Starting phenix.real_space_refine on Thu Jul 2 20:16:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wli_32584/07_2026/7wli_32584_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wli_32584/07_2026/7wli_32584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wli_32584/07_2026/7wli_32584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wli_32584/07_2026/7wli_32584.map" model { file = "/net/cci-nas-00/data/ceres_data/7wli_32584/07_2026/7wli_32584_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wli_32584/07_2026/7wli_32584_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.068 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 Ca 2 9.91 5 P 1 5.49 5 S 78 5.16 5 C 6321 2.51 5 N 1501 2.21 5 O 1590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9493 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9111 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1135, 9100 Classifications: {'peptide': 1135} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 1103} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 1135, 9100 Classifications: {'peptide': 1135} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 1103} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 9289 Chain: "A" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 380 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'3PE': 11, 'NAG': 2, 'Y01': 6} Classifications: {'undetermined': 19} Link IDs: {None: 18} Chain breaks: 2 Unresolved non-hydrogen bonds: 421 Unresolved non-hydrogen angles: 487 Unresolved non-hydrogen dihedrals: 433 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'3PE:plan-1': 10, '3PE:plan-2': 10, 'Y01:plan-1': 3, 'Y01:plan-2': 1} Unresolved non-hydrogen planarities: 78 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 854 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 854 " occ=0.50 Time building chain proxies: 3.43, per 1000 atoms: 0.36 Number of scatterers: 9493 At special positions: 0 Unit cell: (112.32, 123.76, 109.2, 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) Ca 2 19.99 S 78 16.00 P 1 15.00 O 1590 8.00 N 1501 7.00 C 6321 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 280 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A1335 " - pdb=" SG CYS A1349 " distance=2.03 Simple disulfide: pdb=" SG CYS A1646 " - pdb=" SG CYS A1652 " distance=2.03 Simple disulfide: pdb=" SG CYS A1691 " - pdb=" SG CYS A1698 " distance=2.03 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 Links applied NAG-ASN " NAG A2303 " - " ASN A1345 " " NAG A2304 " - " ASN A1342 " Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 647.2 milliseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2150 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 2 sheets defined 76.7% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 66 through 78 removed outlier: 4.192A pdb=" N CYS A 72 " --> pdb=" O PRO A 68 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N MET A 75 " --> pdb=" O TRP A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 98 removed outlier: 3.796A pdb=" N GLU A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 138 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 148 through 170 removed outlier: 3.586A pdb=" N ARG A 152 " --> pdb=" O ASP A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 190 removed outlier: 4.313A pdb=" N VAL A 182 " --> pdb=" O THR A 179 " (cutoff:3.500A) Proline residue: A 185 - end of helix Processing helix chain 'A' and resid 192 through 206 Processing helix chain 'A' and resid 209 through 231 removed outlier: 4.308A pdb=" N PHE A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 260 through 264 removed outlier: 3.561A pdb=" N ASP A 263 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 355 removed outlier: 3.779A pdb=" N ALA A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 removed outlier: 3.586A pdb=" N ILE A 362 " --> pdb=" O GLY A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 374 through 383 Processing helix chain 'A' and resid 389 through 413 removed outlier: 3.742A pdb=" N MET A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 638 removed outlier: 4.111A pdb=" N LYS A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 660 removed outlier: 4.200A pdb=" N GLU A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 695 removed outlier: 3.768A pdb=" N ASN A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 702 removed outlier: 3.895A pdb=" N ASN A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 721 removed outlier: 3.662A pdb=" N ILE A 706 " --> pdb=" O ASN A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 730 Processing helix chain 'A' and resid 731 through 744 removed outlier: 3.861A pdb=" N LEU A 735 " --> pdb=" O THR A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 785 removed outlier: 3.643A pdb=" N ARG A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN A 