Starting phenix.real_space_refine on Thu Feb 15 05:03:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klc_0706/02_2024/6klc_0706.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klc_0706/02_2024/6klc_0706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klc_0706/02_2024/6klc_0706.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klc_0706/02_2024/6klc_0706.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klc_0706/02_2024/6klc_0706.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klc_0706/02_2024/6klc_0706.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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: 5 Type Number sf(0) Gaussians Mn 1 7.51 5 S 72 5.16 5 C 7134 2.51 5 N 1866 2.21 5 O 2137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 106": "NH1" <-> "NH2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A ASP 359": "OD1" <-> "OD2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A ASP 454": "OD1" <-> "OD2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 581": "NH1" <-> "NH2" Residue "A PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "A ASP 657": "OD1" <-> "OD2" Residue "A ARG 663": "NH1" <-> "NH2" Residue "A GLU 664": "OE1" <-> "OE2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A PHE 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A ASP 689": "OD1" <-> "OD2" Residue "A GLU 714": "OE1" <-> "OE2" Residue "A ASP 717": "OD1" <-> "OD2" Residue "A ARG 718": "NH1" <-> "NH2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "A PHE 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 858": "OE1" <-> "OE2" Residue "A ASP 872": "OD1" <-> "OD2" Residue "A GLU 874": "OE1" <-> "OE2" Residue "A ASP 894": "OD1" <-> "OD2" Residue "A GLU 897": "OE1" <-> "OE2" Residue "A GLU 902": "OE1" <-> "OE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A GLU 921": "OE1" <-> "OE2" Residue "A ASP 925": "OD1" <-> "OD2" Residue "A GLU 929": "OE1" <-> "OE2" Residue "A TYR 1101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1115": "OD1" <-> "OD2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1133": "NH1" <-> "NH2" Residue "A TYR 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1141": "NH1" <-> "NH2" Residue "A GLU 1150": "OE1" <-> "OE2" Residue "A GLU 1154": "OE1" <-> "OE2" Residue "A GLU 1168": "OE1" <-> "OE2" Residue "A ARG 1226": "NH1" <-> "NH2" Residue "A GLU 1272": "OE1" <-> "OE2" Residue "A ASP 1293": "OD1" <-> "OD2" Residue "A ASP 1334": "OD1" <-> "OD2" Residue "A ARG 1349": "NH1" <-> "NH2" Residue "A ASP 1350": "OD1" <-> "OD2" Residue "A GLU 1353": "OE1" <-> "OE2" Residue "A ARG 1355": "NH1" <-> "NH2" Residue "A PHE 1371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1394": "OD1" <-> "OD2" Residue "A GLU 1420": "OE1" <-> "OE2" Residue "A TYR 1452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1476": "NH1" <-> "NH2" Residue "A ARG 1482": "NH1" <-> "NH2" Residue "A GLU 1513": "OE1" <-> "OE2" Residue "A ARG 1559": "NH1" <-> "NH2" Residue "A GLU 1637": "OE1" <-> "OE2" Residue "A PHE 1683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1750": "NH1" <-> "NH2" Residue "A ASP 1783": "OD1" <-> "OD2" Residue "A ASP 1789": "OD1" <-> "OD2" Residue "A GLU 1793": "OE1" <-> "OE2" Residue "A TYR 1810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1816": "OE1" <-> "OE2" Residue "A ARG 1818": "NH1" <-> "NH2" Residue "A PHE 1819": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 11210 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 11210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1437, 11210 Unusual residues: {' MN': 1} Classifications: {'peptide': 1436, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 41, 'TRANS': 1394, None: 1} Not linked: pdbres="HIS A1821 " pdbres=" MN A2400 " Chain breaks: 18 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 343 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 6, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 9, 'GLU:plan': 13, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 255 Time building chain proxies: 6.23, per 1000 atoms: 0.56 Number of scatterers: 11210 At special positions: 0 Unit cell: (119.68, 112.88, 125.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 1 24.99 S 72 16.00 O 2137 8.00 N 1866 7.00 C 7134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.06 Conformation dependent library (CDL) restraints added in 2.0 seconds 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 8 sheets defined 58.6% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 1 through 16 removed outlier: 3.603A pdb=" N ILE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 31 removed outlier: 3.997A pdb=" N VAL A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 59 Processing helix chain 'A' and resid 68 through 76 Processing helix chain 'A' and resid 108 through 133 Processing helix chain 'A' and resid 153 through 168 Processing helix chain 'A' and resid 170 through 177 removed outlier: 4.282A pdb=" N SER A 174 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 190 Processing helix chain 'A' and resid 213 through 222 Processing helix chain 'A' and resid 232 through 249 removed outlier: 3.884A pdb=" N LEU A 236 " --> pdb=" O HIS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 258 removed outlier: 3.896A pdb=" N PHE A 258 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 283 through 292 Processing helix chain 'A' and resid 295 through 301 removed outlier: 3.533A pdb=" N LEU A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 336 removed outlier: 4.241A pdb=" N MET A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 394 through 409 removed outlier: 3.530A pdb=" N ARG A 398 " --> pdb=" O TRP A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 411 No H-bonds generated for 'chain 'A' and resid 410 through 411' Processing helix chain 'A' and resid 415 through 415 No H-bonds generated for 'chain 'A' and resid 415 through 415' Processing helix chain 'A' and resid 416 through 436 removed outlier: 3.560A pdb=" N ASN A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 452 Processing