Starting phenix.real_space_refine on Sun Dec 29 07:38:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wli_32584/12_2024/7wli_32584_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wli_32584/12_2024/7wli_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_32584/12_2024/7wli_32584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wli_32584/12_2024/7wli_32584.map" model { file = "/net/cci-nas-00/data/ceres_data/7wli_32584/12_2024/7wli_32584_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wli_32584/12_2024/7wli_32584_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.068 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'ARG:plan': 3, 'TRP:plan': 1} 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: {'ARG:plan': 3, 'TRP:plan': 1} 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, 382 Unusual residues: {' CA': 2, '3PE': 11, 'NAG': 2, 'Y01': 6} Classifications: {'undetermined': 21} Link IDs: {None: 20} 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: {'Y01:plan-2': 1, '3PE:plan-1': 10, '3PE:plan-2': 10, 'Y01:plan-1': 3} 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: 11.39, per 1000 atoms: 1.20 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: 2.61 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 0.76 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: 3.39 Time building geometry restraints manager: 2.93 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.110 Process input model: 31.690 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.070 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 9702 Z= 0.739 Angle : 1.012 14.878 13130 Z= 0.525 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 : 15.00 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 (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: -0.17 (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 TRP 0.015 0.001 TRP A 823 HIS 0.005 0.001 HIS A1358 PHE 0.043 0.002 PHE A1626 TYR 0.019 0.002 TYR A1361 ARG 0.004 0.000 ARG A 749 *********************** 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 : 1.079 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: 0.1933 time to fit residues: 61.2947 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 : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9702 Z= 0.235 Angle : 0.684 11.796 13130 Z= 0.347 Chirality : 0.043 0.241 1535 Planarity : 0.005 0.055 1577 Dihedral : 9.737 58.242 1807 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.09 % Allowed : 9.74 % Favored : 89.17 % 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: 0.16 (0.26), residues: 1130 helix: 0.89 (0.19), residues: 776 sheet: None (None), residues: 0 loop : -1.63 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1551 HIS 0.003 0.001 HIS A1358 PHE 0.033 0.002 PHE A1626 TYR 0.016 0.002 TYR A1633 ARG 0.006 0.000 ARG A 731 *********************** 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 213 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 203 time to evaluate : 1.081 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: 0.8793 (t0) cc_final: 0.8558 (t0) REVERT: A 134 MET cc_start: 0.8082 (mpp) cc_final: 0.7838 (mpp) REVERT: A 146 LEU cc_start: 0.8038 (mt) cc_final: 0.7347 (tt) REVERT: A 648 MET cc_start: 0.6553 (mmp) cc_final: 0.5976 (tpt) REVERT: A 686 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8145 (mm-30) REVERT: A 1172 PHE cc_start: 0.8043 (t80) cc_final: 0.7320 (t80) REVERT: A 1174 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.7330 (m-80) REVERT: A 1218 GLU cc_start: 0.7828 (pp20) cc_final: 0.7042 (tm-30) REVERT: A 1434 PHE cc_start: 0.8394 (t80) cc_final: 0.8034 (t80) REVERT: A 1600 LYS cc_start: 0.8242 (tptt) cc_final: 0.7548 (tptp) REVERT: A 1650 ASN cc_start: 0.7545 (m110) cc_final: 0.7178 (m-40) REVERT: A 1655 MET cc_start: 0.8033 (mtm) cc_final: 0.7714 (mtp) outliers start: 10 outliers final: 6 residues processed: 207 average time/residue: 0.1878 time to fit residues: 57.1735 Evaluate side-chains 191 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 184 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 57 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 101 optimal weight: 0.0770 chunk 35 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 ASN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 866 GLN A1398 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9702 Z= 0.229 Angle : 0.646 14.338 13130 Z= 0.326 Chirality : 0.042 0.228 1535 Planarity : 0.004 0.049 1577 Dihedral : 9.197 59.210 1807 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.39 % Allowed : 12.43 % Favored : 86.18 % 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: 0.23 (0.26), residues: 1130 helix: 0.98 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -1.70 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1551 HIS 0.005 0.001 HIS A1358 PHE 0.033 0.002 PHE A 744 TYR 0.014 0.001 TYR A1633 ARG 0.006 0.000 ARG A 731 *********************** 