761 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N THR A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE A 765 " --> pdb=" O ASN A 761 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'A' and resid 806 through 820 Processing helix chain 'A' and resid 822 through 832 removed outlier: 3.599A pdb=" N VAL A 826 " --> pdb=" O ASP A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 838 through 850 removed outlier: 3.990A pdb=" N PHE A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 866 Processing helix chain 'A' and resid 1171 through 1188 Processing helix chain 'A' and resid 1198 through 1227 Processing helix chain 'A' and resid 1234 through 1237 removed outlier: 3.520A pdb=" N ARG A1237 " --> pdb=" O ALA A1234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1234 through 1237' Processing helix chain 'A' and resid 1238 through 1260 Processing helix chain 'A' and resid 1267 through 1281 Processing helix chain 'A' and resid 1289 through 1302 Processing helix chain 'A' and resid 1306 through 1328 Processing helix chain 'A' and resid 1345 through 1353 Processing helix chain 'A' and resid 1365 through 1378 Processing helix chain 'A' and resid 1381 through 1392 removed outlier: 3.695A pdb=" N ILE A1385 " --> pdb=" O GLY A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1406 No H-bonds generated for 'chain 'A' and resid 1404 through 1406' Processing helix chain 'A' and resid 1407 through 1463 removed outlier: 3.918A pdb=" N LEU A1415 " --> pdb=" O PHE A1411 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A1436 " --> pdb=" O GLU A1432 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A1451 " --> pdb=" O ARG A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1505 removed outlier: 3.564A pdb=" N ASP A1490 " --> pdb=" O SER A1486 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE A1492 " --> pdb=" O TYR A1488 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A1493 " --> pdb=" O LEU A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1541 Processing helix chain 'A' and resid 1542 through 1549 removed outlier: 3.575A pdb=" N PHE A1546 " --> pdb=" O GLY A1542 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A1547 " --> pdb=" O LEU A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1551 through 1575 removed outlier: 3.577A pdb=" N LEU A1568 " --> pdb=" O MET A1564 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A1569 " --> pdb=" O GLY A1565 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A1570 " --> pdb=" O ILE A1566 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A1571 " --> pdb=" O THR A1567 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A1572 " --> pdb=" O LEU A1568 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A1573 " --> pdb=" O GLU A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1590 removed outlier: 3.528A pdb=" N ILE A1584 " --> pdb=" O ASN A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1600 removed outlier: 3.660A pdb=" N LYS A1597 " --> pdb=" O ARG A1594 " (cutoff:3.500A) Processing helix chain 'A' and resid 1602 through 1614 Processing helix chain 'A' and resid 1615 through 1642 Processing helix chain 'A' and resid 1664 through 1676 removed outlier: 3.863A pdb=" N THR A1670 " --> pdb=" O MET A1666 " (cutoff:3.500A) Processing helix chain 'A' and resid 1679 through 1688 Processing helix chain 'A' and resid 1695 through 1700 removed outlier: 4.173A pdb=" N LEU A1699 " --> pdb=" O GLU A1695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1701 through 1738 removed outlier: 3.576A pdb=" N VAL A1705 " --> pdb=" O SER A1701 " (cutoff:3.500A) Proline residue: A1707 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 256 through 257 removed outlier: 4.753A pdb=" N CYS A 239 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG A 238 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1333 through 1334 616 hydrogen bonds defined for protein. 1755 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.56 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1426 1.31 - 1.44: 2571 1.44 - 1.57: 5441 1.57 - 1.69: 137 1.69 - 1.82: 127 Bond restraints: 9702 Sorted by residual: bond pdb=" C ALA A1443 " pdb=" O ALA A1443 " ideal model delta sigma weight residual 1.236 1.356 -0.120 1.15e-02 7.56e+03 1.08e+02 bond pdb=" C GLN A1439 " pdb=" O GLN A1439 " ideal model delta sigma weight residual 1.236 1.328 -0.092 1.15e-02 7.56e+03 6.37e+01 bond pdb=" C LYS A1459 " pdb=" O LYS A1459 " ideal model delta sigma weight residual 1.237 1.330 -0.093 1.17e-02 7.31e+03 6.35e+01 bond pdb=" C21 3PE A2305 " pdb=" O21 3PE A2305 " ideal model delta sigma weight residual 1.316 1.468 -0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" C GLU A1450 " pdb=" O GLU A1450 " ideal model delta sigma weight residual 1.237 1.316 -0.079 1.16e-02 7.43e+03 4.66e+01 ... (remaining 9697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 