helix chain 'A' and resid 460 through 468 Processing helix chain 'A' and resid 493 through 510 Processing helix chain 'A' and resid 578 through 586 removed outlier: 3.725A pdb=" N ARG A 581 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N PHE A 583 " --> pdb=" O LYS A 580 " (cutoff:3.500A) Proline residue: A 584 - end of helix Processing helix chain 'A' and resid 590 through 602 Processing helix chain 'A' and resid 612 through 630 Processing helix chain 'A' and resid 632 through 651 removed outlier: 3.564A pdb=" N GLN A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 662 Processing helix chain 'A' and resid 669 through 686 removed outlier: 3.791A pdb=" N LEU A 673 " --> pdb=" O ASP A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 709 Processing helix chain 'A' and resid 717 through 737 Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 748 through 762 removed outlier: 3.555A pdb=" N LEU A 752 " --> pdb=" O THR A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 795 Processing helix chain 'A' and resid 846 through 862 Processing helix chain 'A' and resid 870 through 886 removed outlier: 3.640A pdb=" N LEU A 886 " --> pdb=" O SER A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 907 Processing helix chain 'A' and resid 912 through 929 removed outlier: 3.563A pdb=" N GLU A 929 " --> pdb=" O ASP A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1098 removed outlier: 4.004A pdb=" N LEU A1098 " --> pdb=" O MET A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1159 Processing helix chain 'A' and resid 1167 through 1184 removed outlier: 3.608A pdb=" N MET A1184 " --> pdb=" O LEU A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1211 removed outlier: 3.532A pdb=" N PHE A1205 " --> pdb=" O CYS A1201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN A1211 " --> pdb=" O THR A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1238 removed outlier: 3.848A pdb=" N LEU A1229 " --> pdb=" O GLY A1225 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS A1236 " --> pdb=" O LEU A1232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A1237 " --> pdb=" O LEU A1233 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS A1238 " --> pdb=" O MET A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1261 Processing helix chain 'A' and resid 1270 through 1282 removed outlier: 3.646A pdb=" N GLY A1282 " --> pdb=" O ASN A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1323 Processing helix chain 'A' and resid 1340 through 1350 removed outlier: 3.515A pdb=" N THR A1344 " --> pdb=" O ASP A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1368 removed outlier: 3.642A pdb=" N PHE A1354 " --> pdb=" O ASP A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1408 removed outlier: 4.173A pdb=" N PHE A1402 " --> pdb=" O LEU A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1432 Processing helix chain 'A' and resid 1435 through 1452 removed outlier: 3.975A pdb=" N CYS A1439 " --> pdb=" O PRO A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1488 Processing helix chain 'A' and resid 1490 through 1506 removed outlier: 3.593A pdb=" N LYS A1494 " --> pdb=" O ASP A1490 " (cutoff:3.500A) Processing helix chain 'A' and resid 1511 through 1518 removed outlier: 4.395A pdb=" N PHE A1515 " --> pdb=" O LEU A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1533 Processing helix chain 'A' and resid 1580 through 1590 removed outlier: 4.232A pdb=" N LYS A1584 " --> pdb=" O PRO A1580 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A1590 " --> pdb=" O ILE A1586 " (cutoff:3.500A) Processing helix chain 'A' and resid 1614 through 1626 removed outlier: 3.670A pdb=" N GLY A1618 " --> pdb=" O SER A1614 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A1619 " --> pdb=" O ILE A1615 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1649 removed outlier: 3.773A pdb=" N ILE A1644 " --> pdb=" O TYR A1640 " (cutoff:3.500A) Processing helix chain 'A' and resid 1686 through 1701 Processing helix chain 'A' and resid 1703 through 1707 Processing helix chain 'A' and resid 1742 through 1752 Processing helix chain 'A' and resid 1781 through 1788 Processing helix chain 'A' and resid 1797 through 1802 removed outlier: 3.807A pdb=" N VAL A1802 " --> pdb=" O VAL A1798 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1820 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 7.003A pdb=" N LEU A 98 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N LEU A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU A 100 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ASP A 142 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU A 102 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ARG A 144 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 537 through 542 removed outlier: 3.557A pdb=" N PHE A 541 " --> pdb=" O PHE A 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1121 through 1126 removed outlier: 3.548A pdb=" N ARG A1133 " --> pdb=" O LYS A1126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1326 through 1330 removed outlier: 3.894A pdb=" N GLY A1379 " --> pdb=" O SER A1188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1241 through 1242 Processing sheet with id=AA6, first strand: chain 'A' and resid 1382 through 1385 Processing sheet with id=AA7, first strand: chain 'A' and resid 1548 through 1550 Processing sheet with id=AA8, first strand: chain 'A' and resid 1631 through 1632 600 hydrogen bonds defined for protein. 