' and resid 506 through 512 removed outlier: 4.018A pdb=" N TYR B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 559 removed outlier: 3.655A pdb=" N ARG B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 528 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA B 535 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR B 548 " --> pdb=" O ILE B 544 " (cutoff:3.500A) Proline residue: B 551 - end of helix removed outlier: 3.554A pdb=" N VAL B 555 " --> pdb=" O PRO B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 614 Proline residue: B 589 - end of helix removed outlier: 4.446A pdb=" N LEU B 592 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 593 " --> pdb=" O PRO B 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 595 " --> pdb=" O PHE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 Processing helix chain 'B' and resid 784 through 789 Processing helix chain 'B' and resid 797 through 806 Processing helix chain 'B' and resid 809 through 814 Processing helix chain 'B' and resid 832 through 845 Processing helix chain 'B' and resid 862 through 871 Processing helix chain 'B' and resid 894 through 896 No H-bonds generated for 'chain 'B' and resid 894 through 896' Processing helix chain 'B' and resid 914 through 918 Processing helix chain 'B' and resid 998 through 1008 removed outlier: 3.803A pdb=" N ALA B1008 " --> pdb=" O TYR B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1038 removed outlier: 4.195A pdb=" N SER B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU B1015 " --> pdb=" O LEU B1011 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER B1019 " --> pdb=" O LEU B1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP B1031 " --> pdb=" O LEU B1027 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B1036 " --> pdb=" O TYR B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1106 Processing helix chain 'B' and resid 1110 through 1115 Processing helix chain 'B' and resid 1118 through 1126 removed outlier: 4.264A pdb=" N PHE B1125 " --> pdb=" O ILE B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1128 through 1160 Proline residue: B1137 - end of helix Processing helix chain 'B' and resid 1162 through 1216 removed outlier: 3.820A pdb=" N VAL B1166 " --> pdb=" O PRO B1162 " (cutoff:3.500A) Proline residue: B1170 - end of helix removed outlier: 3.539A pdb=" N PHE B1177 " --> pdb=" O VAL B1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B1181 " --> pdb=" O PHE B1177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B1182 " --> pdb=" O ILE B1178 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B1185 " --> pdb=" O TYR B1181 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP B1188 " --> pdb=" O VAL B1184 " (cutoff:3.500A) Proline residue: B1199 - end of helix removed outlier: 3.525A pdb=" N GLY B1210 " --> pdb=" O GLU B1206 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR B1212 " --> pdb=" O VAL B1208 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR B1213 " --> pdb=" O GLU B1209 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1270 removed outlier: 3.724A pdb=" N ALA B1237 " --> pdb=" O SER B1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B1242 " --> pdb=" O SER B1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B1260 " --> pdb=" O GLY B1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER B1269 " --> pdb=" O ALA B1265 " (cutoff:3.500A) Processing helix chain 'B' and resid 1278 through 1288 removed outlier: 4.013A pdb=" N GLY B1282 " --> pdb=" O ALA B1278 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU B1283 " --> pdb=" O GLY B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1291 through 1319 removed outlier: 4.142A pdb=" N ARG B1314 " --> pdb=" O GLY B1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE B1315 " --> pdb=" O ALA B1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS B1316 " --> pdb=" O VAL B1312 " (cutoff:3.500A) Processing helix chain 'B' and resid 1385 through 1392 Processing helix chain 'B' and resid 1415 through 1419 Processing helix chain 'B' and resid 1436 through 1440 Processing helix chain 'B' and resid 1448 through 1457 Processing helix chain 'B' and resid 1461 through 1465 Processing helix chain 'B' and resid 1484 through 1498 Processing helix chain 'B' and resid 1514 through 1527 removed outlier: 4.097A pdb=" N ILE B1519 " --> pdb=" O ALA B1515 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1545 Processing helix chain 'B' and resid 1563 through 1569 removed outlier: 4.306A pdb=" N SER B1568 " --> pdb=" O GLU B1564 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 701 through 703 Processing