Starting phenix.real_space_refine (version: dev) on Fri Mar 17 10:54:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgh_22327/03_2023/7jgh_22327_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgh_22327/03_2023/7jgh_22327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgh_22327/03_2023/7jgh_22327.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgh_22327/03_2023/7jgh_22327.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgh_22327/03_2023/7jgh_22327_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgh_22327/03_2023/7jgh_22327_updated.pdb" } resolution = 3.36 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= -0.000 sd= 1.000 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 Process input model Symmetric amino acids flipped Residue "A TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 59": "OD1" <-> "OD2" Residue "A ASP 144": "OD1" <-> "OD2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A ASP 296": "OD1" <-> "OD2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 632": "OE1" <-> "OE2" Residue "A PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 897": "OD1" <-> "OD2" Residue "A TYR 951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1142": "OE1" <-> "OE2" Residue "A GLU 1143": "OE1" <-> "OE2" Residue "A PHE 1182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1304": "OE1" <-> "OE2" Residue "A GLU 1369": "OE1" <-> "OE2" Residue "A ASP 1468": "OD1" <-> "OD2" Residue "A ASP 1502": "OD1" <-> "OD2" Residue "A GLU 1523": "OE1" <-> "OE2" Residue "A TYR 1547": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1617": "OE1" <-> "OE2" Residue "A TYR 1663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1694": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1874": "OD1" <-> "OD2" Residue "A TYR 1948": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 19608 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 19428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1421, 19428 Classifications: {'peptide': 1421} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 40, 'TRANS': 1380} Chain breaks: 28 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 162 Unusual residues: {'ASG': 5, 'BDP': 6} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'ASG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" C1 BDP B 1 " occ=0.93 ... (11 atoms not shown) pdb=" O6B BDP B 1 " occ=0.93 residue: pdb=" C1 ASG B 2 " occ=0.93 ... (16 atoms not shown) pdb=" S ASG B 2 " occ=0.93 residue: pdb=" C1 BDP B 3 " occ=0.93 ... (10 atoms not shown) pdb=" O6B BDP B 3 " occ=0.93 residue: pdb=" C1 ASG B 4 " occ=0.93 ... (16 atoms not shown) pdb=" S ASG B 4 " occ=0.93 residue: pdb=" C1 BDP B 5 " occ=0.93 ... (10 atoms not shown) pdb=" O6B BDP B 5 " occ=0.93 residue: pdb=" C1 ASG B 6 " occ=0.93 ... (16 atoms not shown) pdb=" S ASG B 6 " occ=0.93 residue: pdb=" C1 BDP B 7 " occ=0.93 ... (10 atoms not shown) pdb=" O6B BDP B 7 " occ=0.93 residue: pdb=" C1 ASG B 8 " occ=0.93 ... (16 atoms not shown) pdb=" S ASG B 8 " occ=0.93 residue: pdb=" C1 BDP B 9 " occ=0.93 ... (10 atoms not shown) pdb=" O6B BDP B 9 " occ=0.93 residue: pdb=" C1 ASG B 10 " occ=0.93 ... (16 atoms not shown) pdb=" S ASG B 10 " occ=0.93 residue: pdb=" C1 BDP B 11 " occ=0.93 ... (9 atoms not shown) pdb=" O6B BDP B 11 " occ=0.93 residue: pdb=" C1 ASG A2701 " occ=0.93 ... (16 atoms not shown) pdb=" S ASG A2701 " occ=0.93 Time building chain proxies: 10.13, per 1000 atoms: 0.52 Number of scatterers: 19608 At special positions: 0 Unit cell: (110.032, 132.25, 138.598, 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) S 92 16.00 O 2322 8.00 N 2007 7.00 C 7462 6.00 H 7725 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 105 " distance=2.04 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 258 " distance=2.03 Simple disulfide: pdb=" SG CYS A 643 " - pdb=" SG CYS A 745 " distance=2.03 Simple disulfide: pdb=" SG CYS A 769 " - pdb=" SG CYS A 901 " distance=2.03 Simple disulfide: pdb=" SG CYS A 783 " - pdb=" SG CYS A 801 " distance=2.03 Simple disulfide: pdb=" SG CYS A 797 " - pdb=" SG CYS A 957 " distance=2.03 Simple disulfide: pdb=" SG