1752 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: 3.72 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2957 1.33 - 1.45: 1968 1.45 - 1.57: 6361 1.57 - 1.70: 0 1.70 - 1.82: 109 Bond restraints: 11395 Sorted by residual: bond pdb=" N ASP A1334 " pdb=" CA ASP A1334 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.19e-02 7.06e+03 5.89e+00 bond pdb=" C VAL A1434 " pdb=" O VAL A1434 " ideal model delta sigma weight residual 1.240 1.213 0.027 1.26e-02 6.30e+03 4.48e+00 bond pdb=" N TYR A1452 " pdb=" CA TYR A1452 " ideal model delta sigma weight residual 1.458 1.430 0.027 1.33e-02 5.65e+03 4.12e+00 bond pdb=" CA ILE A 152 " pdb=" CB ILE A 152 " ideal model delta sigma weight residual 1.537 1.563 -0.026 1.29e-02 6.01e+03 3.98e+00 bond pdb=" C TYR A1455 " pdb=" O TYR A1455 " ideal model delta sigma weight residual 1.246 1.231 0.015 9.20e-03 1.18e+04 2.72e+00 ... (remaining 11390 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.34: 242 106.34 - 113.26: 6328 113.26 - 120.17: 4205 120.17 - 127.08: 4544 127.08 - 133.99: 91 Bond angle restraints: 15410 Sorted by residual: angle pdb=" C TYR A1455 " pdb=" N PRO A1456 " pdb=" CA PRO A1456 " ideal model delta sigma weight residual 119.84 126.53 -6.69 1.25e+00 6.40e-01 2.86e+01 angle pdb=" N VAL A 690 " pdb=" CA VAL A 690 " pdb=" C VAL A 690 " ideal model delta sigma weight residual 113.47 108.15 5.32 1.01e+00 9.80e-01 2.78e+01 angle pdb=" N VAL A1436 " pdb=" CA VAL A1436 " pdb=" C VAL A1436 " ideal model delta sigma weight residual 110.36 115.66 -5.30 1.05e+00 9.07e-01 2.54e+01 angle pdb=" N THR A1116 " pdb=" CA THR A1116 " pdb=" C THR A1116 " ideal model delta sigma weight residual 114.04 109.13 4.91 1.24e+00 6.50e-01 1.56e+01 angle pdb=" N TYR A1665 " pdb=" CA TYR A1665 " pdb=" C TYR A1665 " ideal model delta sigma weight residual 108.13 114.23 -6.10 1.72e+00 3.38e-01 1.26e+01 ... (remaining 15405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 6309 17.59 - 35.19: 506 35.19 - 52.78: 85 52.78 - 70.37: 13 70.37 - 87.96: 6 Dihedral angle restraints: 6919 sinusoidal: 2698 harmonic: 4221 Sorted by residual: dihedral pdb=" CA ARG A 336 " pdb=" C ARG A 336 " pdb=" N ILE A 337 " pdb=" CA ILE A 337 " ideal model delta harmonic sigma weight residual -180.00 -152.03 -27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA TYR A 706 " pdb=" C TYR A 706 " pdb=" N MET A 707 " pdb=" CA MET A 707 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ALA A 744 " pdb=" C ALA A 744 " pdb=" N ASP A 745 " pdb=" CA ASP A 745 " ideal model delta harmonic sigma weight residual 180.00 162.28 17.72 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 6916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1653 0.071 - 0.143: 145 0.143 - 0.214: 10 0.214 - 0.286: 1 0.286 - 0.357: 1 Chirality restraints: 1810 Sorted by residual: chirality pdb=" CA HIS A 443 " pdb=" N HIS A 443 " pdb=" C HIS A 443 " pdb=" CB HIS A 443 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA HIS A1437 " pdb=" N HIS A1437 " pdb=" C HIS A1437 " pdb=" CB HIS A1437 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ASN A1432 " pdb=" N ASN A1432 " pdb=" C ASN A1432 " pdb=" CB ASN A1432 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.18e-01 ... (remaining 1807 not shown) Planarity restraints: 1949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A1431 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.58e+01 pdb=" C ALA A1431 " -0.069 2.00e-02 2.50e+03 pdb=" O ALA A1431 " 0.026 2.00e-02 2.50e+03 pdb=" N ASN A1432 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1333 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.13e+00 pdb=" C ASP A1333 " 0.039 2.00e-02 2.50e+03 pdb=" O ASP A1333 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP A1334 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 152 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO A 153 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " 0.029 5.00e-02 4.00e+02 ... (remaining 1946 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1013 2.74 - 3.28: 11920 3.28 - 3.82: 17702 3.82 - 4.36: 20024 4.36 - 4.90: 34375 Nonbonded interactions: 85034 Sorted by model distance: nonbonded pdb=" O PRO A1459 " pdb=" NE2 GLN A1483 " model vdw 2.198 2.520 nonbonded pdb=" OE2 GLU A 731 " pdb=" OG1 THR A1271 " model vdw 2.217 2.440 nonbonded pdb=" O SER A 440 " pdb=" OG SER A 440 " model vdw 2.222 2.440 nonbonded pdb=" OD2 ASP A 89 " pdb=" N CYS A 103 " model vdw 2.281 2.520 nonbonded pdb=" NH1 ARG A 643 " pdb=" OH TYR A 706 " model vdw 2.282 2.520 ... (remaining 85029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 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: 1.400 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 31.410 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11395 Z= 0.195 Angle : 0.700 7.040 15410 Z= 0.426 Chirality : 0.043 0.357 1810 Planarity : 0.003 0.053 1949 Dihedral : 13.241 87.964 4165 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.30 % Favored : 90.49 % Rotamer: Outliers : 0.64 % Allowed : 5.06 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.27 (0.19), residues: 1398 helix: -1.02 (0.16), residues: 789 sheet: -1.64 (0.49), residues: 108 loop : -4.21 (0.21), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1704 HIS 0.005 0.001 HIS A 738 PHE 0.011 0.001 PHE A 104 TYR 0.014 0.001 TYR A 706 ARG 0.003 0.000 ARG A 643 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 359 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.5901 (ttm) cc_final: 0.5571 (ttm) REVERT: A 113 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7272 (mm-30) REVERT: A 114 GLN cc_start: 0.7941 (tp40) cc_final: 0.7684 (tt0) REVERT: A 115 LYS cc_start: 0.8041 (tptt) cc_final: 0.7423 (tptt) REVERT: A 118 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6421 (tm-30) REVERT: A 240 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7467 (tm-30) REVERT: A 241 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7421 (mt-10) REVERT: A 325 TRP cc_start: 0.7701 (m100) cc_final: 0.7179 (m100) REVERT: A 407 MET cc_start: 0.8844 (mmp) cc_final: 0.8114 (mmt) REVERT: A 448 MET cc_start: 0.7376 (tmm) cc_final: 0.7106 (tmm) REVERT: A 660 ASP cc_start: 0.7612 (t0) cc_final: 0.7253 (t0) REVERT: A 727 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8249 (tm-30) REVERT: A 856 LEU cc_start: 0.9525 (tp) cc_final: 0.8910 (tp) REVERT: A 860 PHE cc_start: 0.7793 (m-80) cc_final: 0.7425 (m-80) REVERT: A 925 ASP cc_start: 0.8953 (t0) cc_final: 0.8688 (t0) REVERT: A 926 GLN cc_start: 0.9020 (pp30) cc_final: 0.8733 (pp30) REVERT: A 1094 MET cc_start: 0.3657 (pmm) cc_final: 0.3317 (pmm) REVERT: A 1151 ASP cc_start: 0.8649 (p0) cc_final: 0.8420 (p0) REVERT: A 1160 LEU cc_start: 0.9142 (mt) cc_final: 0.8917 (mp) REVERT: A 1242 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7774 (mm-30) REVERT: A 1253 LYS cc_start: 0.8353 (tptp) cc_final: 0.8042 (mmtt) REVERT: A 1341 GLN cc_start: 0.8304 (pp30) cc_final: 0.7747 (pp30) REVERT: A 1364 MET cc_start: 0.7935 (mmm) cc_final: 0.7592 (tpp) REVERT: A 1436 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8482 (p) REVERT: A 1479 ARG cc_start: 0.7935 (mtt90) cc_final: 0.6928 (mtm180) REVERT: A 1485 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8210 (mm-30) REVERT: A 1551 ASN cc_start: 0.7951 (t0) cc_final: 0.7448 (t0) REVERT: A 1629 LYS cc_start: 0.8437 (mmtt) cc_final: 0.7901 (mmtp) REVERT: A 1797 LEU cc_start: 0.6333 (mt) cc_final: 0.5891 (mm) outliers start: 8 outliers final: 5 residues processed: 365 average time/residue: 0.2529 time to fit residues: 127.1057 Evaluate side-chains 252 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 246 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1457 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.1980 chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 83 optimal weight: 0.3980 chunk 129 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A 289 HIS A 508 ASN A 549 GLN A 593 GLN A 758 ASN A 794 ASN A 795 ASN A 869 ASN A1128 GLN ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1193 HIS ** A1287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1451 GLN A1475 ASN A1551 ASN A1791 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11395 Z= 0.168 Angle : 0.653 9.891 15410 Z= 0.328 Chirality : 0.042 0.310 1810 Planarity : 0.004 0.040 1949 Dihedral : 5.186 52.464 1528 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.66 % Favored : 90.27 % Rotamer: Outliers : 2.57 % Allowed : 15.10 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.22), residues: 1398 helix: 0.29 (0.18), residues: 800 sheet: -1.03 (0.51), residues: 108 loop : -3.97 (0.22), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 155 HIS 0.006 0.001 HIS A 213 PHE 0.019 0.001 PHE A 300 TYR 0.014 0.001 TYR A1109 ARG 0.007 0.001 ARG A 663 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 279 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.6053 (ttm) cc_final: 0.5713 (ttm) REVERT: A 113 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7319 (mm-30) REVERT: A 114 GLN cc_start: 0.8046 (tp40) cc_final: 0.7719 (pt0) REVERT: A 115 LYS cc_start: 0.8218 (tptt) cc_final: 0.7647 (tptt) REVERT: A 118 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6574 (tm-30) REVERT: A 240 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7549 (tm-30) REVERT: A 241 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7419 (mt-10) REVERT: A 267 LEU cc_start: 0.8218 (mp) cc_final: 0.8015 (mp) REVERT: A 323 GLN cc_start: 0.8641 (mp10) cc_final: 0.8331 (mp10) REVERT: A 407 MET cc_start: 0.8921 (mmp) cc_final: 0.8402 (mmt) REVERT: A 657 ASP cc_start: 0.7197 (t0) cc_final: 0.6707 (t0) REVERT: A 660 ASP cc_start: 0.7387 (t0) cc_final: 0.6951 (t0) REVERT: A 727 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8252 (tm-30) REVERT: A 856 LEU cc_start: 0.9531 (tp) cc_final: 0.8850 (tp) REVERT: A 860 PHE cc_start: 0.7886 (m-80) cc_final: 0.7505 (m-80) REVERT: A 881 MET cc_start: 0.8257 (mtm) cc_final: 0.7892 (mtm) REVERT: A 889 LYS cc_start: 0.7246 (mptt) cc_final: 0.7013 (mptt) REVERT: A 1094 MET cc_start: 0.3851 (pmm) cc_final: 0.3405 (pmm) REVERT: A 1151 ASP cc_start: 0.8823 (p0) cc_final: 0.8463 (p0) REVERT: A 1240 MET cc_start: 0.6027 (ttm) cc_final: 0.5342 (tmm) REVERT: A 1242 GLU cc_start: 0.7886 (mm-30) cc_final: 0.6972 (mm-30) REVERT: A 1253 LYS cc_start: 0.8357 (tptp) cc_final: 0.8116 (mmtt) REVERT: A 1301 ASN cc_start: 0.8618 (m110) cc_final: 0.8141 (m-40) REVERT: A 1341 GLN cc_start: 0.8264 (pp30) cc_final: 0.7508 (pp30) REVERT: A 1364 MET cc_start: 0.8087 (mmm) cc_final: 0.7690 (mmt) REVERT: A 1454 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.8023 (mmp-170) REVERT: A 1479 ARG cc_start: 0.7748 (mtt90) cc_final: 0.7444 (mtt-85) REVERT: A 1485 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8592 (mt-10) REVERT: A 1551 ASN cc_start: 0.7958 (t0) cc_final: 0.7369 (t0) REVERT: A 1629 LYS cc_start: 0.8462 (mmtt) cc_final: 0.7857 (mmtp) outliers start: 32 outliers final: 18 residues processed: 299 average time/residue: 0.2163 time to fit residues: 93.6556 Evaluate side-chains 274 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 255 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1293 ASP Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1499 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 140 optimal weight: 0.0570 chunk 115 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1236 HIS ** A1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1451 GLN ** A1664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11395 Z= 0.236 Angle : 0.671 10.123 15410 Z= 0.339 Chirality : 0.043 0.239 1810 Planarity : 0.004 0.038 1949 Dihedral : 5.199 51.613 1524 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.66 % Favored : 90.27 % Rotamer: Outliers : 4.18 % Allowed : 16.87 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.22), residues: 1398 helix: 0.79 (0.18), residues: 802 sheet: -0.85 (0.50), residues: 110 loop : -3.73 (0.23), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 325 HIS 0.008 0.001 HIS A 213 PHE 0.012 0.002 PHE A 541 TYR 0.021 0.001 TYR A1665 ARG 0.006 0.001 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 264 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.6209 (ttm) cc_final: 0.5983 (ttm) REVERT: A 113 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7469 (mm-30) REVERT: A 115 LYS cc_start: 0.8216 (tptt) cc_final: 0.8005 (tptt) REVERT: A 241 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7541 (mt-10) REVERT: A 302 TYR cc_start: 0.8105 (m-80) cc_final: 0.7886 (m-80) REVERT: A 325 TRP cc_start: 0.7368 (m100) cc_final: 0.7115 (m100) REVERT: A 344 LEU cc_start: 0.8933 (pt) cc_final: 