12756 2.98 - 5.95: 328 5.95 - 8.93: 37 8.93 - 11.90: 6 11.90 - 14.88: 3 Bond angle restraints: 13130 Sorted by residual: angle pdb=" N ALA A1443 " pdb=" CA ALA A1443 " pdb=" C ALA A1443 " ideal model delta sigma weight residual 110.97 123.96 -12.99 1.09e+00 8.42e-01 1.42e+02 angle pdb=" N LYS A1463 " pdb=" CA LYS A1463 " pdb=" C LYS A1463 " ideal model delta sigma weight residual 108.31 123.19 -14.88 1.52e+00 4.33e-01 9.58e+01 angle pdb=" C ALA A1446 " pdb=" N ARG A1447 " pdb=" CA ARG A1447 " ideal model delta sigma weight residual 120.28 109.12 11.16 1.44e+00 4.82e-01 6.00e+01 angle pdb=" N ALA A1446 " pdb=" CA ALA A1446 " pdb=" C ALA A1446 " ideal model delta sigma weight residual 111.07 103.08 7.99 1.07e+00 8.73e-01 5.57e+01 angle pdb=" N ARG A1453 " pdb=" CA ARG A1453 " pdb=" C ARG A1453 " ideal model delta sigma weight residual 112.23 103.94 8.29 1.26e+00 6.30e-01 4.33e+01 ... (remaining 13125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.12: 5328 18.12 - 36.25: 606 36.25 - 54.37: 132 54.37 - 72.49: 21 72.49 - 90.61: 5 Dihedral angle restraints: 6092 sinusoidal: 2773 harmonic: 3319 Sorted by residual: dihedral pdb=" CB CYS A1646 " pdb=" SG CYS A1646 " pdb=" SG CYS A1652 " pdb=" CB CYS A1652 " ideal model delta sinusoidal sigma weight residual 93.00 174.76 -81.76 1 1.00e+01 1.00e-02 8.22e+01 dihedral pdb=" CB CYS A 239 " pdb=" SG CYS A 239 " pdb=" SG CYS A 280 " pdb=" CB CYS A 280 " ideal model delta sinusoidal sigma weight residual 93.00 145.97 -52.97 1 1.00e+01 1.00e-02 3.82e+01 dihedral pdb=" CA ASN A 332 " pdb=" C ASN A 332 " pdb=" N PRO A 333 " pdb=" CA PRO A 333 " ideal model delta harmonic sigma weight residual -180.00 -151.66 -28.34 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 6089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1444 0.101 - 0.202: 64 0.202 - 0.303: 15 0.303 - 0.404: 6 0.404 - 0.505: 6 Chirality restraints: 1535 Sorted by residual: chirality pdb=" CBG Y01 A2312 " pdb=" CAQ Y01 A2312 " pdb=" CBD Y01 A2312 " pdb=" CBI Y01 A2312 " both_signs ideal model delta sigma weight residual False -2.33 -2.84 0.51 2.00e-01 2.50e+01 6.39e+00 chirality pdb=" CBG Y01 A2315 " pdb=" CAQ Y01 A2315 " pdb=" CBD Y01 A2315 " pdb=" CBI Y01 A2315 " both_signs ideal model delta sigma weight residual False -2.33 -2.82 0.49 2.00e-01 2.50e+01 6.04e+00 chirality pdb=" CBG Y01 A2309 " pdb=" CAQ Y01 A2309 " pdb=" CBD Y01 A2309 " pdb=" CBI Y01 A2309 " both_signs ideal model delta sigma weight residual False -2.33 -2.82 0.49 2.00e-01 2.50e+01 6.03e+00 ... (remaining 1532 not shown) Planarity restraints: 1579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A1449 " -0.024 2.00e-02 2.50e+03 4.64e-02 2.16e+01 pdb=" C ARG A1449 " 0.080 2.00e-02 2.50e+03 pdb=" O ARG A1449 " -0.029 2.00e-02 2.50e+03 pdb=" N GLU A1450 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 702 " 0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO A 703 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 703 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 703 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 403 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" CD GLU A 403 " 0.056 2.00e-02 2.50e+03 pdb=" OE1 GLU A 403 " -0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU A 403 " -0.021 2.00e-02 2.50e+03 ... (remaining 1576 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 47 2.49 - 3.09: 7232 3.09 - 3.70: 14554 3.70 - 4.30: 21308 4.30 - 4.90: 34299 Nonbonded interactions: 77440 Sorted by model distance: nonbonded pdb=" OE1 GLN A1441 " pdb=" OD2 ASP A1734 " model vdw 1.888 3.040 nonbonded pdb=" OD1 ASP A1380 " pdb=" ND2 ASN A1681 " model vdw 2.139 3.120 nonbonded pdb=" O HIS A1481 " pdb=" OG1 THR A1485 " model vdw 2.144 3.040 nonbonded pdb=" OG SER A 270 " pdb=" O ASP A 274 " model vdw 2.149 3.040 nonbonded pdb=" OH TYR A1524 " pdb=" OE1 GLU A1569 " model vdw 2.151 3.040 ... (remaining 77435 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=0.50 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.010 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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 : 0.012 0.152 9709 Z= 0.611 Angle : 1.014 14.878 13146 Z= 0.526 Chirality : 0.064 0.505 1535 Planarity : 0.005 0.081 1577 Dihedral : 15.399 90.614 3927 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.28 % Favored : 92.55 % Rotamer: Outliers : 0.20 % Allowed : 0.60 % Favored : 99.20 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.26), residues: 1130 helix: 0.53 (0.19), residues: 759 sheet: None (None), residues: 0 loop : -1.36 (0.36), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 749 TYR 0.019 0.002 TYR A1361 PHE 0.043 0.002 PHE A1626 TRP 0.015 0.001 TRP A 823 HIS 0.005 0.001 HIS A1358 Details of bonding type rmsd/Z covalent geometry : bond 0.01155 / 0.61 ( 9702) covalent geometry : angle 1.01237 / 0.53 (13130) SS BOND : bond 0.00179 / 0.09 ( 5) SS BOND : angle 1.40360 / 0.82 ( 10) hydrogen bonds : bond 0.13566 / 9.24 ( 616) hydrogen bonds : angle 6.17206 / 4.42 ( 1755) link_NAG-ASN : bond 0.00507 / 0.27 ( 2) link_NAG-ASN : angle 2.90621 / 1.