Starting phenix.real_space_refine on Wed Feb 14 14:35:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wli_32584/02_2024/7wli_32584_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wli_32584/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wli_32584/02_2024/7wli_32584.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wli_32584/02_2024/7wli_32584.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wli_32584/02_2024/7wli_32584_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wli_32584/02_2024/7wli_32584_neut.pdb" } 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 Residue "A ARG 238": "NH1" <-> "NH2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "A GLU 666": "OE1" <-> "OE2" Residue "A GLU 863": "OE1" <-> "OE2" Residue "A GLU 1190": "OE1" <-> "OE2" Residue "A GLU 1297": "OE1" <-> "OE2" Residue "A ARG 1466": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9493 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9493 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1156, 9482 Unusual residues: {' CA': 2, '3PE': 11, 'NAG': 2, 'Y01': 6} Classifications: {'peptide': 1135, 'undetermined': 21} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 1103, None: 21} Not linked: pdbres="LYS A1738 " pdbres=" CA A2301 " Not linked: pdbres=" CA A2301 " pdbres=" CA A2302 " Not linked: pdbres=" CA A2302 " pdbres="NAG A2303 " Not linked: pdbres="NAG A2303 " pdbres="NAG A2304 " Not linked: pdbres="NAG A2304 " pdbres="3PE A2305 " ... (remaining 16 not shown) Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 466 Unresolved non-hydrogen angles: 543 Unresolved non-hydrogen dihedrals: 471 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'3PE:plan-1': 10, '3PE:plan-2': 10, 'TRP:plan': 1, 'Y01:plan-2': 1, 'Y01:plan-1': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 102 Conformer: "B" Number of residues, atoms: 1156, 9482 Unusual residues: {' CA': 2, '3PE': 11, 'NAG': 2, 'Y01': 6} Classifications: {'peptide': 1135, 'undetermined': 21} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 1103, None: 21} Not linked: pdbres="LYS A1738 " pdbres=" CA A2301 " Not linked: pdbres=" CA A2301 " pdbres=" CA A2302 " Not linked: pdbres=" CA A2302 " pdbres="NAG A2303 " Not linked: pdbres="NAG A2303 " pdbres="NAG A2304 " Not linked: pdbres="NAG A2304 " pdbres="3PE A2305 " ... (remaining 16 not shown) Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 466 Unresolved non-hydrogen angles: 543 Unresolved non-hydrogen dihedrals: 471 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'3PE:plan-1': 10, '3PE:plan-2': 10, 'TRP:plan': 1, 'Y01:plan-2': 1, 'Y01:plan-1': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 102 bond proxies already assigned to first conformer: 9676 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: 10.27, per 1000 atoms: 1.08 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A2303 " - " ASN A1345 " " NAG A2304 " - " ASN A1342 " Time building additional restraints: 4.33 Conformation dependent library (CDL) restraints added in 3.4 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: 1.31 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: 2.97 Time building geometry restraints manager: 4.62 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: 98.40 - 105.56: 184 105.56 - 112.72: 5303 112.72 - 119.87: 3240 119.87 - 127.03: 4316 127.03 - 134.19: 87 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 2.520 nonbonded pdb=" O HIS A1481 " pdb=" OG1 THR A1485 " model vdw 2.144 2.440 nonbonded pdb=" OG SER A 270 " pdb=" O ASP A 274 " model vdw 2.149 2.440 nonbonded pdb=" OH TYR A1524 " pdb=" OE1 GLU A1569 " model vdw 2.151 2.440 ... (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: 0.890 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: 4.060 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 36.180 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.310 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 1.052 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: 0.1896 time to fit residues: 60.7193 Evaluate side-chains 189 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 6.9990 chunk 87 optimal weight: 0.2980 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 0.0970 chunk 104 optimal weight: 7.