0.8722 (pp) REVERT: A 660 ASP cc_start: 0.7458 (t0) cc_final: 0.7194 (t0) REVERT: A 682 MET cc_start: 0.8499 (tpp) cc_final: 0.8208 (tpp) REVERT: A 727 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8156 (tm-30) REVERT: A 733 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8584 (mptt) REVERT: A 856 LEU cc_start: 0.9520 (tp) cc_final: 0.8792 (tp) REVERT: A 860 PHE cc_start: 0.8081 (m-80) cc_final: 0.7722 (m-80) REVERT: A 881 MET cc_start: 0.8277 (mtm) cc_final: 0.7980 (mtm) REVERT: A 889 LYS cc_start: 0.7274 (mptt) cc_final: 0.6985 (mptt) REVERT: A 925 ASP cc_start: 0.9020 (t0) cc_final: 0.8808 (t0) REVERT: A 1094 MET cc_start: 0.3788 (pmm) cc_final: 0.3406 (pmm) REVERT: A 1147 ARG cc_start: 0.8271 (tpp80) cc_final: 0.8019 (tpp80) REVERT: A 1151 ASP cc_start: 0.8850 (p0) cc_final: 0.8435 (p0) REVERT: A 1240 MET cc_start: 0.6073 (ttm) cc_final: 0.5368 (tmm) REVERT: A 1242 GLU cc_start: 0.7906 (mm-30) cc_final: 0.6782 (mm-30) REVERT: A 1253 LYS cc_start: 0.8434 (tptp) cc_final: 0.8204 (mmtt) REVERT: A 1301 ASN cc_start: 0.8599 (m110) cc_final: 0.8247 (m-40) REVERT: A 1341 GLN cc_start: 0.8082 (pp30) cc_final: 0.7468 (pp30) REVERT: A 1364 MET cc_start: 0.8210 (mmm) cc_final: 0.8001 (mmt) REVERT: A 1479 ARG cc_start: 0.7953 (mtt90) cc_final: 0.7618 (mtt-85) REVERT: A 1485 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8303 (mm-30) REVERT: A 1551 ASN cc_start: 0.8131 (t0) cc_final: 0.7556 (t0) REVERT: A 1560 MET cc_start: 0.8650 (ptp) cc_final: 0.8219 (mtt) REVERT: A 1629 LYS cc_start: 0.8551 (mmtt) cc_final: 0.7920 (mmtp) outliers start: 52 outliers final: 30 residues processed: 298 average time/residue: 0.2084 time to fit residues: 90.7294 Evaluate side-chains 269 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 238 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1467 ASP Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1623 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 111 ASN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1451 GLN ** A1664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11395 Z= 0.388 Angle : 0.774 12.045 15410 Z= 0.395 Chirality : 0.047 0.358 1810 Planarity : 0.004 0.046 1949 Dihedral : 5.349 25.872 1518 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.23 % Favored : 88.70 % Rotamer: Outliers : 4.90 % Allowed : 20.40 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.23), residues: 1398 helix: 0.71 (0.18), residues: 806 sheet: -0.77 (0.53), residues: 102 loop : -3.59 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 155 HIS 0.007 0.001 HIS A 213 PHE 0.021 0.002 PHE A 423 TYR 0.029 0.002 TYR A1665 ARG 0.007 0.001 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 246 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 TYR cc_start: 0.4412 (p90) cc_final: 0.4197 (p90) REVERT: A 274 TYR cc_start: 0.6668 (t80) cc_final: 0.6386 (t80) REVERT: A 325 TRP cc_start: 0.8109 (m100) cc_final: 0.7543 (m100) REVERT: A 381 LEU cc_start: 0.4964 (OUTLIER) cc_final: 0.4643 (mm) REVERT: A 388 LYS cc_start: 0.8352 (mptt) cc_final: 0.7774 (mptt) REVERT: A 660 ASP cc_start: 0.7707 (t0) cc_final: 0.7473 (t0) REVERT: A 661 LYS cc_start: 0.8520 (tptt) cc_final: 0.8268 (tptm) REVERT: A 727 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8390 (tm-30) REVERT: A 856 LEU cc_start: 0.9526 (tp) cc_final: 0.8909 (tp) REVERT: A 860 PHE cc_start: 0.8181 (m-80) cc_final: 0.7805 (m-80) REVERT: A 917 LYS cc_start: 0.9277 (mmmt) cc_final: 0.8817 (mmmt) REVERT: A 929 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8465 (mm-30) REVERT: A 1094 MET cc_start: 0.3837 (pmm) cc_final: 0.3474 (pmm) REVERT: A 1147 ARG cc_start: 0.8404 (tpp80) cc_final: 0.8063 (tpp80) REVERT: A 1151 ASP cc_start: 0.8789 (p0) cc_final: 0.8396 (p0) REVERT: A 1226 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7029 (ttm170) REVERT: A 1251 MET cc_start: 0.8168 (mmm) cc_final: 0.7931 (mmm) REVERT: A 1252 MET cc_start: 0.8767 (mmm) cc_final: 0.8519 (mmm) REVERT: A 1341 GLN cc_start: 0.8302 (pp30) cc_final: 0.7759 (pp30) REVERT: A 1364 MET cc_start: 0.8364 (mmm) cc_final: 0.8124 (mmt) REVERT: A 1479 ARG cc_start: 0.8209 (mtt90) cc_final: 0.7877 (mtt-85) REVERT: A 1485 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8362 (mm-30) REVERT: A 1551 ASN cc_start: 0.8278 (t0) cc_final: 0.7891 (t0) REVERT: A 1560 MET cc_start: 0.8732 (ptp) cc_final: 0.8279 (mtt) REVERT: A 1629 LYS cc_start: 0.8579 (mmtt) cc_final: 0.7956 (mmtp) outliers start: 61 outliers final: 43 residues processed: 283 average time/residue: 0.2211 time to fit residues: 90.9307 Evaluate side-chains 271 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 226 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1194 SER Chi-restraints excluded: chain A residue 1226 ARG Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1392 TRP Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1467 ASP Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain A residue 1701 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 0 optimal weight: 10.9990 chunk 70 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 34 optimal weight: 0.0970 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11395 Z= 0.191 Angle : 0.699 12.687 15410 Z= 0.344 Chirality : 0.044 0.345 1810 Planarity : 0.004 0.041 1949 Dihedral : 5.013 24.897 1518 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.16 % Favored : 89.77 % Rotamer: Outliers : 4.10 % Allowed : 21.69 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.23), residues: 1398 helix: 1.10 (0.19), residues: 805 sheet: -0.41 (0.55), residues: 101 loop : -3.42 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1688 HIS 0.006 0.001 HIS A 213 PHE 0.018 0.001 PHE A 423 TYR 0.016 0.001 TYR A 116 ARG 0.007 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 250 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8054 (m-80) cc_final: 0.7848 (m-80) REVERT: A 323 GLN cc_start: 0.8516 (mp10) cc_final: 0.7845 (pm20) REVERT: A 325 TRP cc_start: 0.8021 (m100) cc_final: 0.7564 (m100) REVERT: A 335 MET cc_start: 0.8115 (pmm) cc_final: 0.7660 (pmm) REVERT: A 381 LEU cc_start: 0.4649 (OUTLIER) cc_final: 0.4363 (mm) REVERT: A 388 LYS cc_start: 0.8276 (mptt) cc_final: 0.7702 (mptt) REVERT: A 435 ARG cc_start: 0.8789 (tpm170) cc_final: 0.8002 (ttm110) REVERT: A 493 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.8948 (m) REVERT: A 602 TRP cc_start: 0.9106 (OUTLIER) cc_final: 0.8169 (m-10) REVERT: A 660 ASP cc_start: 0.7672 (t0) cc_final: 0.7453 (t0) REVERT: A 682 MET cc_start: 0.8500 (tpp) cc_final: 0.8298 (tpp) REVERT: A 727 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8054 (tm-30) REVERT: A 856 LEU cc_start: 0.9484 (tp) cc_final: 0.8725 (tp) REVERT: A 860 PHE cc_start: 0.8074 (m-80) cc_final: 0.7663 (m-80) REVERT: A 881 MET cc_start: 0.8398 (mtm) cc_final: 0.8168 (mtm) REVERT: A 917 LYS cc_start: 0.9276 (mmmt) cc_final: 0.8797 (mmmt) REVERT: A 925 ASP cc_start: 0.8988 (t0) cc_final: 0.8782 (t0) REVERT: A 1147 ARG cc_start: 0.8278 (tpp80) cc_final: 0.7955 (tpp80) REVERT: A 1151 ASP cc_start: 0.8745 (p0) cc_final: 0.8463 (p0) REVERT: A 1251 MET cc_start: 0.8165 (mmm) cc_final: 0.7862 (mmm) REVERT: A 1252 MET cc_start: 0.8583 (mmm) cc_final: 0.8383 (mmm) REVERT: A 1253 LYS cc_start: 0.8433 (tptp) cc_final: 0.8230 (mmtt) REVERT: A 1341 GLN cc_start: 0.8371 (pp30) cc_final: 0.7689 (pp30) REVERT: A 1364 MET cc_start: 0.8271 (mmm) cc_final: 0.7899 (tpp) REVERT: A 1420 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8319 (mm-30) REVERT: A 1479 ARG cc_start: 0.7958 (mtt90) cc_final: 0.7673 (mtt-85) REVERT: A 1485 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8318 (mm-30) REVERT: A 1551 ASN cc_start: 0.8388 (t0) cc_final: 0.8046 (t0) REVERT: A 1560 MET cc_start: 0.8706 (ptp) cc_final: 0.8260 (mtt) REVERT: A 1629 LYS cc_start: 0.8562 (mmtt) cc_final: 0.7891 (mmtp) outliers start: 51 outliers final: 36 residues processed: 279 average time/residue: 0.2051 time to fit residues: 84.3477 Evaluate side-chains 274 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 235 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1194 SER Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1392 TRP Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1467 ASP Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1701 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 72 optimal weight: 4.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN A 636 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11395 Z= 0.335 Angle : 0.759 12.654 15410 Z= 0.381 Chirality : 0.046 0.347 1810 Planarity : 0.004 0.041 1949 Dihedral : 5.234 23.561 1517 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.30 % Favored : 88.63 % Rotamer: Outliers : 5.22 % Allowed : 22.81 % Favored : 71.97 % 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: -0.93 (0.23), residues: 1398 helix: 0.97 (0.19), residues: 809 sheet: -0.73 (0.54), residues: 97 loop : -3.45 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 155 HIS 0.008 0.001 HIS A 213 PHE 0.018 0.002 PHE A 423 TYR 0.024 0.002 TYR A1665 ARG 0.004 0.001 ARG A 617 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 237 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8534 (mp) REVERT: A 388 LYS cc_start: 0.8337 (mptt) cc_final: 0.7753 (mptt) REVERT: A 493 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8875 (m) REVERT: A 510 MET cc_start: 0.8642 (tpp) cc_final: 0.8425 (tpp) REVERT: A 624 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8509 (tt) REVERT: A 660 ASP cc_start: 0.7814 (t0) cc_final: 0.7596 (t0) REVERT: A 697 ARG cc_start: 0.8173 (mtm-85) cc_final: 0.7840 (mtm180) REVERT: A 727 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8559 (tm-30) REVERT: A 856 LEU cc_start: 0.9531 (tp) cc_final: 0.8911 (tp) REVERT: A 860 PHE cc_start: 0.8037 (m-80) cc_final: 0.7732 (m-80) REVERT: A 917 LYS cc_start: 0.9260 (mmmt) cc_final: 0.8793 (mmmt) REVERT: A 1147 ARG cc_start: 0.8353 (tpp80) cc_final: 0.8009 (tpp80) REVERT: A 1151 ASP cc_start: 0.8751 (p0) cc_final: 0.8480 (p0) REVERT: A 1226 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.6966 (ttm170) REVERT: A 1251 MET cc_start: 0.8212 (mmm) cc_final: 0.7929 (mmm) REVERT: A 1341 GLN cc_start: 0.8418 (pp30) cc_final: 0.7620 (pp30) REVERT: A 1479 ARG cc_start: 0.8138 (mtt90) cc_final: 0.7821 (mtt-85) REVERT: A 1485 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8314 (mm-30) REVERT: A 1551 ASN cc_start: 0.8220 (t0) cc_final: 0.7897 (t0) REVERT: A 1560 MET cc_start: 0.8712 (ptp) cc_final: 0.8308 (mtt) REVERT: A 1629 LYS cc_start: 0.8542 (mmtt) cc_final: 0.7897 (mmtp) outliers start: 65 outliers final: 49 residues processed: 281 average time/residue: 0.2152 time to fit residues: 87.8869 Evaluate side-chains 282 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 229 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 483 TYR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1194 SER Chi-restraints excluded: chain A residue 1226 ARG Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1392 TRP Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1411 LYS Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1467 ASP Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1797 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11395 Z= 0.345 Angle : 0.774 11.826 15410 Z= 0.389 Chirality : 0.046 0.304 1810 Planarity : 0.004 0.041 1949 Dihedral : 5.376 24.301 1517 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.52 % Favored : 88.41 % Rotamer: Outliers : 5.62 % Allowed : 23.45 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.23), residues: 1398 helix: 0.87 (0.18), residues: 806 sheet: -0.67 (0.55), residues: 96 loop : -3.47 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 155 HIS 0.008 0.001 HIS A 213 PHE 0.033 0.002 PHE A 300 TYR 0.022 0.002 TYR A 116 ARG 0.006 0.001 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 239 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.7929 (tp30) cc_final: 0.7535 (pt0) REVERT: A 274 TYR cc_start: 0.6875 (t80) cc_final: 0.6673 (t80) REVERT: A 335 MET cc_start: 0.8257 (pmm) cc_final: 0.7736 (pmm) REVERT: A 388 LYS cc_start: 0.8305 (mptt) cc_final: 0.7675 (mptt) REVERT: A 493 THR cc_start: 0.9209 (OUTLIER) cc_final: 0.8866 (m) REVERT: A 602 TRP cc_start: 0.9178 (OUTLIER) cc_final: 0.8029 (m-10) REVERT: A 624 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8548 (tt) REVERT: A 657 ASP cc_start: 0.7131 (t70) cc_final: 0.6426 (t0) REVERT: A 660 ASP cc_start: 0.7871 (t0) cc_final: 0.7568 (t0) REVERT: A 697 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7770 (mtm180) REVERT: A 727 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8480 (tm-30) REVERT: A 856 LEU cc_start: 0.9536 (tp) cc_final: 0.8966 (tp) REVERT: A 860 PHE cc_start: 0.8080 (m-80) cc_final: 0.7779 (m-80) REVERT: A 917 LYS cc_start: 0.9268 (mmmt) cc_final: 0.8933 (mmmt) REVERT: A 1147 ARG cc_start: 0.8377 (tpp80) cc_final: 0.8047 (tpp80) REVERT: A 1151 ASP cc_start: 0.8746 (p0) cc_final: 0.8491 (p0) REVERT: A 1199 MET cc_start: 0.8674 (mmt) cc_final: 0.8339 (mmm) REVERT: A 1226 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.6907 (ttm170) REVERT: A 1252 MET cc_start: 0.8522 (mmm) cc_final: 0.8283 (mmm) REVERT: A 1341 GLN cc_start: 0.8507 (pp30) cc_final: 0.7676 (pp30) REVERT: A 1479 ARG cc_start: 0.8197 (mtt90) cc_final: 0.7674 (mtt-85) REVERT: A 1485 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8323 (mm-30) REVERT: A 1551 ASN cc_start: 0.7953 (t0) cc_final: 0.7617 (t0) REVERT: A 1560 MET cc_start: 0.8722 (ptp) cc_final: 0.8331 (mtt) REVERT: A 1629 LYS cc_start: 0.8591 (mmtt) cc_final: 0.7927 (mmtp) REVERT: A 1670 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6756 (pp) REVERT: A 1782 LEU cc_start: 0.8376 (mt) cc_final: 0.8161 (tt) outliers start: 70 outliers final: 52 residues processed: 286 average time/residue: 0.2143 time to fit residues: 89.6489 Evaluate side-chains 281 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 224 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 483 TYR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1194 SER Chi-restraints excluded: chain A residue 1226 ARG Chi-restraints excluded: chain A residue 1256 ILE Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1392 TRP Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1411 LYS Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1467 ASP Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain A residue 1670 LEU Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1797 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 41 optimal weight: 0.0870 chunk 27 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 93 optimal weight: 0.3980 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 108 optimal weight: 0.4980 chunk 125 optimal weight: 2.9990 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11395 Z= 0.189 Angle : 0.747 15.909 15410 Z= 0.364 Chirality : 0.045 0.301 1810 Planarity : 0.003 0.043 1949 Dihedral : 4.993 23.111 1517 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.30 % Favored : 89.63 % Rotamer: Outliers : 3.21 % Allowed : 26.43 % Favored : 70.36 % 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: -0.71 (0.23), residues: 1398 helix: 1.18 (0.19), residues: 808 sheet: -0.20 (0.58), residues: 84 loop : -3.46 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1549 HIS 0.006 0.001 HIS A 213 PHE 0.027 0.001 PHE A 300 TYR 0.018 0.001 TYR A 214 ARG 0.008 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 245 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5078 (tmm) cc_final: 0.4803 (ppp) REVERT: A 335 MET cc_start: 0.8145 (pmm) cc_final: 0.7755 (pmm) REVERT: A 388 LYS cc_start: 0.8206 (mptt) cc_final: 0.7557 (mptt) REVERT: A 493 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8798 (m) REVERT: A 602 TRP cc_start: 0.9089 (OUTLIER) cc_final: 0.8312 (m-10) REVERT: A 657 ASP cc_start: 0.7264 (t70) cc_final: 0.6640 (t0) REVERT: A 660 ASP cc_start: 0.7762 (t0) cc_final: 0.7449 (t0) REVERT: A 727 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8581 (tm-30) REVERT: A 856 LEU cc_start: 0.9548 (tp) cc_final: 0.9090 (tp) REVERT: A 860 PHE cc_start: 0.8009 (m-80) cc_final: 0.7724 (m-80) REVERT: A 917 LYS cc_start: 0.9271 (mmmt) cc_final: 0.8843 (mmmt) REVERT: A 1147 ARG cc_start: 0.8158 (tpp80) cc_final: 0.7871 (tpp80) REVERT: A 1151 ASP cc_start: 0.8641 (p0) cc_final: 0.8388 (p0) REVERT: A 1251 MET cc_start: 0.8079 (mmm) cc_final: 0.7591 (tpt) REVERT: A 1301 ASN cc_start: 0.8636 (m110) cc_final: 0.8356 (m-40) REVERT: A 1341 GLN cc_start: 0.8415 (pp30) cc_final: 0.7737 (pp30) REVERT: A 1364 MET cc_start: 0.8441 (mmt) cc_final: 0.8088 (mmt) REVERT: A 1479 ARG cc_start: 0.8039 (mtt90) cc_final: 0.7798 (mtt-85) REVERT: A 1485 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8499 (mt-10) REVERT: A 1551 ASN cc_start: 0.8359 (t0) cc_final: 0.8044 (t0) REVERT: A 1560 MET cc_start: 0.8696 (ptp) cc_final: 0.8277 (mtt) REVERT: A 1629 LYS cc_start: 0.8479 (mmtt) cc_final: 0.7780 (mmtp) REVERT: A 1670 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6721 (pp) outliers start: 40 outliers final: 32 residues processed: 267 average time/residue: 0.2177 time to fit residues: 84.3826 Evaluate side-chains 268 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 233 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1256 ILE Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1392 TRP Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1670 LEU Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1797 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 0.4980 chunk 121 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1110 ASN ** A1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11395 Z= 0.218 Angle : 0.759 16.727 15410 Z= 0.371 Chirality : 0.045 0.370 1810 Planarity : 0.004 0.042 1949 Dihedral : 4.924 22.126 1517 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.37 % Favored : 89.56 % Rotamer: Outliers : 3.45 % Allowed : 26.51 % Favored : 70.04 % 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: -0.66 (0.23), residues: 1398 helix: 1.21 (0.18), residues: 809 sheet: -0.13 (0.58), residues: 84 loop : -3.44 