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 0.329 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8806 (t0) cc_final: 0.8558 (t0) REVERT: A 146 LEU cc_start: 0.8135 (mt) cc_final: 0.7385 (tt) REVERT: A 648 MET cc_start: 0.6592 (mmp) cc_final: 0.6069 (tpt) REVERT: A 1219 MET cc_start: 0.8386 (tpt) cc_final: 0.8080 (tpt) REVERT: A 1564 MET cc_start: 0.8205 (ttm) cc_final: 0.7944 (tmm) REVERT: A 1650 ASN cc_start: 0.7501 (m110) cc_final: 0.7122 (m-40) outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 0.0807 time to fit residues: 26.2635 Evaluate side-chains 189 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN A 653 ASN A 761 ASN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 ASN A1404 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.205377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.142650 restraints weight = 19378.441| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 3.58 r_work: 0.3432 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9709 Z= 0.163 Angle : 0.689 11.767 13146 Z= 0.348 Chirality : 0.043 0.239 1535 Planarity : 0.005 0.055 1577 Dihedral : 9.741 57.064 1807 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.09 % Allowed : 9.64 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.26), residues: 1130 helix: 0.87 (0.18), residues: 777 sheet: None (None), residues: 0 loop : -1.69 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 731 TYR 0.016 0.002 TYR A1709 PHE 0.034 0.002 PHE A1626 TRP 0.015 0.001 TRP A1551 HIS 0.004 0.001 HIS A1358 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 9702) covalent geometry : angle 0.68639 / 0.35 (13130) SS BOND : bond 0.00182 / 0.09 ( 5) SS BOND : angle 1.22877 / 0.75 ( 10) hydrogen bonds : bond 0.04798 / 3.18 ( 616) hydrogen bonds : angle 5.08404 / 3.59 ( 1755) link_NAG-ASN : bond 0.00290 / 0.15 ( 2) link_NAG-ASN : angle 2.36507 / 1.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 206 time to evaluate : 0.405 Fit side-chains TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8795 (t0) cc_final: 0.8549 (t0) REVERT: A 134 MET cc_start: 0.8289 (mpp) cc_final: 0.7989 (mpp) REVERT: A 146 LEU cc_start: 0.8014 (mt) cc_final: 0.7255 (tt) REVERT: A 648 MET cc_start: 0.6687 (mmp) cc_final: 0.6019 (tpt) REVERT: A 686 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8179 (mm-30) REVERT: A 1172 PHE cc_start: 0.8108 (t80) cc_final: 0.7343 (t80) REVERT: A 1174 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.7398 (m-80) REVERT: A 1218 GLU cc_start: 0.7959 (pp20) cc_final: 0.7113 (tm-30) REVERT: A 1434 PHE cc_start: 0.8723 (t80) cc_final: 0.8376 (t80) REVERT: A 1650 ASN cc_start: 0.7618 (m110) cc_final: 0.7224 (m-40) REVERT: A 1655 MET cc_start: 0.8149 (mtm) cc_final: 0.7838 (mtp) outliers start: 10 outliers final: 6 residues processed: 210 average time/residue: 0.0767 time to fit residues: 24.1977 Evaluate side-chains 190 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 183 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 1174 TYR Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1601 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 60 optimal weight: 7.9990 chunk 66 optimal weight: 0.0770 chunk 69 optimal weight: 2.9990 chunk 95 optimal weight: 0.0270 chunk 102 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 chunk 41 optimal weight: 0.4980 chunk 82 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 ASN A 816 GLN ** A1398 GLN ** 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 = 0.4404 r_free = 0.4404 target = 0.208986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.147308 restraints weight = 27689.427| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 4.01 r_work: 0.3470 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3468 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9709 Z= 0.134 Angle : 0.629 13.343 13146 Z= 0.317 Chirality : 0.041 0.230 1535 Planarity : 0.004 0.050 1577 Dihedral : 8.864 59.963 1807 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.39 % Allowed : 12.62 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.26), residues: 1130 helix: 1.05 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -1.76 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 743 TYR 0.013 0.001 TYR A1387 PHE 0.025 0.002 PHE A1626 TRP 0.010 0.001 TRP A1551 HIS 0.004 0.001 HIS A1358 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 9702) covalent geometry : angle 0.62649 / 0.32 (13130) SS BOND : bond 0.00120 / 0.05 ( 5) SS BOND : angle 0.91656 / 0.54 ( 10) hydrogen bonds : bond 0.04274 / 2.82 ( 616) hydrogen bonds : angle 4.76486 / 3.39 ( 1755) link_NAG-ASN : bond 0.00346 / 0.18 ( 2) link_NAG-ASN : angle 2.32356 / 1.