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 214 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.939 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: 0.8782 (t0) cc_final: 0.8547 (t0) REVERT: A 134 MET cc_start: 0.7875 (mpp) cc_final: 0.7433 (mpp) REVERT: A 146 LEU cc_start: 0.8025 (mt) cc_final: 0.7326 (tt) REVERT: A 648 MET cc_start: 0.6468 (mmp) cc_final: 0.5915 (tpt) REVERT: A 657 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7977 (ttm) REVERT: A 1174 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.7337 (m-80) REVERT: A 1434 PHE cc_start: 0.8344 (t80) cc_final: 0.8085 (t80) REVERT: A 1655 MET cc_start: 0.8012 (mtm) cc_final: 0.7508 (mtp) REVERT: A 1730 MET cc_start: 0.7373 (mmm) cc_final: 0.7051 (mmm) outliers start: 14 outliers final: 6 residues processed: 206 average time/residue: 0.2001 time to fit residues: 61.0130 Evaluate side-chains 193 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 185 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 1295 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 29 optimal weight: 0.1980 chunk 90 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 ASN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9702 Z= 0.190 Angle : 0.615 10.181 13130 Z= 0.313 Chirality : 0.041 0.229 1535 Planarity : 0.004 0.049 1577 Dihedral : 8.720 59.679 1807 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.29 % Allowed : 14.12 % 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 (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: 0.39 (0.26), residues: 1130 helix: 1.13 (0.19), residues: 778 sheet: None (None), residues: 0 loop : -1.73 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1551 HIS 0.005 0.001 HIS A1358 PHE 0.022 0.001 PHE A1626 TYR 0.013 0.001 TYR A1387 ARG 0.007 0.000 ARG A 731 *********************** 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 220 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 207 time to evaluate : 1.060 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: symmetry clash REVERT: A 86 MET cc_start: 0.7877 (mmm) cc_final: 0.7436 (mmp) REVERT: A 134 MET cc_start: 0.7910 (mpp) cc_final: 0.7595 (mpp) REVERT: A 648 MET cc_start: 0.6426 (mmp) cc_final: 0.5838 (tpt) REVERT: A 657 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.8091 (ttm) REVERT: A 1174 TYR cc_start: 0.7912 (OUTLIER) cc_final: 0.7369 (m-80) REVERT: A 1434 PHE cc_start: 0.8284 (t80) cc_final: 0.8043 (t80) REVERT: A 1504 MET cc_start: 0.8403 (mtm) cc_final: 0.8100 (mtp) REVERT: A 1655 MET cc_start: 0.7851 (mtm) cc_final: 0.7405 (mtp) outliers start: 13 outliers final: 7 residues processed: 211 average time/residue: 0.1886 time to fit residues: 58.1413 Evaluate side-chains 197 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 379 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 409 HIS 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 1295 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9702 Z= 0.228 Angle : 0.619 9.484 13130 Z= 0.315 Chirality : 0.041 0.223 1535 Planarity : 0.004 0.047 1577 Dihedral : 8.676 59.890 1807 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.79 % Allowed : 14.61 % Favored : 83.60 % 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: 0.44 (0.26), residues: 1130 helix: 1.15 (0.19), residues: 777 sheet: None (None), residues: 0 loop : -1.64 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1551 HIS 0.004 0.001 HIS A1358 PHE 0.020 0.002 PHE A1626 TYR 0.014 0.001 TYR A1387 ARG 0.007 0.000 ARG A1355 *********************** 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 208 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 1.009 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 648 MET cc_start: 0.6350 (mmp) cc_final: 0.5786 (tpt) REVERT: A 657 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8080 (ttm) REVERT: A 1174 TYR cc_start: 0.7919 (OUTLIER) cc_final: 0.7395 (m-80) REVERT: A 1218 GLU cc_start: 0.7935 (pp20) cc_final: 0.7731 (pp20) REVERT: A 1434 PHE cc_start: 0.8315 (t80) cc_final: 0.8045 (t80) REVERT: A 1504 MET cc_start: 0.8492 (mtm) cc_final: 0.8135 (mtp) REVERT: A 1655 MET cc_start: 0.7910 (mtm) cc_final: 0.7460 (mtp) outliers start: 18 outliers final: 10 residues processed: 197 average time/residue: 0.1959 time to fit residues: 55.8113 Evaluate side-chains 195 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 379 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 1174 TYR Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1350 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 105 optimal weight: 0.0170 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9702 Z= 0.193 Angle : 0.619 13.952 13130 Z= 0.313 Chirality : 0.041 0.222 1535 Planarity : 0.004 0.062 1577 Dihedral : 8.403 59.752 1807 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.69 % Allowed : 15.21 % Favored : 83.10 % 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 (0.26), residues: 1130 helix: 1.24 (0.19), residues: 778 sheet: None (None), residues: 0 loop : -1.59 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1551 HIS 0.006 0.001 HIS A1358 PHE 0.020 0.001 PHE A 125 TYR 0.015 0.001 TYR A1387 ARG 0.008 0.000 ARG A 731 *********************** 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 209 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 1.079 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 86 MET cc_start: 0.7778 (mmm) cc_final: 0.7417 (mmp) REVERT: A 648 MET cc_start: 0.6270 (mmp) cc_final: 0.5729 (tpt) REVERT: A 1174 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.7444 (m-80) REVERT: A 1218 GLU cc_start: 0.7904 (pp20) cc_final: 0.7674 (pp20) REVERT: A 1504 MET cc_start: 0.8450 (mtm) cc_final: 0.8065 (mtp) REVERT: A 1636 LEU cc_start: 0.9082 (tt) cc_final: 0.8809 (tp) REVERT: A 1655 MET cc_start: 0.7847 (mtm) cc_final: 0.7400 (mtp) outliers start: 17 outliers final: 12 residues processed: 198 average time/residue: 0.1963 time to fit residues: 56.8059 Evaluate side-chains 195 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 157 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 668 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9702 Z= 0.226 Angle : 0.629 13.604 13130 Z= 0.314 Chirality : 0.041 0.220 1535 Planarity : 0.004 0.046 1577 Dihedral : 8.383 59.006 1807 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.79 % Allowed : 15.81 % Favored : 82.41 % 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: 0.58 (0.26), residues: 1130 helix: 1.26 (0.19), residues: 777 sheet: None (None), residues: 0 loop : -1.60 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1551 HIS 0.007 0.001 HIS A1358 PHE 0.019 0.002 PHE A 125 TYR 0.012 0.001 TYR A1633 ARG 0.008 0.000 ARG A 731 *********************** 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 212 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 1.086 Fit side-chains TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 86 MET cc_start: 0.7785 (mmm) cc_final: 0.7386 (mmp) REVERT: A 648 MET cc_start: 0.6332 (mmp) cc_final: 0.5757 (tpt) REVERT: A 1174 TYR cc_start: 0.7974 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: A 1218 GLU cc_start: 0.7922 (pp20) cc_final: 0.7636 (pp20) REVERT: A 1504 MET cc_start: 0.8535 (mtm) cc_final: 0.8122 (mtp) REVERT: A 1655 MET cc_start: 0.7852 (mtm) cc_final: 0.7416 (mtp) REVERT: A 1686 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7363 (m-30) outliers start: 18 outliers final: 13 residues processed: 202 average time/residue: 0.1887 time to fit residues: 56.1689 Evaluate side-chains 202 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 379 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 668 LEU 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 1590 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 65 optimal weight: 6.9990 chunk 32 optimal weight: 0.0770 chunk 21 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 866 GLN ** A1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9702 Z= 0.267 Angle : 0.659 13.991 13130 Z= 0.329 Chirality : 0.042 0.219 1535 Planarity : 0.004 0.045 1577 Dihedral : 8.489 59.387 1807 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.89 % Allowed : 16.70 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.26), residues: 1130 helix: 1.22 (0.19), residues: 779 sheet: None (None), residues: 0 loop : -1.68 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1551 HIS 0.006 0.001 HIS A1358 PHE 0.021 0.002 PHE A 125 TYR 0.017 0.001 TYR A 364 ARG 0.009 0.000 ARG A 731 *********************** 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 212 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 1.062 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 648 MET cc_start: 0.6334 (mmp) cc_final: 0.5802 (tpt) REVERT: A 1174 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.7406 (m-80) REVERT: A 1179 PHE cc_start: 0.8671 (m-80) cc_final: 0.8319 (m-80) REVERT: A 1218 GLU cc_start: 0.7942 (pp20) cc_final: 0.7650 (pp20) REVERT: A 1391 ASP cc_start: 0.7372 (m-30) cc_final: 0.7142 (m-30) REVERT: A 1483 MET cc_start: 0.7094 (ttt) cc_final: 0.6561 (ptt) REVERT: A 1504 MET cc_start: 0.8567 (mtm) cc_final: 0.8156 (mtp) REVERT: A 1636 LEU cc_start: 0.9137 (tt) cc_final: 0.8873 (tp) REVERT: A 1655 MET cc_start: 0.7925 (mtm) cc_final: 0.7490 (mtp) REVERT: A 1686 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7377 (m-30) outliers start: 19 outliers final: 13 residues processed: 203 average time/residue: 0.1889 time to fit residues: 56.4406 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 : 1.104 ------------------------------------------------------------------------------- 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 379 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 668 LEU 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 1590 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 101 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9702 