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1688 HIS 0.008 0.001 HIS A 213 PHE 0.029 0.002 PHE A 112 TYR 0.020 0.001 TYR A 214 ARG 0.009 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 232 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4623 (tmm) cc_final: 0.4324 (ppp) REVERT: A 335 MET cc_start: 0.8123 (pmm) cc_final: 0.7666 (pmm) REVERT: A 388 LYS cc_start: 0.8246 (mptt) cc_final: 0.7599 (mptt) REVERT: A 493 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8710 (m) REVERT: A 510 MET cc_start: 0.8587 (tpp) cc_final: 0.8336 (tpp) REVERT: A 647 MET cc_start: 0.8415 (tpp) cc_final: 0.7774 (ttp) REVERT: A 657 ASP cc_start: 0.7303 (t70) cc_final: 0.6654 (t0) REVERT: A 660 ASP cc_start: 0.7824 (t0) cc_final: 0.7512 (t0) REVERT: A 727 GLU cc_start: 0.8805 (tm-30) cc_final: 0.7966 (tm-30) REVERT: A 856 LEU cc_start: 0.9548 (tp) cc_final: 0.9120 (tp) REVERT: A 860 PHE cc_start: 0.7958 (m-80) cc_final: 0.7688 (m-80) REVERT: A 917 LYS cc_start: 0.9272 (mmmt) cc_final: 0.8802 (mmmt) REVERT: A 1147 ARG cc_start: 0.8156 (tpp80) cc_final: 0.7881 (tpp80) REVERT: A 1151 ASP cc_start: 0.8634 (p0) cc_final: 0.8386 (p0) REVERT: A 1301 ASN cc_start: 0.8661 (m110) cc_final: 0.8396 (m-40) REVERT: A 1341 GLN cc_start: 0.8394 (pp30) cc_final: 0.7505 (pp30) REVERT: A 1364 MET cc_start: 0.8405 (mmt) cc_final: 0.8032 (mmt) REVERT: A 1479 ARG cc_start: 0.8012 (mtt90) cc_final: 0.7738 (mtt-85) REVERT: A 1485 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8497 (mt-10) REVERT: A 1551 ASN cc_start: 0.8188 (t0) cc_final: 0.7867 (t0) REVERT: A 1629 LYS cc_start: 0.8453 (mmtt) cc_final: 0.7768 (mmtp) outliers start: 43 outliers final: 35 residues processed: 258 average time/residue: 0.2092 time to fit residues: 79.9685 Evaluate side-chains 263 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 227 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1256 ILE Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1392 TRP Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1458 ASP Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1701 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 2.9990 chunk 82 optimal weight: 0.0970 chunk 64 optimal weight: 0.0060 chunk 94 optimal weight: 7.9990 chunk 142 optimal weight: 20.0000 chunk 131 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11395 Z= 0.256 Angle : 0.781 17.057 15410 Z= 0.383 Chirality : 0.045 0.373 1810 Planarity : 0.004 0.042 1949 Dihedral : 5.017 22.787 1517 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.02 % Favored : 88.91 % Rotamer: Outliers : 3.61 % Allowed : 26.43 % Favored : 69.96 % 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: -0.67 (0.23), residues: 1398 helix: 1.19 (0.18), residues: 807 sheet: -0.16 (0.58), residues: 84 loop : -3.39 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 155 HIS 0.004 0.001 HIS A 891 PHE 0.030 0.002 PHE A 300 TYR 0.025 0.001 TYR A 214 ARG 0.009 0.000 ARG A 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 231 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4617 (tmm) cc_final: 0.4389 (ppp) REVERT: A 274 TYR cc_start: 0.6995 (t80) cc_final: 0.6750 (t80) REVERT: A 335 MET cc_start: 0.8114 (pmm) cc_final: 0.7641 (pmm) REVERT: A 388 LYS cc_start: 0.8279 (mptt) cc_final: 0.7626 (mptt) REVERT: A 493 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8725 (m) REVERT: A 647 MET cc_start: 0.8388 (tpp) cc_final: 0.7769 (ttp) REVERT: A 657 ASP cc_start: 0.7187 (t70) cc_final: 0.6550 (t0) REVERT: A 660 ASP cc_start: 0.7851 (t0) cc_final: 0.7548 (t0) REVERT: A 697 ARG cc_start: 0.8051 (mtm-85) cc_final: 0.7838 (mtm180) REVERT: A 727 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8034 (tm-30) REVERT: A 856 LEU cc_start: 0.9529 (tp) cc_final: 0.9103 (tp) REVERT: A 860 PHE cc_start: 0.7953 (m-80) cc_final: 0.7688 (m-80) REVERT: A 917 LYS cc_start: 0.9336 (mmmt) cc_final: 0.8901 (mmmt) REVERT: A 1147 ARG cc_start: 0.8210 (tpp80) cc_final: 0.7944 (tpp80) REVERT: A 1151 ASP cc_start: 0.8645 (p0) cc_final: 0.8402 (p0) REVERT: A 1251 MET cc_start: 0.8228 (mmm) cc_final: 0.7983 (mmm) REVERT: A 1341 GLN cc_start: 0.8508 (pp30) cc_final: 0.7609 (pp30) REVERT: A 1364 MET cc_start: 0.8457 (mmt) cc_final: 0.8183 (mmt) REVERT: A 1479 ARG cc_start: 0.7992 (mtt90) cc_final: 0.7749 (mtt-85) REVERT: A 1485 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8492 (mt-10) REVERT: A 1551 ASN cc_start: 0.8162 (t0) cc_final: 0.7837 (t0) REVERT: A 1629 LYS cc_start: 0.8512 (mmtt) cc_final: 0.7814 (mmtp) outliers start: 45 outliers final: 42 residues processed: 255 average time/residue: 0.2187 time to fit residues: 81.7762 Evaluate side-chains 267 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 224 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1256 ILE Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1392 TRP Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1458 ASP Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1817 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.153709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.117507 restraints weight = 20429.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118544 restraints weight = 11853.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120388 restraints weight = 8958.537| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11395 Z= 0.195 Angle : 0.765 16.994 15410 Z= 0.373 Chirality : 0.045 0.380 1810 Planarity : 0.003 0.043 1949 Dihedral : 4.856 22.836 1517 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.37 % Favored : 89.56 % Rotamer: Outliers : 3.21 % Allowed : 26.59 % Favored : 70.20 % 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: -0.52 (0.23), residues: 1398 helix: 1.35 (0.18), residues: 806 sheet: -0.16 (0.57), residues: 84 loop : -3.39 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1549 HIS 0.003 0.001 HIS A 738 PHE 0.028 0.002 PHE A 112 TYR 0.023 0.001 TYR A 214 ARG 0.009 0.000 ARG A 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2376.17 seconds wall clock time: 44 minutes 6.12 seconds (2646.12 seconds total)