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 213 time to evaluate : 0.225 Fit side-chains TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8777 (t0) cc_final: 0.8535 (t0) REVERT: A 134 MET cc_start: 0.8135 (mpp) cc_final: 0.7654 (mpp) REVERT: A 648 MET cc_start: 0.6554 (mmp) cc_final: 0.5965 (tpt) REVERT: A 657 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8223 (ttm) REVERT: A 828 TYR cc_start: 0.8476 (m-10) cc_final: 0.7782 (m-80) REVERT: A 1174 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.7468 (m-80) REVERT: A 1434 PHE cc_start: 0.8668 (t80) cc_final: 0.8377 (t80) REVERT: A 1600 LYS cc_start: 0.8427 (tptt) cc_final: 0.8097 (pttt) REVERT: A 1655 MET cc_start: 0.7928 (mtm) cc_final: 0.7398 (mtp) REVERT: A 1730 MET cc_start: 0.8083 (mmm) cc_final: 0.7813 (mmm) outliers start: 14 outliers final: 5 residues processed: 217 average time/residue: 0.0764 time to fit residues: 24.3135 Evaluate side-chains 197 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 190 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 1174 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 77 optimal weight: 0.0980 chunk 41 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 97 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.210885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.155037 restraints weight = 26506.565| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 3.38 r_work: 0.3591 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9709 Z= 0.138 Angle : 0.617 10.258 13146 Z= 0.312 Chirality : 0.041 0.227 1535 Planarity : 0.004 0.048 1577 Dihedral : 8.646 59.874 1807 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.59 % Allowed : 13.82 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.26), residues: 1130 helix: 1.15 (0.19), residues: 778 sheet: None (None), residues: 0 loop : -1.64 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1355 TYR 0.024 0.001 TYR A1709 PHE 0.022 0.002 PHE A1626 TRP 0.018 0.001 TRP A1551 HIS 0.004 0.001 HIS A1358 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 9702) covalent geometry : angle 0.61523 / 0.31 (13130) SS BOND : bond 0.00106 / 0.05 ( 5) SS BOND : angle 0.81117 / 0.48 ( 10) hydrogen bonds : bond 0.04131 / 2.73 ( 616) hydrogen bonds : angle 4.62885 / 3.33 ( 1755) link_NAG-ASN : bond 0.00428 / 0.22 ( 2) link_NAG-ASN : angle 2.28308 / 1.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.298 Fit side-chains TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.7708 (mmm) cc_final: 0.7385 (mmp) REVERT: A 134 MET cc_start: 0.8004 (mpp) cc_final: 0.7696 (mpp) REVERT: A 648 MET cc_start: 0.6659 (mmp) cc_final: 0.6020 (tpt) REVERT: A 657 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8215 (ttm) REVERT: A 828 TYR cc_start: 0.8456 (m-10) cc_final: 0.8058 (m-80) REVERT: A 1174 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: A 1434 PHE cc_start: 0.8398 (t80) cc_final: 0.8121 (t80) REVERT: A 1504 MET cc_start: 0.8510 (mtm) cc_final: 0.8204 (mtp) REVERT: A 1655 MET cc_start: 0.7887 (mtm) cc_final: 0.7431 (mtp) outliers start: 16 outliers final: 8 residues processed: 204 average time/residue: 0.0701 time to fit residues: 21.7672 Evaluate side-chains 193 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 183 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 1174 TYR Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1350 MET Chi-restraints excluded: chain A residue 1525 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 76 optimal weight: 2.9990 chunk 105 optimal weight: 0.0070 chunk 47 optimal weight: 0.3980 chunk 111 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 107 optimal weight: 0.4980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1193 GLN A1663 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.212037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.150884 restraints weight = 22355.278| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 3.24 r_work: 0.3601 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9709 Z= 0.128 Angle : 0.603 9.569 13146 Z= 0.306 Chirality : 0.041 0.223 1535 Planarity : 0.004 0.048 1577 Dihedral : 8.339 59.506 1807 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.49 % Allowed : 15.21 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.26), residues: 1130 helix: 1.25 (0.19), residues: 779 sheet: None (None), residues: 0 loop : -1.65 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1355 TYR 0.014 0.001 TYR A1387 PHE 0.020 0.001 PHE A1172 TRP 0.014 0.001 TRP A1551 HIS 0.004 0.001 HIS A1358 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 9702) covalent geometry : angle 0.60125 / 0.31 (13130) SS BOND : bond 0.00099 / 0.05 ( 5) SS BOND : angle 0.79019 / 0.46 ( 10) hydrogen bonds : bond 0.03962 / 2.59 ( 616) hydrogen bonds : angle 4.56768 / 3.29 ( 1755) link_NAG-ASN : bond 0.00396 / 0.21 ( 2) link_NAG-ASN : angle 2.25555 