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 A1241 ASN A1404 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9702 Z= 0.206 Angle : 0.660 11.944 13130 Z= 0.333 Chirality : 0.042 0.241 1535 Planarity : 0.004 0.055 1577 Dihedral : 9.583 57.969 1807 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 1.09 % Allowed : 9.44 % Favored : 89.46 % 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: 0.24 (0.26), residues: 1130 helix: 0.96 (0.19), residues: 777 sheet: None (None), residues: 0 loop : -1.62 (0.36), residues: 353 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 0.014 0.001 TYR A1709 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 215 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 204 time to evaluate : 1.100 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: 0.8801 (t0) cc_final: 0.8557 (t0) REVERT: A 86 MET cc_start: 0.8085 (mmm) cc_final: 0.7606 (mmp) REVERT: A 134 MET cc_start: 0.8092 (mpp) cc_final: 0.7840 (mpp) REVERT: A 146 LEU cc_start: 0.8031 (mt) cc_final: 0.7362 (tt) REVERT: A 648 MET cc_start: 0.6489 (mmp) cc_final: 0.5903 (tpt) REVERT: A 1172 PHE cc_start: 0.8052 (t80) cc_final: 0.7302 (t80) REVERT: A 1174 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7343 (m-80) REVERT: A 1218 GLU cc_start: 0.7844 (pp20) cc_final: 0.7056 (tm-30) REVERT: A 1434 PHE cc_start: 0.8388 (t80) cc_final: 0.8025 (t80) REVERT: A 1600 LYS cc_start: 0.8261 (tptt) cc_final: 0.7664 (tptp) REVERT: A 1650 ASN cc_start: 0.7516 (m110) cc_final: 0.7133 (m-40) outliers start: 11 outliers final: 7 residues processed: 208 average time/residue: 0.1811 time to fit residues: 56.1970 Evaluate side-chains 193 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 185 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 689 LEU 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: 115 random chunks: chunk 58 optimal weight: 0.2980 chunk 32 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 103 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 866 GLN ** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9702 Z= 0.203 Angle : 0.630 14.081 13130 Z= 0.315 Chirality : 0.041 0.235 1535 Planarity : 0.004 0.049 1577 Dihedral : 9.029 59.901 1807 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.09 % Allowed : 12.43 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 1130 helix: 1.09 (0.19), residues: 781 sheet: None (None), residues: 0 loop : -1.64 (0.36), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1551 HIS 0.003 0.001 HIS A1358 PHE 0.027 0.002 PHE A1626 TYR 0.013 0.001 TYR A1387 ARG 0.005 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 213 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 202 time to evaluate : 0.977 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: 0.8799 (t0) cc_final: 0.8546 (t0) REVERT: A 134 MET cc_start: 0.7853 (mpp) cc_final: 0.7422 (mpp) REVERT: A 648 MET cc_start: 0.6448 (mmp) cc_final: 0.5900 (tpt) REVERT: A 1174 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.7342 (m-80) REVERT: A 1187 ILE cc_start: 0.7753 (mt) cc_final: 0.7415 (mt) REVERT: A 1434 PHE cc_start: 0.8314 (t80) cc_final: 0.8062 (t80) REVERT: A 1730 MET cc_start: 0.7441 (mmm) cc_final: 0.7090 (mmm) outliers start: 11 outliers final: 5 residues processed: 207 average time/residue: 0.1874 time to fit residues: 56.8126 Evaluate side-chains 190 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 184 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 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 1295 VAL Chi-restraints excluded: chain A residue 1525 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 104 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1732 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9702 Z= 0.219 Angle : 0.614 10.214 13130 Z= 0.307 Chirality : 0.041 0.234 1535 Planarity : 0.004 0.048 1577 Dihedral : 8.841 59.518 1807 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.69 % Allowed : 14.51 % Favored : 83.80 % 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: 1.20 (0.19), residues: 779 sheet: None (None), residues: 0 loop : -1.62 (0.36), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1382 HIS 0.003 0.001 HIS A1358 PHE 0.023 0.002 PHE A1626 TYR 0.013 0.001 TYR A1387 ARG 0.006 0.000 ARG A1355 *********************** 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 213 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 196 time to evaluate : 1.059 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 134 MET cc_start: 0.7887 (mpp) cc_final: 0.7547 (mpp) REVERT: A 648 MET cc_start: 0.6469 (mmp) cc_final: 0.5887 (tpt) REVERT: A 657 