CYS A 805 " - pdb=" SG CYS A 955 " distance=2.03 Simple disulfide: pdb=" SG CYS A 966 " - pdb=" SG CYS A1090 " distance=2.03 Simple disulfide: pdb=" SG CYS A 978 " - pdb=" SG CYS A 996 " distance=2.03 Simple disulfide: pdb=" SG CYS A1088 " - pdb=" SG CYS A1193 " distance=2.03 Simple disulfide: pdb=" SG CYS A1140 " - pdb=" SG CYS A1171 " distance=2.03 Simple disulfide: pdb=" SG CYS A1210 " - pdb=" SG CYS A1411 " distance=2.03 Simple disulfide: pdb=" SG CYS A1221 " - pdb=" SG CYS A1264 " distance=2.03 Simple disulfide: pdb=" SG CYS A1242 " - pdb=" SG CYS A1255 " distance=2.04 Simple disulfide: pdb=" SG CYS A1339 " - pdb=" SG CYS A1431 " distance=2.03 Simple disulfide: pdb=" SG CYS A1456 " - pdb=" SG CYS A1528 " distance=2.02 Simple disulfide: pdb=" SG CYS A1470 " - pdb=" SG CYS A1483 " distance=2.03 Simple disulfide: pdb=" SG CYS A1487 " - pdb=" SG CYS A1556 " distance=2.03 Simple disulfide: pdb=" SG CYS A1578 " - pdb=" SG CYS A1614 " distance=2.03 Simple disulfide: pdb=" SG CYS A1670 " - pdb=" SG CYS A1777 " distance=2.03 Simple disulfide: pdb=" SG CYS A1671 " - pdb=" SG CYS A1901 " distance=2.03 Simple disulfide: pdb=" SG CYS A1802 " - pdb=" SG CYS A1904 " distance=2.03 Simple disulfide: pdb=" SG CYS A1816 " - pdb=" SG CYS A1833 " distance=2.03 Simple disulfide: pdb=" SG CYS A1837 " - pdb=" SG CYS A1927 " distance=2.03 Simple disulfide: pdb=" SG CYS A1891 " - pdb=" SG CYS A1902 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " ASG B 2 " - " BDP B 3 " " ASG B 4 " - " BDP B 5 " " ASG B 6 " - " BDP B 7 " " ASG B 8 " - " BDP B 9 " " ASG B 10 " - " BDP B 11 " BETA1-4 " BDP B 1 " - " ASG B 2 " " BDP B 3 " - " ASG B 4 " " BDP B 5 " - " ASG B 6 " " BDP B 7 " - " ASG B 8 " " BDP B 9 " - " ASG B 10 " Time building additional restraints: 14.71 Conformation dependent library (CDL) restraints added in 1.7 seconds 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2700 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 1 sheets defined 54.5% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 120 through 141 Processing helix chain 'A' and resid 150 through 163 Processing helix chain 'A' and resid 176 through 188 Processing helix chain 'A' and resid 208 through 220 Processing helix chain 'A' and resid 222 through 227 removed outlier: 3.965A pdb=" N CYS A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 304 removed outlier: 3.656A pdb=" N TRP A 278 " --> pdb=" O GLN A 274 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 295 " --> pdb=" O GLN A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 353 Processing helix chain 'A' and resid 364 through 377 Processing helix chain 'A' and resid 582 through 586 Processing helix chain 'A' and resid 613 through 635 Proline residue: A 629 - end of helix Processing helix chain 'A' and resid 640 through 658 Processing helix chain 'A' and resid 668 through 682 Processing helix chain 'A' and resid 702 through 721 removed outlier: 4.727A pdb=" N LYS A 715 " --> pdb=" O ASN A 711 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TYR A 716 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 719 " --> pdb=" O LYS A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 782 Proline residue: A 778 - end of helix Processing helix chain 'A' and resid 802 through 812 Processing helix chain 'A' and resid 826 through 846 Processing helix chain 'A' and resid 873 through 883 removed outlier: 3.703A pdb=" N PHE A 877 " --> pdb=" O ILE A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 895 Processing helix chain 'A' and resid 962 through 968 Processing helix chain 'A' and resid 1020 through 1042 Processing helix chain 'A' and resid 1084 through 1118 Processing helix chain 'A' and resid 1132 through 1148 Processing helix chain 'A' and resid 1161 through 1170 Processing helix chain 'A' and resid 1178 through 1198 Processing helix chain 'A' and resid 1259 through 1261 No H-bonds generated for 'chain 'A' and resid 1259 through 1261' Processing helix chain 'A' and resid 1287 through 1308 Processing helix chain 'A' and resid 1338 through 1354 Processing helix chain 'A' and resid 1362 through 1374 