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 0.321 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 648 MET cc_start: 0.6448 (mmp) cc_final: 0.5847 (tpt) REVERT: A 1174 TYR cc_start: 0.8047 (OUTLIER) cc_final: 0.7460 (m-80) REVERT: A 1218 GLU cc_start: 0.7994 (pp20) cc_final: 0.7674 (pp20) REVERT: A 1434 PHE cc_start: 0.8568 (t80) cc_final: 0.8261 (t80) REVERT: A 1504 MET cc_start: 0.8450 (mtm) cc_final: 0.8099 (mtp) REVERT: A 1655 MET cc_start: 0.7828 (mtm) cc_final: 0.7462 (mtp) outliers start: 15 outliers final: 9 residues processed: 203 average time/residue: 0.0693 time to fit residues: 21.3961 Evaluate side-chains 196 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 1174 TYR Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1350 MET Chi-restraints excluded: chain A residue 1525 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 102 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 87 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 chunk 64 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.211641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.154885 restraints weight = 19685.970| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 3.37 r_work: 0.3611 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9709 Z= 0.132 Angle : 0.611 13.210 13146 Z= 0.308 Chirality : 0.041 0.239 1535 Planarity : 0.004 0.047 1577 Dihedral : 8.182 58.837 1807 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.69 % Allowed : 15.61 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.26), residues: 1130 helix: 1.31 (0.19), residues: 778 sheet: None (None), residues: 0 loop : -1.65 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1355 TYR 0.024 0.002 TYR A1709 PHE 0.019 0.001 PHE A 125 TRP 0.016 0.001 TRP A1551 HIS 0.004 0.001 HIS A1358 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 9702) covalent geometry : angle 0.60972 / 0.31 (13130) SS BOND : bond 0.00111 / 0.05 ( 5) SS BOND : angle 0.73991 / 0.44 ( 10) hydrogen bonds : bond 0.03920 / 2.59 ( 616) hydrogen bonds : angle 4.53957 / 3.26 ( 1755) link_NAG-ASN : bond 0.00420 / 0.22 ( 2) link_NAG-ASN : angle 2.15065 / 1.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.318 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.7692 (mmm) cc_final: 0.7307 (mmp) REVERT: A 648 MET cc_start: 0.6332 (mmp) cc_final: 0.5776 (tpt) REVERT: A 733 PHE cc_start: 0.8206 (m-80) cc_final: 0.7454 (m-80) REVERT: A 828 TYR cc_start: 0.8461 (m-10) cc_final: 0.7797 (m-80) REVERT: A 1174 TYR cc_start: 0.8010 (OUTLIER) cc_final: 0.7469 (m-80) REVERT: A 1218 GLU cc_start: 0.8047 (pp20) cc_final: 0.7720 (pp20) REVERT: A 1434 PHE cc_start: 0.8610 (t80) cc_final: 0.8371 (t80) REVERT: A 1504 MET cc_start: 0.8489 (mtm) cc_final: 0.8123 (mtp) REVERT: A 1655 MET cc_start: 0.7783 (mtm) cc_final: 0.7457 (mtp) outliers start: 17 outliers final: 11 residues processed: 203 average time/residue: 0.0682 time to fit residues: 21.4781 Evaluate side-chains 197 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 185 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 1174 TYR Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1350 MET Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1525 MET Chi-restraints excluded: chain A residue 1561 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 14 optimal weight: 0.0980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1439 GLN ** 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 = 0.4434 r_free = 0.4434 target = 0.209996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.155314 restraints weight = 23755.526| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 3.08 r_work: 0.3635 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9709 Z= 0.161 Angle : 0.650 13.677 13146 Z= 0.324 Chirality : 0.043 0.294 1535 Planarity : 0.004 0.047 1577 Dihedral : 8.322 59.848 1807 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.49 % Allowed : 16.20 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.26), residues: 1130 helix: 1.26 (0.19), residues: 777 sheet: None (None), residues: 0 loop : -1.69 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1355 TYR 0.017 0.002 TYR A 364 PHE 0.020 0.002 PHE A 848 TRP 0.015 0.001 TRP A1551 HIS 0.004 0.001 HIS A1358 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 9702) covalent geometry : angle 0.64853 / 0.32 (13130) SS BOND : bond 0.00123 / 0.06 ( 5) SS BOND : angle 0.76519 / 0.46 ( 10) hydrogen bonds : bond 0.04030 / 2.68 ( 616) hydrogen bonds : angle 4.62407 / 3.33 ( 1755) link_NAG-ASN : bond 0.00393 / 0.21 ( 2) link_NAG-ASN : angle 2.19106 / 1.