Starting phenix.real_space_refine (version: dev) on Mon Dec 12 16:49:15 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klc_0706/12_2022/6klc_0706.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klc_0706/12_2022/6klc_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_0706/12_2022/6klc_0706.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klc_0706/12_2022/6klc_0706.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klc_0706/12_2022/6klc_0706.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klc_0706/12_2022/6klc_0706.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 6.40, per 1000 atoms: 0.57 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: 4.85 Conformation dependent library (CDL) restraints added in 1.7 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: 0.94 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: 3.83 Time building geometry restraints manager: 5.23 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 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. 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: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.870 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.090 Process input model: 32.540 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 : 11.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.30 % Favored : 90.49 % Rotamer Outliers : 0.64 % 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 *********************** 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 : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 365 average time/residue: 0.2501 time to fit residues: 126.5606 Evaluate side-chains 243 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 238 time to evaluate : 1.382 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2023 time to fit residues: 3.2604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 4.9990 chunk 108 optimal weight: 0.0010 chunk 60 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 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: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN 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 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1193 HIS ** A1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1451 GLN A1475 ASN A1791 ASN A1800 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 11395 Z= 0.173 Angle : 0.669 9.875 15410 Z= 0.335 Chirality : 0.043 0.287 1810 Planarity : 0.004 0.040 1949 Dihedral : 4.691 25.817 1517 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.80 % Favored : 90.13 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.21), residues: 1398 helix: 0.29 (0.18), residues: 788 sheet: -1.02 (0.54), residues: 99 loop : -3.86 (0.22), residues: 511 *********************** 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 299 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 276 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 290 average time/residue: 0.2147 time to fit residues: 91.3284 Evaluate side-chains 249 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 237 time to evaluate : 1.405 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1054 time to fit residues: 4.3690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 108 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN ** A 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1236 HIS A1315 ASN 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: 0.7708 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 11395 Z= 0.176 Angle : 0.659 10.326 15410 Z= 0.329 Chirality : 0.043 0.236 1810 Planarity : 0.003 0.038 1949 Dihedral : 4.654 25.435 1517 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.08 % Favored : 90.84 % Rotamer Outliers : 2.49 % 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: 799 sheet: -0.65 (0.53), residues: 102 loop : -3.72 (0.22), residues: 497 *********************** 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 289 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 258 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 14 residues processed: 275 average time/residue: 0.2009 time to fit residues: 82.3786 Evaluate side-chains 247 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 233 time to evaluate : 1.380 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1294 time to fit residues: 5.0209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 37 optimal weight: 0.0030 overall best weight: 1.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN A 703 ASN ** A 926 GLN ** 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: 0.7790 moved from start: 0.2868 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 : 0.709 13.146 15410 Z= 0.350 Chirality : 0.044 0.344 1810 Planarity : 0.004 0.038 1949 Dihedral : 4.825 24.554 1517 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.16 % Favored : 89.77 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.23), residues: 1398 helix: 0.87 (0.18), residues: 808 sheet: -0.69 (0.51), residues: 110 loop : -3.59 (0.24), residues: 480 *********************** 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 283 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 248 time to evaluate : 1.340 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 outliers start: 35 outliers final: 25 residues processed: 269 average time/residue: 0.2163 time to fit residues: 87.2989 Evaluate side-chains 252 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 227 time to evaluate : 1.413 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1102 time to fit residues: 7.0298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 2 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1451 GLN ** A1664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 11395 Z= 0.243 Angle : 0.713 12.903 15410 Z= 0.354 Chirality : 0.045 0.353 1810 Planarity : 0.004 0.038 1949 Dihedral : 4.884 25.487 1517 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.66 % Favored : 89.27 % Rotamer Outliers : 1.61 % 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 (0.18), residues: 804 sheet: -0.46 (0.52), residues: 109 loop : -3.55 (0.25), residues: 485 *********************** 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 264 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 244 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 256 average time/residue: 0.2117 time to fit residues: 80.7478 Evaluate side-chains 240 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 229 time to evaluate : 1.403 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1088 time to fit residues: 4.0247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 81 optimal weight: 0.2980 chunk 34 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** A1664 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3271 