sheet with id= B, first strand: chain 'B' and resid 911 through 913 removed outlier: 3.670A pdb=" N GLY B 912 " --> pdb=" O ILE B 900 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA B 771 " --> pdb=" O PHE B 852 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ASP B 854 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA B 773 " --> pdb=" O ASP B 854 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 1367 through 1369 removed outlier: 3.602A pdb=" N GLN B1346 " --> pdb=" O ILE B1404 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN B1348 " --> pdb=" O ARG B1402 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG B1402 " --> pdb=" O GLN B1348 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 1351 through 1353 removed outlier: 3.547A pdb=" N MET B1398 " --> pdb=" O ARG B1353 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 1557 through 1560 removed outlier: 3.774A pdb=" N MET B1550 " --> pdb=" O GLY B1376 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE B1503 " --> pdb=" O VAL B1534 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE B1536 " --> pdb=" O PHE B1503 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET B1505 " --> pdb=" O ILE B1536 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER B1423 " --> pdb=" O ILE B1504 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP B1506 " --> pdb=" O SER B1423 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE B1425 " --> pdb=" O ASP B1506 " (cutoff:3.500A) 533 hydrogen bonds defined for protein. 1551 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: 2.84 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 3342 1.38 - 1.56: 5688 1.56 - 1.73: 8 1.73 - 1.90: 75 1.90 - 2.08: 1 Bond restraints: 9114 Sorted by residual: bond pdb=" C4 AGS B2002 " pdb=" C5 AGS B2002 " ideal model delta sigma weight residual 1.386 1.470 -0.084 1.00e-02 1.00e+04 7.11e+01 bond pdb=" C18 GBM B2001 " pdb=" S2 GBM B2001 " ideal model delta sigma weight residual 1.765 1.604 0.161 2.00e-02 2.50e+03 6.52e+01 bond pdb=" C5 AGS B2002 " pdb=" C6 AGS B2002 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.39e+01 bond pdb=" PG AGS B2002 " pdb=" S1G AGS B2002 " ideal model delta sigma weight residual 1.949 2.075 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C8 AGS B2002 " pdb=" N7 AGS B2002 " ideal model delta sigma weight residual 1.311 1.357 -0.046 1.00e-02 1.00e+04 2.09e+01 ... (remaining 9109 not shown) Histogram of bond angle deviations from ideal: 99.81 - 107.03: 222 107.03 - 114.24: 5578 114.24 - 121.46: 4636 121.46 - 128.68: 1861 128.68 - 135.90: 72 Bond angle restraints: 12369 Sorted by residual: angle pdb=" C5 AGS B2002 " pdb=" C4 AGS B2002 " pdb=" N3 AGS B2002 " ideal model delta sigma weight residual 126.80 118.59 8.21 7.41e-01 1.82e+00 1.23e+02 angle pdb=" C4 AGS B2002 " pdb=" C5 AGS B2002 " pdb=" N7 AGS B2002 " ideal model delta sigma weight residual 110.73 106.71 4.02 4.52e-01 4.89e+00 7.91e+01 angle pdb=" C5 AGS B2002 " pdb=" N7 AGS B2002 " pdb=" C8 AGS B2002 " ideal model delta sigma weight residual 103.67 107.37 -3.70 4.26e-01 5.51e+00 7.52e+01 angle pdb=" N3 AGS B2002 " pdb=" C4 AGS B2002 " pdb=" N9 AGS B2002 " ideal model delta sigma weight residual 127.16 135.21 -8.05 1.06e+00 8.92e-01 5.78e+01 angle pdb=" C SER B 532 " pdb=" N LEU B 533 " pdb=" CA LEU B 533 " ideal model delta sigma weight residual 120.28 130.85 -10.57 1.44e+00 4.82e-01 5.39e+01 ... (remaining 12364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.76: 5216 24.76 - 49.52: 212 49.52 - 74.28: 33 74.28 - 99.05: 4 99.05 - 123.81: 2 Dihedral angle restraints: 5467 sinusoidal: 2147 harmonic: 3320 Sorted by residual: dihedral pdb=" CA PHE B 295 " pdb=" C PHE B 295 " pdb=" N GLY B 296 " pdb=" CA GLY B 296 " ideal model delta harmonic sigma weight residual 180.00 154.49 25.51 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" N SER B1501 " pdb=" C SER B1501 " pdb=" CA SER B1501 " pdb=" CB SER B1501 " ideal model delta harmonic sigma weight residual 122.80 133.62 -10.82 0 2.50e+00 1.60e-01 1.87e+01 dihedral pdb=" CA GLY B 296 " pdb=" C GLY B 296 " pdb=" N ARG B 297 " pdb=" CA ARG B 297 " ideal model delta harmonic sigma weight residual -180.00 -158.77 -21.23 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 5464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1378 0.075 - 0.149: 98 0.149 - 0.224: 10 0.224 - 0.299: 4 0.299 - 0.373: 2 Chirality restraints: 1492 Sorted by residual: chirality pdb=" CA LYS B1444 " pdb=" N LYS B1444 " pdb=" C LYS B1444 " pdb=" CB LYS B1444 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA SER B1501 " pdb=" N SER B1501 " pdb=" C SER B1501 " pdb=" CB SER B1501 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CA ASP B1133 " pdb=" N ASP B1133 " pdb=" C ASP B1133 " pdb=" CB ASP B1133 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 1489 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C25 GBM B2001 " -0.321 2.00e-02 2.50e+03 2.73e-01 9.29e+02 pdb=" C26 GBM B2001 " 0.077 2.00e-02 2.50e+03 pdb=" C27 GBM B2001 " -0.172 2.00e-02 2.50e+03 pdb=" N10 GBM B2001 " 0.478 2.00e-02 2.50e+03 pdb=" O6 GBM B2001 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 GBM B2001 " 0.081 2.00e-02 2.50e+03 7.61e-02 8.68e+01 pdb=" C17 GBM B2001 " -0.037 2.00e-02 2.50e+03 pdb=" N8 GBM B2001 " -0.039 2.00e-02 2.50e+03 pdb=" N9 GBM B2001 " -0.130 2.00e-02 2.50e+03 pdb=" O3 GBM B2001 " 0.047 2.00e-02 2.50e+03 pdb=" S2 GBM B2001 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B1128 " 0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C ASP B1128 " -0.067 2.00e-02 2.50e+03 pdb=" O ASP B1128 " 0.025 2.00e-02 2.50e+03 pdb=" N CYS B1129 " 0.023 2.00e-02 2.50e+03 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1785 2.78 - 3.31: 9136 3.31 - 3.84: 14923 3.84 - 4.37: 16427 4.37 - 4.90: 28016 Nonbonded interactions: 70287 Sorted by model distance: nonbonded pdb=" OD2 ASP B1031 " pdb=" OH TYR B1287 " model vdw 2.246 2.440 nonbonded pdb=" CB TYR B 512 " pdb=" NH2 ARG B1498 " model vdw 2.269 3.520 nonbonded pdb=" O SER B1126 " pdb=" ND2 ASN B1130 " model vdw 2.275 2.520 nonbonded pdb=" O GLN B 846 " pdb=" NH2 ARG B 882 " model vdw 2.308 2.520 nonbonded pdb=" O THR B 783 " pdb=" ND2 ASN B 787 " model vdw 2.309 2.520 ... (remaining 70282 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 group one per residue 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: 5.990 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: 7.560 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 27.960 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 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 : 0.004 0.161 9114 Z= 0.289 Angle : 0.710 11.976 12369 Z= 0.444 Chirality : 0.046 0.373 1492 Planarity : 0.008 0.273 1516 Dihedral : 13.432 123.808 3305 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 6.49 % Allowed : 8.97 % Favored : 84.54 % Cbeta Deviations : 0.09 % 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: -2.58 (0.22), residues: 1122 helix: -1.14 (0.17), residues: 750 sheet: -1.78 (0.54), residues: 79 loop : -2.81 (0.31), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1037 HIS 0.004 0.001 HIS B 584 PHE 0.016 0.001 PHE B 305 TYR 0.014 0.001 TYR B 378 ARG 0.003 0.000 ARG B1494 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 337 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LYS cc_start: 0.8996 (mtpp) cc_final: 0.7908 (tttt) REVERT: B 233 MET cc_start: 0.9511 (mmm) cc_final: 0.9075 (mmm) REVERT: B 263 TYR cc_start: 0.9117 (t80) cc_final: 0.8846 (t80) REVERT: B 270 PHE cc_start: 0.8821 (t80) cc_final: 0.8547 (t80) REVERT: B 299 LEU cc_start: 0.9230 (tp) cc_final: 0.8882 (tt) REVERT: B 306 ARG cc_start: 0.8570 (tpt90) cc_final: 0.8201 (tpp80) REVERT: B 320 ILE cc_start: 0.9508 (mt) cc_final: 0.9237 (mt) REVERT: B 367 LEU cc_start: 0.9377 (pp) cc_final: 0.9160 (pp) REVERT: B 374 GLN cc_start: 0.9396 (OUTLIER) cc_final: 0.9137 (mm-40) REVERT: B 510 LYS cc_start: 0.9375 (mtpp) cc_final: 0.9057 (mtmt) REVERT: B 581 SER cc_start: 0.9663 (m) cc_final: 0.9339 (p) REVERT: B 590 LEU cc_start: 0.9261 (mt) cc_final: 0.8880 (tp) REVERT: B 708 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8277 (tt) REVERT: B 730 MET cc_start: 0.7235 (mtm) cc_final: 0.6721 (mtp) REVERT: B 820 GLN cc_start: 0.9011 (mt0) cc_final: 0.8750 (mp10) REVERT: B 869 MET cc_start: 0.9030 (tmm) cc_final: 0.8488 (tmm) REVERT: B 886 LEU cc_start: 0.9249 (tt) cc_final: 0.8387 (tt) REVERT: B 1078 LEU cc_start: 0.9037 (tp) cc_final: 0.8637 (tp) REVERT: B 1146 SER cc_start: 0.9252 (m) cc_final: 0.8719 (p) REVERT: B 1190 GLN cc_start: 0.9228 (tp40) cc_final: 0.8863 (tt0) REVERT: B 1206 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7936 (mt-10) REVERT: B 1214 ILE cc_start: 0.9600 (mt) cc_final: 0.9295 (tp) REVERT: B 1232 ASP cc_start: 0.8570 (t70) cc_final: 0.8350 (t70) REVERT: B 1246 ARG cc_start: 0.9469 (OUTLIER) cc_final: 0.9247 (mmp80) REVERT: B 1301 ASN cc_start: 0.8902 (m110) cc_final: 0.8694 (m110) REVERT: B 1305 MET cc_start: 0.8941 (tpt) cc_final: 0.8537 (tpt) REVERT: B 1398 MET cc_start: 0.4986 (mmm) cc_final: 0.4592 (mpp) REVERT: B 1490 PHE cc_start: 0.9192 (m-80) cc_final: 0.8674 (m-80) REVERT: B 1505 MET cc_start: 0.7959 (ttm) cc_final: 0.7393 (mmt) REVERT: B 1550 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8475 (mtp) REVERT: B 1551 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8465 (p) REVERT: B 1561 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.7954 (p0) outliers start: 63 outliers final: 20 residues processed: 374 average time/residue: 0.2153 time to fit residues: 109.2891 Evaluate side-chains 223 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 197 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN B 397 ASN B 416 GLN B 485 GLN B1134 GLN ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1541 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9114 Z= 0.240 Angle : 0.693 8.924 12369 Z= 0.349 Chirality : 0.043 0.172 1492 Planarity : 0.005 0.059 1516 Dihedral : 8.140 116.275 1255 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.31 % Allowed : 4.85 % Favored : 94.85 % 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: -0.98 (0.24), residues: 1122 helix: 0.14 (0.18), residues: 746 sheet: -1.50 (0.52), residues: 79 loop : -2.25 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B1247 HIS 0.004 0.001 HIS B1024 PHE 0.022 0.002 PHE B1240 TYR 0.022 0.002 TYR B 512 ARG 0.010 0.001 ARG B 837 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 245 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 VAL cc_start: 0.8771 (m) cc_final: 0.8460 (p) REVERT: B 227 LYS cc_start: 0.9029 (mtpp) cc_final: 0.8112 (tttt) REVERT: B 306 ARG cc_start: 0.8723 (tpt90) cc_final: 0.8405 (tpp80) REVERT: B 429 MET cc_start: 0.8718 (ttp) cc_final: 0.8503 (ttp) REVERT: B 565 PHE cc_start: 0.8183 (t80) cc_final: 0.7961 (m-80) REVERT: B 581 SER cc_start: 0.9686 (m) cc_final: 0.9416 (p) REVERT: B 602 LYS cc_start: 0.9198 (tptt) cc_final: 0.8761 (tptm) REVERT: B 869 MET cc_start: 0.8913 (tmm) cc_final: 0.8365 (tmm) REVERT: B 1078 LEU cc_start: 0.9004 (tp) cc_final: 0.8720 (tp) REVERT: B 1148 LEU cc_start: 0.9203 (mm) cc_final: 0.8998 (mt) REVERT: B 1301 ASN cc_start: 0.8876 (m110) cc_final: 0.8662 (m110) REVERT: B 1305 MET cc_start: 0.8890 (tpt) cc_final: 0.8526 (tpt) REVERT: B 1431 LEU cc_start: 0.8905 (mt) cc_final: 0.8665 (pt) REVERT: B 1460 LEU cc_start: 0.7444 (mt) cc_final: 0.7086 (mt) REVERT: B 1490 PHE cc_start: 0.9256 (m-80) cc_final: 0.9025 (m-80) outliers start: 3 outliers final: 0 residues processed: 247 average time/residue: 0.1890 time to fit residues: 66.8874 Evaluate side-chains 176 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 102 optimal weight: 0.0980 chunk 35 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN B 397 ASN B 909 GLN B1134 GLN ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9114 Z= 0.199 Angle : 0.636 9.679 12369 Z= 0.315 Chirality : 0.040 0.138 1492 Planarity : 0.004 0.043 1516 Dihedral : 7.803 117.348 1255 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % 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: -0.10 (0.25), residues: 1122 helix: 0.80 (0.19), residues: 747 sheet: -1.15 (0.53), residues: 79 loop : -1.88 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 778 HIS 0.002 0.001 HIS B 491 PHE 0.029 0.002 PHE B 295 TYR 0.023 0.002 TYR B 512 ARG 0.003 0.000 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LYS cc_start: 0.9038 (mtpp) cc_final: 0.8125 (tttt) REVERT: B 306 ARG cc_start: 0.8728 (tpt90) cc_final: 0.8461 (tpp80) REVERT: B 319 CYS cc_start: 0.8450 (m) cc_final: 0.7903 (t) REVERT: B 361 LEU cc_start: 0.9700 (mm) cc_final: 0.9232 (tt) REVERT: B 429 MET cc_start: 0.8860 (ttp) cc_final: 0.8458 (ttp) REVERT: B 581 SER cc_start: 0.9651 (m) cc_final: 0.9409 (p) REVERT: B 583 PHE cc_start: 0.9484 (m-10) cc_final: 0.9248 (m-10) REVERT: B 602 LYS cc_start: 0.9196 (tptt) cc_final: 0.8795 (tptp) REVERT: B 808 LEU cc_start: 0.9418 (tp) cc_final: 0.9086 (tp) REVERT: B 877 LEU cc_start: 0.9174 (mt) cc_final: 0.8963 (mt) REVERT: B 1078 LEU cc_start: 0.9066 (tp) cc_final: 0.8777 (tp) REVERT: B 1220 GLU cc_start: 0.8678 (pm20) cc_final: 0.8399 (pm20) REVERT: B 1258 CYS cc_start: 0.9326 (t) cc_final: 0.9083 (t) REVERT: B 1300 ARG cc_start: 0.8498 (ttm170) cc_final: 0.8202 (mtp180) REVERT: B 1305 MET cc_start: 0.8901 (tpt) cc_final: 0.8504 (tpt) REVERT: B 1431 LEU cc_start: 0.8974 (mt) cc_final: 0.8537 (pt) REVERT: B 1490 PHE cc_start: 0.9268 (m-80) cc_final: 0.8845 (m-80) outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 0.1700 time to fit residues: 54.8527 Evaluate side-chains 165 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 54 optimal weight: 0.0050 chunk 98 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN B 392 GLN B 397 ASN B 485 GLN B 846 GLN B1134 GLN ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1301 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 9114 Z= 0.190 Angle : 0.625 9.615 12369 Z= 0.305 Chirality : 0.040 0.137 1492 Planarity : 0.004 0.047 1516 Dihedral : 7.479 118.733 1255 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % 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: 0.18 (0.25), residues: 1122 helix: 1.02 (0.19), residues: 750 sheet: -0.98 (0.56), residues: 79 loop : -1.84 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1247 HIS 0.003 0.001 HIS B 562 PHE 0.019 0.001 PHE B 433 TYR 0.013 0.001 TYR B1064 ARG 0.003 0.000 ARG B1353 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 214 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LYS cc_start: 0.9047 (mtpp) cc_final: 0.8130 (tttt) REVERT: B 319 CYS cc_start: 0.8392 (m) cc_final: 0.7976 (t) REVERT: B 361 LEU cc_start: 0.9660 (mm) cc_final: 0.9218 (tp) REVERT: B 429 MET cc_start: 0.8855 (ttp) cc_final: 0.8465 (ttp) REVERT: B 581 SER cc_start: 0.9659 (m) cc_final: 0.9394 (p) REVERT: B 583 PHE cc_start: 0.9432 (m-10) cc_final: 0.9223 (m-10) REVERT: B 602 LYS cc_start: 0.9173 (tptt) cc_final: 0.8878 (tptm) REVERT: B 786 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8804 (mt-10) REVERT: B 808 LEU cc_start: 0.9277 (tp) cc_final: 0.9052 (tp) REVERT: B 1078 LEU cc_start: 0.9083 (tp) cc_final: 0.8767 (tp) REVERT: B 1091 LEU cc_start: 0.8820 (tt) cc_final: 0.8513 (tt) REVERT: B 1246 ARG cc_start: 0.9557 (mmp80) cc_final: 0.9066 (mmp80) REVERT: B 1258 CYS cc_start: 0.9315 (t) cc_final: 0.9051 (t) REVERT: B 1290 MET cc_start: 0.9187 (ttm) cc_final: 0.8732 (tmm) REVERT: B 1300 ARG cc_start: 0.8372 (ttm170) cc_final: 0.8111 (mtp180) REVERT: B 1305 MET cc_start: 0.8905 (tpt) cc_final: 0.8478 (tpt) REVERT: B 1431 LEU cc_start: 0.9026 (mt) cc_final: 0.8465 (pt) REVERT: B 1490 PHE cc_start: 0.9265 (m-80) cc_final: 0.8832 (m-80) REVERT: B 1504 ILE cc_start: 0.9383 (mm) cc_final: 0.9138 (pt) REVERT: B 1505 MET cc_start: 0.6954 (mmp) cc_final: 0.5696 (ttt) outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 0.1788 time to fit residues: 56.3127 Evaluate side-chains 167 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN B 485 GLN ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 846 GLN B1135 HIS ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9114 Z= 0.194 Angle : 0.613 7.513 12369 Z= 0.303 Chirality : 0.040 0.140 1492 Planarity : 0.004 0.051 1516 Dihedral : 7.262 120.000 1255 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % 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: 0.32 (0.25), residues: 1122 helix: 1.12 (0.19), residues: 748 sheet: -0.95 (0.56), residues: 79 loop : -1.74 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 232 HIS 0.002 0.001 HIS B1024 PHE 0.020 0.001 PHE B1393 TYR 0.032 0.001 TYR B 512 ARG 0.004 0.000 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LYS cc_start: 0.9031 (mtpp) cc_final: 0.8091 (tttt) REVERT: B 257 MET cc_start: 0.8311 (ptp) cc_final: 0.7577 (ptp) REVERT: B 319 CYS cc_start: 0.8392 (m) cc_final: 0.8011 (t) REVERT: B 320 ILE cc_start: 0.9371 (mt) cc_final: 0.9055 (mt) REVERT: B 361 LEU cc_start: 0.9657 (mm) cc_final: 0.9237 (tp) REVERT: B 429 MET cc_start: 0.8853 (ttp) cc_final: 0.8546 (ttp) REVERT: B 503 LEU cc_start: 0.9399 (mm) cc_final: 0.9137 (mm) REVERT: B 506 MET cc_start: 0.7966 (pmm) cc_final: 0.7758 (pmm) REVERT: B 512 TYR cc_start: 0.7662 (p90) cc_final: 0.6837 (p90) REVERT: B 530 MET cc_start: 0.9194 (mmm) cc_final: 0.8984 (mmt) REVERT: B 581 SER cc_start: 0.9625 (m) cc_final: 0.9350 (p) REVERT: B 602 LYS cc_start: 0.9202 (tptt) cc_final: 0.8782 (tppt) REVERT: B 685 PHE cc_start: 0.8237 (t80) cc_final: 0.8031 (m-80) REVERT: B 808 LEU cc_start: 0.9322 (tp) cc_final: 0.9021 (tp) REVERT: B 1078 LEU cc_start: 0.9086 (tp) cc_final: 0.8772 (tp) REVERT: B 1091 LEU cc_start: 0.8820 (tt) cc_final: 0.8578 (tt) REVERT: B 1246 ARG cc_start: 0.9533 (mmp80) cc_final: 0.9079 (mmp80) REVERT: B 1258 CYS cc_start: 0.9333 (t) cc_final: 0.9061 (t) REVERT: B 1290 MET cc_start: 0.9274 (ttm) cc_final: 0.8821 (tmm) REVERT: B 1300 ARG cc_start: 0.8375 (ttm170) cc_final: 0.8093 (mtp180) REVERT: B 1305 MET cc_start: 0.8910 (tpt) cc_final: 0.8475 (tpt) REVERT: B 1398 MET cc_start: 0.4012 (ptp) cc_final: 0.3801 (mtm) REVERT: B 1413 LEU cc_start: 0.7950 (mt) cc_final: 0.7746 (mt) REVERT: B 1490 PHE cc_start: 0.9284 (m-80) cc_final: 0.8762 (m-80) REVERT: B 1503 PHE cc_start: 0.7228 (m-80) cc_final: 0.6934 (m-10) REVERT: B 1504 ILE cc_start: 0.9311 (mm) cc_final: 0.9071 (pt) REVERT: B 1505 MET cc_start: 0.7151 (mmp) cc_final: 0.6111 (ttt) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1738 time to fit residues: 54.7403 Evaluate side-chains 167 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 110 optimal weight: 0.2980 chunk 91 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN B 392 GLN B 397 ASN B 485 GLN B 781 ASN ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1439 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9114 Z= 0.208 Angle : 0.622 7.422 12369 Z= 0.309 Chirality : 0.040 0.145 1492 Planarity : 0.004 0.043 1516 Dihedral : 7.074 122.280 1255 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % 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: 0.42 (0.25), residues: 1122 helix: 1.17 (0.19), residues: 749 sheet: -0.94 (0.55), residues: 79 loop : -1.62 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 430 HIS 0.003 0.001 HIS B1024 PHE 0.022 0.002 PHE B1393 TYR 0.015 0.001 TYR B 512 ARG 0.010 0.000 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LYS cc_start: 0.9005 (mtpp) cc_final: 0.8126 (tttt) REVERT: B 319 CYS cc_start: 0.8349 (m) cc_final: 0.8049 (t) REVERT: B 361 LEU cc_start: 0.9683 (mm) cc_final: 0.9230 (tp) REVERT: B 429 MET cc_start: 0.8905 (ttp) cc_final: 0.8587 (ttp) REVERT: B 503 LEU cc_start: 0.9434 (mm) cc_final: 0.9149 (mm) REVERT: B 506 MET cc_start: 0.8067 (pmm) cc_final: 0.7747 (pmm) REVERT: B 530 MET cc_start: 0.9233 (mmm) cc_final: 0.9014 (mmt) REVERT: B 581 SER cc_start: 0.9590 (m) cc_final: 0.9337 (p) REVERT: B 602 LYS cc_start: 0.9171 (tptt) cc_final: 0.8863 (tptm) REVERT: B 685 PHE cc_start: 0.8257 (t80) cc_final: 0.7953 (m-80) REVERT: B 808 LEU cc_start: 0.9249 (tp) cc_final: 0.8934 (tp) REVERT: B 1078 LEU cc_start: 0.9099 (tp) cc_final: 0.8796 (tp) REVERT: B 1091 LEU cc_start: 0.8812 (tt) cc_final: 0.8529 (tt) REVERT: B 1206 GLU cc_start: 0.8652 (pt0) cc_final: 0.8429 (pt0) REVERT: B 1229 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8788 (tm-30) REVERT: B 1246 ARG cc_start: 0.9535 (mmp80) cc_final: 0.9064 (mmp80) REVERT: B 1258 CYS cc_start: 0.9311 (t) cc_final: 0.9050 (t) REVERT: B 1290 MET cc_start: 0.9143 (ttm) cc_final: 0.8756 (ttp) REVERT: B 1305 MET cc_start: 0.8927 (tpt) cc_final: 0.8496 (tpt) REVERT: B 1398 MET cc_start: 0.3800 (ptp) cc_final: 0.3548 (mtm) REVERT: B 1490 PHE cc_start: 0.9288 (m-80) cc_final: 0.9081 (m-80) REVERT: B 1503 PHE cc_start: 0.7265 (m-80) cc_final: 0.6903 (m-80) REVERT: B 1505 MET cc_start: 0.7338 (mmp) cc_final: 0.6322 (ttt) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1627 time to fit residues: 50.5484 Evaluate side-chains 161 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN B 485 GLN ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1134 GLN ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9114 Z= 0.230 Angle : 0.637 7.703 12369 Z= 0.320 Chirality : 0.041 0.156 1492 Planarity : 0.004 0.044 1516 Dihedral : 7.017 124.756 1255 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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: 0.42 (0.25), residues: 1122 helix: 1.10 (0.19), residues: 752 sheet: -0.80 (0.56), residues: 79 loop : -1.50 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 232 HIS 0.003 0.001 HIS B1273 PHE 0.027 0.002 PHE B1223 TYR 0.036 0.002 TYR B1064 ARG 0.005 0.000 ARG B1215 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LYS cc_start: 0.8975 (mtpp) cc_final: 0.8134 (tttt) REVERT: B 319 CYS cc_start: 0.8372 (m) cc_final: 0.8024 (t) REVERT: B 361 LEU cc_start: 0.9688 (mm) cc_final: 0.9250 (tp) REVERT: B 429 MET cc_start: 0.8960 (ttp) cc_final: 0.8536 (ttp) REVERT: B 503 LEU cc_start: 0.9480 (mm) cc_final: 0.9172 (mm) REVERT: B 506 MET cc_start: 0.8051 (pmm) cc_final: 0.7717 (pmm) REVERT: B 512 TYR cc_start: 0.7681 (p90) cc_final: 0.6682 (p90) REVERT: B 530 MET cc_start: 0.9215 (mmm) cc_final: 0.9001 (mmt) REVERT: B 685 PHE cc_start: 0.8215 (t80) cc_final: 0.7923 (m-80) REVERT: B 808 LEU cc_start: 0.9268 (tp) cc_final: 0.8957 (tp) REVERT: B 1078 LEU cc_start: 0.9122 (tp) cc_final: 0.8838 (tp) REVERT: B 1091 LEU cc_start: 0.8846 (tt) cc_final: 0.8544 (tt) REVERT: B 1229 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8791 (tm-30) REVERT: B 1246 ARG cc_start: 0.9536 (mmp80) cc_final: 0.8997 (mmp80) REVERT: B 1258 CYS cc_start: 0.9285 (t) cc_final: 0.9026 (t) REVERT: B 1300 ARG cc_start: 0.8402 (ttm170) cc_final: 0.8141 (mtt180) REVERT: B 1305 MET cc_start: 0.8934 (tpt) cc_final: 0.8509 (tpt) REVERT: B 1490 PHE cc_start: 0.9285 (m-80) cc_final: 0.9079 (m-80) REVERT: B 1503 PHE cc_start: 0.7308 (m-80) cc_final: 0.6983 (m-80) REVERT: B 1505 MET cc_start: 0.7343 (mmp) cc_final: 0.6372 (ttt) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1741 time to fit residues: 52.9235 Evaluate side-chains 147 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.0980 chunk 69 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN B 392 GLN B 397 ASN ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9114 Z= 0.193 Angle : 0.633 7.879 12369 Z= 0.315 Chirality : 0.041 0.163 1492 Planarity : 0.004 0.043 1516 Dihedral : 6.904 127.337 1255 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.55 (0.25), residues: 1122 helix: 1.23 (0.19), residues: 752 sheet: -0.77 (0.56), residues: 79 loop : -1.53 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 688 HIS 0.003 0.001 HIS B 889 PHE 0.023 0.002 PHE B 295 TYR 0.049 0.002 TYR B 512 ARG 0.003 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LYS cc_start: 0.8951 (mtpp) cc_final: 0.8069 (tttt) REVERT: B 257 MET cc_start: 0.7892 (ptp) cc_final: 0.7195 (ptp) REVERT: B 319 CYS cc_start: 0.8373 (m) cc_final: 0.7803 (t) REVERT: B 323 ILE cc_start: 0.9235 (mm) cc_final: 0.8754 (mm) REVERT: B 361 LEU cc_start: 0.9683 (mm) cc_final: 0.9256 (tp) REVERT: B 429 MET cc_start: 0.8867 (ttp) cc_final: 0.8547 (ttp) REVERT: B 503 LEU cc_start: 0.9517 (mm) cc_final: 0.9254 (mm) REVERT: B 506 MET cc_start: 0.7974 (pmm) cc_final: 0.7679 (pmm) REVERT: B 530 MET cc_start: 0.9216 (mmm) cc_final: 0.8996 (mmt) REVERT: B 590 LEU cc_start: 0.9285 (mt) cc_final: 0.8920 (mt) REVERT: B 602 LYS cc_start: 0.9167 (tptt) cc_final: 0.8755 (tptp) REVERT: B 685 PHE cc_start: 0.8196 (t80) cc_final: 0.7921 (m-80) REVERT: B 786 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8709 (mt-10) REVERT: B 808 LEU cc_start: 0.9283 (tp) cc_final: 0.8985 (tp) REVERT: B 1066 MET cc_start: 0.6439 (mmm) cc_final: 0.6197 (mmm) REVERT: B 1078 LEU cc_start: 0.9118 (tp) cc_final: 0.8823 (tt) REVERT: B 1091 LEU cc_start: 0.8820 (tt) cc_final: 0.8518 (tt) REVERT: B 1206 GLU cc_start: 0.8708 (pt0) cc_final: 0.8483 (pt0) REVERT: B 1229 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8785 (tm-30) REVERT: B 1246 ARG cc_start: 0.9488 (mmp80) cc_final: 0.9014 (mmp80) REVERT: B 1258 CYS cc_start: 0.9281 (t) cc_final: 0.9007 (t) REVERT: B 1290 MET cc_start: 0.8990 (ttm) cc_final: 0.7832 (tmm) REVERT: B 1300 ARG cc_start: 0.8262 (ttm170) cc_final: 0.8036 (mtt180) REVERT: B 1305 MET cc_start: 0.8912 (tpt) cc_final: 0.8464 (tpt) REVERT: B 1431 LEU cc_start: 0.9144 (mt) cc_final: 0.8944 (mm) REVERT: B 1505 MET cc_start: 0.7338 (mmp) cc_final: 0.6362 (ttt) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1670 time to fit residues: 50.0736 Evaluate side-chains 158 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 10.0000 chunk 102 optimal weight: 0.5980 chunk 105 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN B 485 GLN ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1134 GLN ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1301 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.5756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9114 Z= 0.181 Angle : 0.640 7.807 12369 Z= 0.312 Chirality : 0.041 0.157 1492 Planarity : 0.004 0.046 1516 Dihedral : 6.857 128.721 1255 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: 0.53 (0.25), residues: 1122 helix: 1.17 (0.19), residues: 751 sheet: -0.66 (0.56), residues: 79 loop : -1.42 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B1037 HIS 0.003 0.000 HIS B1024 PHE 0.025 0.002 PHE B 295 TYR 0.025 0.002 TYR B 512 ARG 0.003 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LYS cc_start: 0.8918 (mtpp) cc_final: 0.8072 (tttt) REVERT: B 319 CYS cc_start: 0.8317 (m) cc_final: 0.7775 (t) REVERT: B 323 ILE cc_start: 0.9171 (mm) cc_final: 0.8686 (mm) REVERT: B 361 LEU cc_start: 0.9671 (mm) cc_final: 0.9239 (tp) REVERT: B 382 GLU cc_start: 0.8109 (tp30) cc_final: 0.7605 (tp30) REVERT: B 429 MET cc_start: 0.8828 (ttp) cc_final: 0.8504 (ttp) REVERT: B 497 LYS cc_start: 0.9015 (mmmt) cc_final: 0.8720 (mttt) REVERT: B 503 LEU cc_start: 0.9507 (mm) cc_final: 0.9258 (mm) REVERT: B 506 MET cc_start: 0.7872 (pmm) cc_final: 0.7621 (pmm) REVERT: B 512 TYR cc_start: 0.7842 (p90) cc_final: 0.6416 (p90) REVERT: B 530 MET cc_start: 0.9207 (mmm) cc_final: 0.8990 (mmt) REVERT: B 590 LEU cc_start: 0.9287 (mt) cc_final: 0.8916 (mt) REVERT: B 602 LYS cc_start: 0.9170 (tptt) cc_final: 0.8812 (tptm) REVERT: B 685 PHE cc_start: 0.8205 (t80) cc_final: 0.7938 (m-80) REVERT: B 786 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8695 (mt-10) REVERT: B 808 LEU cc_start: 0.9328 (tp) cc_final: 0.8941 (tp) REVERT: B 1066 MET cc_start: 0.6440 (mmm) cc_final: 0.6169 (mmm) REVERT: B 1078 LEU cc_start: 0.9092 (tp) cc_final: 0.8777 (tp) REVERT: B 1091 LEU cc_start: 0.8821 (tt) cc_final: 0.8531 (tt) REVERT: B 1229 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8740 (tm-30) REVERT: B 1246 ARG cc_start: 0.9470 (mmp80) cc_final: 0.8984 (mmp80) REVERT: B 1258 CYS cc_start: 0.9285 (t) cc_final: 0.9017 (t) REVERT: B 1290 MET cc_start: 0.9026 (ttm) cc_final: 0.8675 (ttp) REVERT: B 1305 MET cc_start: 0.8929 (tpt) cc_final: 0.8592 (tpt) REVERT: B 1398 MET cc_start: 0.3322 (ptp) cc_final: 0.3060 (mtm) REVERT: B 1431 LEU cc_start: 0.9162 (mt) cc_final: 0.8774 (mm) REVERT: B 1490 PHE cc_start: 0.9061 (m-80) cc_final: 0.8656 (m-80) REVERT: B 1505 MET cc_start: 0.7204 (mmp) cc_final: 0.6389 (ttt) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.1635 time to fit residues: 49.4735 Evaluate side-chains 157 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 113 optimal weight: 0.0000 chunk 104 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN B 392 GLN B 397 ASN ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1134 GLN ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.5899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9114 Z= 0.179 Angle : 0.626 7.732 12369 Z= 0.307 Chirality : 0.041 0.155 1492 Planarity : 0.004 0.048 1516 Dihedral : 6.761 129.701 1255 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: 0.57 (0.25), residues: 1122 helix: 1.19 (0.19), residues: 751 sheet: -0.53 (0.56), residues: 79 loop : -1.41 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B1037 HIS 0.002 0.000 HIS B1024 PHE 0.025 0.002 PHE B 295 TYR 0.021 0.002 TYR B1354 ARG 0.003 0.000 ARG B1187 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LYS cc_start: 0.8925 (mtpp) cc_final: 0.8067 (tttt) REVERT: B 319 CYS cc_start: 0.8290 (m) cc_final: 0.7778 (t) REVERT: B 323 ILE cc_start: 0.9166 (mm) cc_final: 0.8688 (mm) REVERT: B 361 LEU cc_start: 0.9657 (mm) cc_final: 0.9216 (tp) REVERT: B 382 GLU cc_start: 0.8033 (tp30) cc_final: 0.7601 (tp30) REVERT: B 387 LEU cc_start: 0.9483 (tt) cc_final: 0.9191 (tt) REVERT: B 429 MET cc_start: 0.8824 (ttp) cc_final: 0.8382 (ttp) REVERT: B 503 LEU cc_start: 0.9516 (mm) cc_final: 0.9287 (mm) REVERT: B 506 MET cc_start: 0.7933 (pmm) cc_final: 0.7616 (pmm) REVERT: B 512 TYR cc_start: 0.7873 (p90) cc_final: 0.6471 (p90) REVERT: B 530 MET cc_start: 0.9185 (mmm) cc_final: 0.8980 (mmt) REVERT: B 586 LEU cc_start: 0.9701 (tp) cc_final: 0.9471 (tp) REVERT: B 590 LEU cc_start: 0.9266 (mt) cc_final: 0.8845 (mt) REVERT: B 602 LYS cc_start: 0.9164 (tptt) cc_final: 0.8713 (tptp) REVERT: B 685 PHE cc_start: 0.8190 (t80) cc_final: 0.7925 (m-80) REVERT: B 710 MET cc_start: 0.8917 (tpt) cc_final: 0.8501 (mmm) REVERT: B 786 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8690 (mt-10) REVERT: B 796 LYS cc_start: 0.8600 (tttt) cc_final: 0.8272 (ptpp) REVERT: B 1066 MET cc_start: 0.6439 (mmm) cc_final: 0.6169 (mmm) REVERT: B 1091 LEU cc_start: 0.8812 (tt) cc_final: 0.8509 (tt) REVERT: B 1229 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8768 (tm-30) REVERT: B 1246 ARG cc_start: 0.9461 (mmp80) cc_final: 0.8955 (mmp80) REVERT: B 1258 CYS cc_start: 0.9273 (t) cc_final: 0.8990 (t) REVERT: B 1290 MET cc_start: 0.9077 (ttm) cc_final: 0.8525 (tmm) REVERT: B 1305 MET cc_start: 0.8953 (tpt) cc_final: 0.8542 (tpt) REVERT: B 1431 LEU cc_start: 0.9156 (mt) cc_final: 0.8811 (mm) REVERT: B 1490 PHE cc_start: 0.9075 (m-80) cc_final: 0.8616 (m-80) REVERT: B 1505 MET cc_start: 0.7200 (mmp) cc_final: 0.6438 (ttt) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.1719 time to fit residues: 52.1766 Evaluate side-chains 157 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.082967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.063931 restraints weight = 32562.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.065852 restraints weight = 19651.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.067140 restraints weight = 13508.438| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.6017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9114 Z= 0.196 Angle : 0.638 8.272 12369 Z= 0.312 Chirality : 0.041 0.162 1492 Planarity : 0.004 0.048 1516 Dihedral : 6.740 130.556 1255 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.53 (0.25), residues: 1122 helix: 1.17 (0.19), residues: 749 sheet: -0.57 (0.56), residues: 79 loop : -1.42 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 899 HIS 0.003 0.001 HIS B1024 PHE 0.018 0.001 PHE B1223 TYR 0.015 0.002 TYR B1004 ARG 0.003 0.000 ARG B 258 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2117.86 seconds wall clock time: 39 minutes 10.14 seconds (2350.14 seconds total)