Z= 0.259 Angle : 0.674 18.121 13130 Z= 0.332 Chirality : 0.042 0.219 1535 Planarity : 0.004 0.046 1577 Dihedral : 8.475 59.596 1807 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.59 % Allowed : 17.20 % Favored : 81.21 % 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: 0.51 (0.26), residues: 1130 helix: 1.22 (0.19), residues: 777 sheet: None (None), residues: 0 loop : -1.67 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1551 HIS 0.006 0.001 HIS A1358 PHE 0.026 0.002 PHE A1434 TYR 0.024 0.002 TYR A 828 ARG 0.008 0.000 ARG A 731 *********************** 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 209 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 1.062 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 86 MET cc_start: 0.7860 (mmm) cc_final: 0.7353 (mmp) REVERT: A 648 MET cc_start: 0.6407 (mmp) cc_final: 0.5820 (tpt) REVERT: A 1174 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.7411 (m-80) REVERT: A 1218 GLU cc_start: 0.7965 (pp20) cc_final: 0.7669 (pp20) REVERT: A 1391 ASP cc_start: 0.7382 (m-30) cc_final: 0.7157 (m-30) REVERT: A 1504 MET cc_start: 0.8551 (mtm) cc_final: 0.8127 (mtp) REVERT: A 1636 LEU cc_start: 0.9134 (tt) cc_final: 0.8858 (tp) REVERT: A 1655 MET cc_start: 0.7920 (mtm) cc_final: 0.7489 (mtp) REVERT: A 1686 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7397 (m-30) outliers start: 16 outliers final: 13 residues processed: 199 average time/residue: 0.1834 time to fit residues: 54.3087 Evaluate side-chains 201 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 379 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 668 LEU 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 1590 LEU 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 50 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9702 Z= 0.214 Angle : 0.657 16.423 13130 Z= 0.324 Chirality : 0.041 0.221 1535 Planarity : 0.004 0.046 1577 Dihedral : 8.264 59.272 1807 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.49 % Allowed : 18.19 % Favored : 80.32 % 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: 0.58 (0.26), residues: 1130 helix: 1.27 (0.19), residues: 779 sheet: None (None), residues: 0 loop : -1.65 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1551 HIS 0.006 0.001 HIS A1358 PHE 0.024 0.002 PHE A1434 TYR 0.027 0.002 TYR A1709 ARG 0.009 0.000 ARG A 731 ********************** 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 201 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 1.046 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 86 MET cc_start: 0.7764 (mmm) cc_final: 0.7194 (mmp) REVERT: A 648 MET cc_start: 0.6496 (mmp) cc_final: 0.5928 (tpt) REVERT: A 1174 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.7406 (m-80) REVERT: A 1218 GLU cc_start: 0.7992 (pp20) cc_final: 0.7672 (pp20) REVERT: A 1504 MET cc_start: 0.8503 (mtm) cc_final: 0.8072 (mtp) REVERT: A 1636 LEU cc_start: 0.9099 (tt) cc_final: 0.8834 (tp) REVERT: A 1655 MET cc_start: 0.7824 (mtm) cc_final: 0.7409 (mtp) REVERT: A 1686 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7497 (m-30) outliers start: 15 outliers final: 13 residues processed: 192 average time/residue: 0.1874 time to fit residues: 54.5853 Evaluate side-chains 198 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 379 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 668 LEU 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 1590 LEU 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 82 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 0.0270 chunk 5 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 GLN A 866 GLN ** A1193 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 = 0.4452 r_free = 0.4452 target = 0.212289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.153286 restraints weight = 17791.228| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.69 r_work: 0.3628 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- 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 = 0.50 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 | |-----------------------------------------------------------------------------| r_final: 0.3627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9702 Z= 0.192 Angle : 0.642 15.953 13130 Z= 0.318 Chirality : 0.041 0.251 1535 Planarity : 0.004 0.048 1577 Dihedral : 8.032 57.924 1807 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.49 % Allowed : 18.39 % 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 (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: 0.68 (0.26), residues: 1130 helix: 1.35 (0.19), residues: 781 sheet: None (None), residues: 0 loop : -1.63 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1551 HIS 0.006 0.001 HIS A1358 PHE 0.033 0.002 PHE A 125 TYR 0.025 0.002 TYR A 364 ARG 0.009 0.000 ARG A 731 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2227.98 seconds wall clock time: 41 minutes 22.08 seconds (2482.08 seconds total)