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= 0.187 Angle : 0.699 13.075 15410 Z= 0.345 Chirality : 0.044 0.343 1810 Planarity : 0.003 0.038 1949 Dihedral : 4.766 21.506 1517 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.80 % Favored : 90.13 % Rotamer Outliers : 1.45 % 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: -0.76 (0.23), residues: 1398 helix: 1.11 (0.19), residues: 806 sheet: -0.35 (0.52), residues: 109 loop : -3.51 (0.25), residues: 483 *********************** 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 263 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 245 time to evaluate : 1.383 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 outliers start: 18 outliers final: 10 residues processed: 253 average time/residue: 0.2121 time to fit residues: 79.8120 Evaluate side-chains 238 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 228 time to evaluate : 1.390 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1045 time to fit residues: 3.8195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 78 optimal weight: 0.0030 chunk 101 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 137 optimal weight: 0.0980 chunk 86 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3428 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= 0.192 Angle : 0.699 13.631 15410 Z= 0.347 Chirality : 0.044 0.346 1810 Planarity : 0.003 0.039 1949 Dihedral : 4.722 21.889 1517 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.09 % Favored : 89.84 % Rotamer Outliers : 1.29 % 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: -0.70 (0.23), residues: 1398 helix: 1.15 (0.19), residues: 808 sheet: -0.07 (0.55), residues: 90 loop : -3.43 (0.24), residues: 500 *********************** 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 255 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 239 time to evaluate : 1.426 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 outliers start: 16 outliers final: 7 residues processed: 249 average time/residue: 0.2059 time to fit residues: 76.5084 Evaluate side-chains 234 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 227 time to evaluate : 1.252 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1007 time to fit residues: 3.2001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.5980 chunk 82 optimal weight: 20.0000 chunk 41 optimal weight: 0.0970 chunk 27 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 108 optimal weight: 0.0470 chunk 125 optimal weight: 0.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 878 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 11395 Z= 0.161 Angle : 0.701 16.118 15410 Z= 0.343 Chirality : 0.043 0.325 1810 Planarity : 0.003 0.040 1949 Dihedral : 4.605 22.261 1517 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.51 % Favored : 90.41 % Rotamer Outliers : 0.96 % 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: -0.59 (0.23), residues: 1398 helix: 1.24 (0.19), residues: 808 sheet: 0.03 (0.55), residues: 90 loop : -3.40 (0.24), residues: 500 *********************** 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 257 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 245 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 outliers start: 12 outliers final: 6 residues processed: 250 average time/residue: 0.2126 time to fit residues: 79.1165 Evaluate side-chains 231 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 225 time to evaluate : 1.341 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1250 time to fit residues: 3.4158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 39 optimal weight: 0.0470 chunk 116 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3725 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= 0.179 Angle : 0.725 16.814 15410 Z= 0.356 Chirality : 0.044 0.343 1810 Planarity : 0.003 0.039 1949 Dihedral : 4.625 21.879 1517 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.87 % Favored : 90.06 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.23), residues: 1398 helix: 1.31 (0.19), residues: 807 sheet: 0.10 (0.54), residues: 90 loop : -3.36 (0.24), residues: 501 *********************** 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 249 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 239 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 243 average time/residue: 0.2107 time to fit residues: 75.6386 Evaluate side-chains 234 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 229 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1008 time to fit residues: 2.9229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.1980 chunk 82 optimal weight: 20.0000 chunk 64 optimal weight: 0.0570 chunk 94 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 90 optimal weight: 0.0470 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3834 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= 0.178 Angle : 0.749 17.150 15410 Z= 0.367 Chirality : 0.044 0.333 1810 Planarity : 0.004 0.039 1949 Dihedral : 4.606 22.388 1517 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.51 % Favored : 90.41 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.23), residues: 1398 helix: 1.28 (0.19), residues: 811 sheet: 0.34 (0.57), residues: 82 loop : -3.36 (0.24), residues: 505 ********************** 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 237 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 234 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 234 average time/residue: 0.2327 time to fit residues: 80.6065 Evaluate side-chains 214 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 1.376 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1007 time to fit residues: 2.1253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 358 HIS A 508 ASN A 846 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.154752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.117710 restraints weight = 20449.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.119462 restraints weight = 13974.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.121509 restraints weight = 9622.443| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3934 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= 0.233 Angle : 0.765 16.962 15410 Z= 0.382 Chirality : 0.045 0.320 1810 Planarity : 0.004 0.038 1949 Dihedral : 4.732 22.305 1517 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.16 % Favored : 89.77 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.23), residues: 1398 helix: 1.21 (0.19), residues: 813 sheet: 0.25 (0.55), residues: 91 loop : -3.44 (0.24), residues: 494 =============================================================================== Job complete usr+sys time: 2300.51 seconds wall clock time: 42 minutes 41.66 seconds (2561.66 seconds total)