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 0.281 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.7734 (mmm) cc_final: 0.7356 (mmp) REVERT: A 648 MET cc_start: 0.6544 (mmp) cc_final: 0.5923 (tpt) REVERT: A 828 TYR cc_start: 0.8449 (m-10) cc_final: 0.8085 (m-80) REVERT: A 1174 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7481 (m-80) REVERT: A 1179 PHE cc_start: 0.8810 (m-80) cc_final: 0.8436 (m-80) REVERT: A 1434 PHE cc_start: 0.8600 (t80) cc_final: 0.8349 (t80) REVERT: A 1483 MET cc_start: 0.7001 (ttt) cc_final: 0.6721 (ptt) REVERT: A 1504 MET cc_start: 0.8581 (mtm) cc_final: 0.8204 (mtp) REVERT: A 1655 MET cc_start: 0.7902 (mtm) cc_final: 0.7464 (mtp) REVERT: A 1686 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.7792 (m-30) outliers start: 15 outliers final: 11 residues processed: 200 average time/residue: 0.0659 time to fit residues: 20.1948 Evaluate side-chains 199 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 1174 TYR Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1350 MET Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1525 MET Chi-restraints excluded: chain A residue 1561 LEU Chi-restraints excluded: chain A residue 1686 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 27 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 74 optimal weight: 0.0770 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1439 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.209416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.154609 restraints weight = 23247.849| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 3.06 r_work: 0.3628 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9709 Z= 0.159 Angle : 0.654 13.766 13146 Z= 0.328 Chirality : 0.043 0.293 1535 Planarity : 0.004 0.045 1577 Dihedral : 8.306 59.369 1807 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.69 % Allowed : 17.00 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.26), residues: 1130 helix: 1.23 (0.19), residues: 777 sheet: None (None), residues: 0 loop : -1.68 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1355 TYR 0.020 0.002 TYR A1354 PHE 0.020 0.002 PHE A 125 TRP 0.016 0.001 TRP A1551 HIS 0.003 0.001 HIS A1358 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 9702) covalent geometry : angle 0.65276 / 0.33 (13130) SS BOND : bond 0.00130 / 0.07 ( 5) SS BOND : angle 0.75722 / 0.46 ( 10) hydrogen bonds : bond 0.04024 / 2.69 ( 616) hydrogen bonds : angle 4.66512 / 3.34 ( 1755) link_NAG-ASN : bond 0.00395 / 0.21 ( 2) link_NAG-ASN : angle 2.15921 / 1.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.252 Fit side-chains TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7211 (tmm) REVERT: A 648 MET cc_start: 0.6511 (mmp) cc_final: 0.5894 (tpt) REVERT: A 1174 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.7497 (m-80) REVERT: A 1179 PHE cc_start: 0.8812 (m-80) cc_final: 0.8447 (m-80) REVERT: A 1434 PHE cc_start: 0.8560 (t80) cc_final: 0.8329 (t80) REVERT: A 1504 MET cc_start: 0.8588 (mtm) cc_final: 0.8202 (mtp) REVERT: A 1552 ASN cc_start: 0.8719 (m110) cc_final: 0.8512 (m110) REVERT: A 1655 MET cc_start: 0.7927 (mtm) cc_final: 0.7482 (mtp) REVERT: A 1686 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.7751 (m-30) outliers start: 17 outliers final: 12 residues processed: 196 average time/residue: 0.0663 time to fit residues: 20.0670 Evaluate side-chains 199 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 1174 TYR Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1350 MET Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1525 MET Chi-restraints excluded: chain A residue 1561 LEU Chi-restraints excluded: chain A residue 1686 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 72 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 0.0770 chunk 5 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.210830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.153813 restraints weight = 14226.588| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.34 r_work: 0.3635 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9709 Z= 0.140 Angle : 0.659 13.984 13146 Z= 0.326 Chirality : 0.042 0.279 1535 Planarity : 0.004 0.047 1577 Dihedral : 8.114 59.033 1807 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.49 % Allowed : 17.50 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.26), residues: 1130 helix: 1.27 (0.19), residues: 779 sheet: None (None), residues: 0 loop : -1.67 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1355 TYR 0.022 0.002 TYR A 364 PHE 0.019 0.001 PHE A 848 TRP 0.017 0.001 TRP A1551 HIS 0.003 0.001 HIS A1358 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9702) covalent geometry : angle 0.65712 / 0.33 (13130) SS BOND : bond 0.00123 / 0.06 ( 5) SS BOND : angle 0.71960 / 0.44 ( 10) hydrogen bonds : bond 0.03936 / 2.63 ( 616) hydrogen bonds : angle 4.60496 / 3.29 ( 1755) link_NAG-ASN : bond 0.00403 / 0.21 ( 2) link_NAG-ASN : angle 2.06860 / 1.