removed outlier: 3.661A pdb=" N LYS A1366 " --> pdb=" O GLU A1362 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU A1367 " --> pdb=" O TYR A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1419 Processing helix chain 'A' and resid 1429 through 1431 No H-bonds generated for 'chain 'A' and resid 1429 through 1431' Processing helix chain 'A' and resid 1444 through 1469 Processing helix chain 'A' and resid 1484 through 1511 Processing helix chain 'A' and resid 1518 through 1524 Processing helix chain 'A' and resid 1533 through 1536 No H-bonds generated for 'chain 'A' and resid 1533 through 1536' Processing helix chain 'A' and resid 1542 through 1546 removed outlier: 4.230A pdb=" N TYR A1546 " --> pdb=" O TYR A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1553 through 1557 Processing helix chain 'A' and resid 1610 through 1612 No H-bonds generated for 'chain 'A' and resid 1610 through 1612' Processing helix chain 'A' and resid 1617 through 1624 removed outlier: 4.343A pdb=" N ILE A1621 " --> pdb=" O GLU A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1631 through 1655 removed outlier: 3.526A pdb=" N GLU A1635 " --> pdb=" O ALA A1632 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A1636 " --> pdb=" O LYS A1633 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A1644 " --> pdb=" O GLN A1641 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A1650 " --> pdb=" O GLU A1647 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A1652 " --> pdb=" O TYR A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1663 through 1685 Processing helix chain 'A' and resid 1693 through 1705 removed outlier: 4.070A pdb=" N TYR A1697 " --> pdb=" O GLU A1693 " (cutoff:3.500A) Processing helix chain 'A' and resid 1713 through 1725 Processing helix chain 'A' and resid 1745 through 1762 Processing helix chain 'A' and resid 1789 through 1814 Processing helix chain 'A' and resid 1833 through 1860 Proline residue: A1846 - end of helix removed outlier: 4.318A pdb=" N ILE A1849 " --> pdb=" O ASN A1845 " (cutoff:3.500A) Processing helix chain 'A' and resid 1883 through 1887 Processing helix chain 'A' and resid 1910 through 1914 Processing helix chain 'A' and resid 1924 through 1951 removed outlier: 3.617A pdb=" N GLU A1928 " --> pdb=" O GLU A1924 " (cutoff:3.500A) Proline residue: A1933 - end of helix Proline residue: A1946 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 912 through 914 556 hydrogen bonds defined for protein. 1608 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: 7.05 Time building geometry restraints manager: 15.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 7713 1.04 - 1.25: 1609 1.25 - 1.45: 3697 1.45 - 1.65: 6715 1.65 - 1.86: 111 Bond restraints: 19845 Sorted by residual: bond pdb=" C1 ASG B 8 " pdb=" O5 ASG B 8 " ideal model delta sigma weight residual 1.408 1.509 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" C1 ASG B 10 " pdb=" O5 ASG B 10 " ideal model delta sigma weight residual 1.408 1.508 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C1 ASG B 2 " pdb=" O5 ASG B 2 " ideal model delta sigma weight residual 1.408 1.507 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C1 ASG A2701 " pdb=" O5 ASG A2701 " ideal model delta sigma weight residual 1.408 1.507 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C1 BDP B 5 " pdb=" O5 BDP B 5 " ideal model delta sigma weight residual 1.406 1.505 -0.099 2.00e-02 2.50e+03 2.44e+01 ... (remaining 19840 not shown) Histogram of bond angle deviations from ideal: 70.04 - 82.83: 7 82.83 - 95.62: 4 95.62 - 108.40: 5523 108.40 - 121.19: 24192 121.19 - 133.98: 4282 Bond angle restraints: 34008 Sorted by residual: angle pdb=" CB VAL A 827 " pdb=" CA VAL A 827 " pdb=" HA VAL A 827 " ideal model delta sigma weight residual 109.00 70.04 38.96 3.00e+00 1.11e-01 1.69e+02 angle pdb=" N VAL A 827 " pdb=" CA VAL A 827 " pdb=" HA VAL A 827 " ideal model delta sigma weight residual 110.00 77.02 32.98 3.00e+00 1.11e-01 1.21e+02 angle pdb=" C VAL A 827 " pdb=" CA VAL A 827 " pdb=" HA VAL A 827 " ideal model delta sigma weight residual 109.00 78.03 30.97 