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.8089 (ttm) REVERT: A 1174 TYR cc_start: 0.7914 (OUTLIER) cc_final: 0.7356 (m-80) REVERT: A 1218 GLU cc_start: 0.8031 (pp20) cc_final: 0.7723 (pp20) REVERT: A 1434 PHE cc_start: 0.8260 (t80) cc_final: 0.8006 (t80) REVERT: A 1504 MET cc_start: 0.8475 (mtm) cc_final: 0.8173 (mtp) outliers start: 17 outliers final: 9 residues processed: 200 average time/residue: 0.1895 time to fit residues: 55.6201 Evaluate side-chains 193 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 182 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 379 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 1199 THR Chi-restraints excluded: chain A residue 1214 ILE 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: 115 random chunks: chunk 63 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 99 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2076 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= 0.219 Angle : 0.603 9.542 13130 Z= 0.302 Chirality : 0.041 0.234 1535 Planarity : 0.004 0.047 1577 Dihedral : 8.680 59.547 1807 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.59 % Allowed : 15.21 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1130 helix: 1.27 (0.19), residues: 779 sheet: None (None), residues: 0 loop : -1.62 (0.35), residues: 351 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 A1284 *********************** 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 216 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 200 time to evaluate : 1.082 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: symmetry clash REVERT: A 86 MET cc_start: 0.7830 (mmm) cc_final: 0.7476 (mmp) REVERT: A 165 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.7629 (m-80) REVERT: A 648 MET cc_start: 0.6315 (mmp) cc_final: 0.5758 (tpt) REVERT: A 657 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8074 (ttm) REVERT: A 1174 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.7396 (m-80) REVERT: A 1218 GLU cc_start: 0.8068 (pp20) cc_final: 0.7708 (pp20) REVERT: A 1434 PHE cc_start: 0.8322 (t80) cc_final: 0.8065 (t80) REVERT: A 1504 MET cc_start: 0.8499 (mtm) cc_final: 0.8194 (mtp) outliers start: 16 outliers final: 8 residues processed: 204 average time/residue: 0.1926 time to fit residues: 57.2528 Evaluate side-chains 200 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 189 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 TYR Chi-restraints excluded: chain A residue 379 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 668 LEU Chi-restraints excluded: chain A residue 1174 TYR Chi-restraints excluded: chain A residue 1199 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: 115 random chunks: chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9702 Z= 0.310 Angle : 0.656 12.814 13130 Z= 0.329 Chirality : 0.043 0.263 1535 Planarity : 0.004 0.046 1577 Dihedral : 8.919 59.663 1807 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.49 % Allowed : 15.90 % Favored : 82.60 % 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: 0.48 (0.26), residues: 1130 helix: 1.17 (0.19), residues: 779 sheet: None (None), residues: 0 loop : -1.62 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1551 HIS 0.005 0.001 HIS A1358 PHE 0.019 0.002 PHE A1626 TYR 0.015 0.002 TYR A1387 ARG 0.007 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 207 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 192 time to evaluate : 1.078 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 165 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.7690 (m-80) REVERT: A 648 MET cc_start: 0.6349 (mmp) cc_final: 0.5806 (tpt) REVERT: A 657 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.8054 (ttm) REVERT: A 1174 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: A 1218 GLU cc_start: 0.8091 (pp20) cc_final: 0.7762 (pp20) REVERT: A 1434 PHE cc_start: 0.8350 (t80) cc_final: 0.8073 (t80) REVERT: A 1504 MET cc_start: 0.8592 (mtm) cc_final: 0.8271 (mtp) REVERT: A 1552 ASN cc_start: 0.8885 (m110) cc_final: 0.8682 (m110) REVERT: A 1650 ASN cc_start: 0.7637 (m110) cc_final: 0.7189 (m-40) REVERT: A 1655 MET cc_start: 0.8158 (mtm) cc_final: 0.7725 (mtp) outliers start: 15 outliers final: 10 residues processed: 197 average time/residue: 0.1867 time to fit residues: 54.1059 Evaluate side-chains 196 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 183 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 165 TYR Chi-restraints