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.265 Fit side-chains TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7203 (tmm) REVERT: A 648 MET cc_start: 0.6629 (mmp) cc_final: 0.5977 (tpt) REVERT: A 828 TYR cc_start: 0.8413 (m-10) cc_final: 0.7816 (m-80) REVERT: A 1174 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.7460 (m-80) REVERT: A 1175 VAL cc_start: 0.9639 (p) cc_final: 0.9343 (p) REVERT: A 1179 PHE cc_start: 0.8748 (m-80) cc_final: 0.8332 (m-80) REVERT: A 1434 PHE cc_start: 0.8568 (t80) cc_final: 0.8336 (t80) REVERT: A 1504 MET cc_start: 0.8524 (mtm) cc_final: 0.8115 (mtp) REVERT: A 1636 LEU cc_start: 0.9156 (tt) cc_final: 0.8898 (tp) REVERT: A 1655 MET cc_start: 0.7845 (mtm) cc_final: 0.7493 (mtp) REVERT: A 1686 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.7751 (m-30) outliers start: 15 outliers final: 10 residues processed: 198 average time/residue: 0.0644 time to fit residues: 20.0780 Evaluate side-chains 200 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 1174 TYR Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1350 MET Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1525 MET Chi-restraints excluded: chain A residue 1686 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 7 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 53 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 94 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.210192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.153451 restraints weight = 22078.557| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 3.26 r_work: 0.3565 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9709 Z= 0.158 Angle : 0.681 17.391 13146 Z= 0.338 Chirality : 0.043 0.271 1535 Planarity : 0.004 0.045 1577 Dihedral : 8.181 58.485 1807 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.39 % Allowed : 17.59 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.26), residues: 1130 helix: 1.25 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -1.69 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1355 TYR 0.029 0.002 TYR A 364 PHE 0.020 0.001 PHE A 125 TRP 0.014 0.001 TRP A1551 HIS 0.003 0.001 HIS A1732 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 9702) covalent geometry : angle 0.68000 / 0.34 (13130) SS BOND : bond 0.00124 / 0.06 ( 5) SS BOND : angle 0.76431 / 0.46 ( 10) hydrogen bonds : bond 0.03995 / 2.68 ( 616) hydrogen bonds : angle 4.62987 / 3.31 ( 1755) link_NAG-ASN : bond 0.00416 / 0.22 ( 2) link_NAG-ASN : angle 2.10072 / 1.31 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.272 Fit side-chains TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 389 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7308 (tmm) REVERT: A 648 MET cc_start: 0.6597 (mmp) cc_final: 0.5943 (tpt) REVERT: A 828 TYR cc_start: 0.8527 (m-10) cc_final: 0.7912 (m-80) REVERT: A 1174 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.7501 (m-80) REVERT: A 1391 ASP cc_start: 0.7645 (m-30) cc_final: 0.7403 (m-30) REVERT: A 1434 PHE cc_start: 0.8693 (t80) cc_final: 0.8469 (t80) REVERT: A 1504 MET cc_start: 0.8573 (mtm) cc_final: 0.8177 (mtp) REVERT: A 1636 LEU cc_start: 0.9165 (tt) cc_final: 0.8878 (tp) REVERT: A 1655 MET cc_start: 0.7907 (mtm) cc_final: 0.7534 (mtp) REVERT: A 1686 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.7841 (m-30) outliers start: 14 outliers final: 11 residues processed: 198 average time/residue: 0.0651 time to fit residues: 19.8762 Evaluate side-chains 201 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 1174 TYR Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1350 MET Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1525 MET Chi-restraints excluded: chain A residue 1686 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 56 optimal weight: 9.9990 chunk 49 optimal weight: 0.0570 chunk 97 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.211756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.155411 restraints weight = 26709.601| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 3.26 r_work: 0.3649 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9709 Z= 0.139 Angle : 0.671 15.685 13146 Z= 0.334 Chirality : 0.042 0.260 1535 Planarity : 0.004 0.047 1577 Dihedral : 8.034 58.672 1807 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.29 % Allowed : 18.59 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.26), residues: 1130 helix: 1.31 (0.19), residues: 779 sheet: None (None), residues: 0 loop : -1.73 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1355 TYR 0.023 0.002 TYR A 364 PHE 0.037 0.001 PHE A 125 TRP 0.015 0.001 TRP A1551 HIS 0.004 0.001 HIS A1732 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9702) covalent geometry : angle 0.67027 / 0.33 (13130) SS BOND : bond 0.00104 / 0.05 ( 5) SS BOND : angle 0.73501 / 0.44 ( 10) hydrogen bonds : bond 0.03942 / 2.64 ( 616) hydrogen bonds : angle 4.59079 / 3.28 ( 1755) link_NAG-ASN : bond 0.00402 / 0.21 ( 2) link_NAG-ASN : angle 1.97674 / 1.24 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2656.74 seconds wall clock time: 46 minutes 6.68 seconds (2766.68 seconds total)