excluded: chain A residue 379 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 668 LEU Chi-restraints excluded: chain A residue 1174 TYR Chi-restraints excluded: chain A residue 1199 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9702 Z= 0.219 Angle : 0.638 14.154 13130 Z= 0.318 Chirality : 0.042 0.235 1535 Planarity : 0.004 0.048 1577 Dihedral : 8.589 59.066 1807 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.79 % Allowed : 16.40 % Favored : 81.81 % 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: 0.60 (0.26), residues: 1130 helix: 1.26 (0.19), residues: 778 sheet: None (None), residues: 0 loop : -1.56 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1551 HIS 0.006 0.001 HIS A1358 PHE 0.021 0.002 PHE A 848 TYR 0.017 0.001 TYR A1387 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 205 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 187 time to evaluate : 1.138 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 165 TYR cc_start: 0.8028 (OUTLIER) cc_final: 0.7645 (m-80) REVERT: A 648 MET cc_start: 0.6254 (mmp) cc_final: 0.5703 (tpt) REVERT: A 657 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.8074 (ttm) REVERT: A 1174 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7416 (m-80) REVERT: A 1218 GLU cc_start: 0.8083 (pp20) cc_final: 0.7744 (pp20) REVERT: A 1434 PHE cc_start: 0.8330 (t80) cc_final: 0.8120 (t80) REVERT: A 1655 MET cc_start: 0.8048 (mtm) cc_final: 0.7590 (mtp) outliers start: 18 outliers final: 10 residues processed: 193 average time/residue: 0.2043 time to fit residues: 58.4200 Evaluate side-chains 194 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 181 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 165 TYR Chi-restraints excluded: chain A residue 379 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 668 LEU Chi-restraints excluded: chain A residue 1174 TYR Chi-restraints excluded: chain A residue 1199 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9702 Z= 0.283 Angle : 0.672 14.310 13130 Z= 0.335 Chirality : 0.043 0.261 1535 Planarity : 0.004 0.058 1577 Dihedral : 8.691 59.950 1807 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.79 % Allowed : 17.10 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.50 (0.26), residues: 1130 helix: 1.20 (0.19), residues: 778 sheet: None (None), residues: 0 loop : -1.63 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1551 HIS 0.007 0.001 HIS A1358 PHE 0.020 0.002 PHE A 125 TYR 0.012 0.001 TYR A1387 ARG 0.008 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 205 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 187 time to evaluate : 1.090 Fit side-chains TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 165 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.7695 (m-80) REVERT: A 389 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.6873 (tmm) REVERT: A 648 MET cc_start: 0.6301 (mmp) cc_final: 0.5732 (tpt) REVERT: A 657 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.8067 (ttm) REVERT: A 1174 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: A 1218 GLU cc_start: 0.8086 (pp20) cc_final: 0.7746 (pp20) REVERT: A 1650 ASN cc_start: 0.7556 (m110) cc_final: 0.7099 (m-40) REVERT: A 1655 MET cc_start: 0.8092 (mtm) cc_final: 0.7625 (mtp) REVERT: A 1709 TYR cc_start: 0.8607 (t80) cc_final: 0.8278 (t80) outliers start: 18 outliers final: 12 residues processed: 194 average time/residue: 0.1832 time to fit residues: 52.3468 Evaluate side-chains 199 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 183 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 165 TYR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 389 MET 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 668 LEU Chi-restraints excluded: chain A residue 1174 TYR Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1298 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 109 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 352 GLN ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2409 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= 0.203 Angle : 0.653 14.323 13130 Z= 0.324 Chirality : 0.041 0.242 1535 Planarity : 0.004 0.064 1577 Dihedral : 8.308 59.804 1807 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.09 % Allowed : 17.99 % Favored : 80.91 % 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: 0.62 (0.26), residues: 1130 helix: 1.29 (0.19), residues: 779 sheet: None (None), residues: 0 loop : -1.60 (0.36), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1551 HIS 0.006 0.001 HIS A1359 PHE 0.048 0.002 PHE A 125 TYR 0.013 0.001 TYR A1387 ARG 0.009 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 201 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 190 time to evaluate : 1.107 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 165 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7659 (m-80) REVERT: A 389 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7027 (tmm) REVERT: A 648 MET cc_start: 0.6297 (mmp) cc_final: 0.5737 (tpt) REVERT: A 657 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.8089 (ttm) REVERT: A 1174 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7398 (m-80) REVERT: A 1218 GLU cc_start: 0.8066 (pp20) cc_final: 0.7743 (pp20) REVERT: A 1504 MET cc_start: 0.8460 (mtm) cc_final: 0.8072 (mtp) REVERT: A 1655 MET cc_start: 0.8023 (mtm) cc_final: 0.7533 (mtp) REVERT: A 1709 TYR cc_start: 0.8517 (t80) cc_final: 0.8268 (t80) outliers start: 11 outliers final: 5 residues processed: 193 average time/residue: 0.1796 time to fit residues: 51.2638 Evaluate side-chains 192 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 183 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 TYR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 389 MET 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 Chi-restraints excluded: chain A residue 1350 MET Chi-restraints excluded: chain A residue 1393 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 9.9990 chunk 51 optimal weight: 0.0980 chunk 75 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 866 GLN ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9702 Z= 0.213 Angle : 0.666 14.467 13130 Z= 0.333 Chirality : 0.042 0.233 1535 Planarity : 0.004 0.069 1577 Dihedral : 8.214 58.642 1807 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.09 % Allowed : 18.39 % Favored : 80.52 % 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: 0.63 (0.26), residues: 1130 helix: 1.29 (0.19), residues: 779 sheet: None (None), residues: 0 loop : -1.60 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1551 HIS 0.008 0.001 HIS A1358 PHE 0.047 0.002 PHE A 125 TYR 0.012 0.001 TYR A 365 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 203 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 192 time to evaluate : 1.069 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 165 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: A 389 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7123 (tmm) REVERT: A 648 MET cc_start: 0.6338 (mmp) cc_final: 0.5815 (tpt) REVERT: A 1174 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7374 (m-80) REVERT: A 1504 MET cc_start: 0.8525 (mtm) cc_final: 0.8118 (mtp) REVERT: A 1655 MET cc_start: 0.7991 (mtm) cc_final: 0.7495 (mtp) REVERT: A 1709 TYR cc_start: 0.8511 (t80) cc_final: 0.8293 (t80) outliers start: 11 outliers final: 6 residues processed: 195 average time/residue: 0.1793 time to fit residues: 51.9141 Evaluate side-chains 193 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 184 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 TYR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 1174 TYR Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1350 MET Chi-restraints excluded: chain A residue 1393 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 80 optimal weight: 0.4980 chunk 5 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1614 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 = 0.4421 r_free = 0.4421 target = 0.208659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.150313 restraints weight = 17422.500| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 3.04 r_work: 0.3537 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2539 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= 0.268 Angle : 0.693 18.512 13130 Z= 0.344 Chirality : 0.043 0.256 1535 Planarity : 0.004 0.067 1577 Dihedral : 8.379 59.035 1807 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.99 % Allowed : 18.99 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.56 (0.26), residues: 1130 helix: 1.25 (0.19), residues: 779 sheet: None (None), residues: 0 loop : -1.63 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1551 HIS 0.009 0.001 HIS A1358 PHE 0.047 0.002 PHE A 125 TYR 0.024 0.002 TYR A1361 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: 2325.76 seconds wall clock time: 42 minutes 47.21 seconds (2567.21 seconds total)