3.00e+00 1.11e-01 1.07e+02 angle pdb=" SD MET A 185 " pdb=" CE MET A 185 " pdb=" HE2 MET A 185 " ideal model delta sigma weight residual 109.00 78.89 30.11 3.00e+00 1.11e-01 1.01e+02 angle pdb=" SD MET A 185 " pdb=" CE MET A 185 " pdb=" HE3 MET A 185 " ideal model delta sigma weight residual 109.00 79.61 29.39 3.00e+00 1.11e-01 9.60e+01 ... (remaining 34003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8132 17.92 - 35.83: 507 35.83 - 53.75: 87 53.75 - 71.66: 14 71.66 - 89.58: 7 Dihedral angle restraints: 8747 sinusoidal: 3985 harmonic: 4762 Sorted by residual: dihedral pdb=" CB CYS A1088 " pdb=" SG CYS A1088 " pdb=" SG CYS A1193 " pdb=" CB CYS A1193 " ideal model delta sinusoidal sigma weight residual -86.00 -160.49 74.49 1 1.00e+01 1.00e-02 7.03e+01 dihedral pdb=" CB CYS A1578 " pdb=" SG CYS A1578 " pdb=" SG CYS A1614 " pdb=" CB CYS A1614 " ideal model delta sinusoidal sigma weight residual 93.00 127.24 -34.24 1 1.00e+01 1.00e-02 1.66e+01 dihedral pdb=" C VAL A 827 " pdb=" N VAL A 827 " pdb=" CA VAL A 827 " pdb=" CB VAL A 827 " ideal model delta harmonic sigma weight residual -122.00 -132.13 10.13 0 2.50e+00 1.60e-01 1.64e+01 ... (remaining 8744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.346: 1698 0.346 - 0.691: 7 0.691 - 1.037: 1 1.037 - 1.383: 0 1.383 - 1.728: 2 Chirality restraints: 1708 Sorted by residual: chirality pdb=" CG LEU A 293 " pdb=" CB LEU A 293 " pdb=" CD1 LEU A 293 " pdb=" CD2 LEU A 293 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.47e+01 chirality pdb=" C3 ASG B 4 " pdb=" C2 ASG B 4 " pdb=" C4 ASG B 4 " pdb=" O3 ASG B 4 " both_signs ideal model delta sigma weight residual False 2.24 0.84 1.40 2.00e-01 2.50e+01 4.87e+01 chirality pdb=" C4 BDP B 3 " pdb=" C3 BDP B 3 " pdb=" C5 BDP B 3 " pdb=" O4 BDP B 3 " both_signs ideal model delta sigma weight residual False -2.49 -1.76 -0.73 2.00e-01 2.50e+01 1.35e+01 ... (remaining 1705 not shown) Planarity restraints: 3104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 942 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO A 943 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 943 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 943 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A1222 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO A1223 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A1223 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1223 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A1787 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO A1788 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A1788 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1788 " 0.020 5.00e-02 4.00e+02 ... (remaining 3101 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 2745 2.31 - 2.88: 36734 2.88 - 3.45: 42210 3.45 - 4.03: 56286 4.03 - 4.60: 87589 Nonbonded interactions: 225564 Sorted by model distance: nonbonded pdb=" H VAL A 827 " pdb=" HA VAL A 827 " model vdw 1.733 1.816 nonbonded pdb="HH22 ARG A1674 " pdb=" O CYS A1777 " model vdw 1.746 1.850 nonbonded pdb=" OD2 ASP A1682 " pdb="HH22 ARG A1792 " model vdw 1.757 1.850 nonbonded pdb="HH22 ARG A1610 " pdb=" OD2 ASP A1688 " model vdw 1.763 1.850 nonbonded pdb=" H TYR A1563 " pdb=" OE1 GLU A1638 " model vdw 1.766 1.850 ... (remaining 225559 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 S 92 5.16 5 C 7462 2.51 5 N 2007 2.21 5 O 2322 1.98 5 H 7725 0.53 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=0.93 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.340 Extract box with map and model: 7.410 Check model and map are aligned: 0.300 Process input model: 58.660 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.180 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6265 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 : 0.007 0.101 12120 Z= 0.431 Angle : 0.828 23.354 16291 Z= 0.361 Chirality : 0.075 1.728 1708 Planarity : 0.003 0.038 2056 Dihedral : 11.513 89.581 4536 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.07 % 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: -0.15 (0.21), residues: 1363 helix: 1.61 (0.17), residues: 785 sheet: -0.61 (1.81), residues: 10 loop : -2.75 (0.23), residues: 568 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 36 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue VAL 591 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue ILE 617 is missing expected H atoms. Skipping. Residue ILE 618 is missing expected H atoms. Skipping. Residue ALA 619 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue LEU 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LYS 640 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue ILE 678 is missing expected H atoms. Skipping. Residue LEU 719 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 824 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 828 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue TYR 834 is missing expected H atoms. Skipping. Residue TYR 837 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 839 is missing expected H atoms. Skipping. Residue TYR 840 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue ALA 844 is missing expected H atoms. Skipping. Residue LYS 849 is missing expected H atoms. Skipping. Residue ALA 850 is missing expected H atoms. Skipping. Residue THR 852 is missing expected H atoms. Skipping. Residue THR 887 is missing expected H atoms. Skipping. Residue SER 889 is missing expected H atoms. Skipping. Residue SER 890 is missing expected H atoms. Skipping. Residue TYR 891 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 894 is missing expected H atoms. Skipping. Residue VAL 895 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue TYR 972 is missing expected H atoms. Skipping. Residue SER 977 is missing expected H atoms. Skipping. Residue SER 1092 is missing expected H atoms. Skipping. Residue THR 1180 is missing expected H atoms. Skipping. Residue SER 1183 is missing expected H atoms. Skipping. Residue LYS 1185 is missing expected H atoms. Skipping. Residue LEU 1186 is missing expected H atoms. Skipping. Residue ALA 1189 is missing expected H atoms. Skipping. Residue LYS 1191 is missing expected H atoms. Skipping. Residue SER 1198 is missing expected H atoms. Skipping. Residue THR 1199 is missing expected H atoms. Skipping. Residue SER 1213 is missing expected H atoms. Skipping. Residue ILE 1216 is missing expected H atoms. Skipping. Residue ILE 1225 is missing expected H atoms. Skipping. Residue SER 1286 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Residue MET 1318 is missing expected H atoms. Skipping. Residue SER 1331 is missing expected H atoms. Skipping. Residue TYR 1363 is missing expected H atoms. Skipping. Residue LYS 1422 is missing expected H atoms. Skipping. Residue THR 1425 is missing expected H atoms. Skipping. Residue SER 1427 is missing expected H atoms. Skipping. Residue ILE 1433 is missing expected H atoms. Skipping. Residue LYS 1464 is missing expected H atoms. Skipping. Residue LYS 1626 is missing expected H atoms. Skipping. Residue ILE 1629 is missing expected H atoms. Skipping. Residue THR 1630 is missing expected H atoms. Skipping. Residue LYS 1634 is missing expected H atoms. Skipping. Residue ALA 1657 is missing expected H atoms. Skipping. Residue TYR 1663 is missing expected H atoms. Skipping. Residue LEU 1664 is missing expected H atoms. Skipping. Residue LYS 1711 is missing expected H atoms. Skipping. Residue LYS 1759 is missing expected H atoms. Skipping. Residue ILE 1761 is missing expected H atoms. Skipping. Residue THR 1841 is missing expected H atoms. Skipping. Residue TYR 1862 is missing expected H atoms. Skipping. Residue SER 1911 is missing expected H atoms. Skipping. Residue LYS 1939 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 107 average time/residue: 0.4221 time to fit residues: 67.3420 Evaluate side-chains 70 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.717 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 870 GLN ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1573 ASN A1641 GLN A1942 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 12120 Z= 0.298 Angle : 0.621 9.452 16291 Z= 0.321 Chirality : 0.057 1.689 1708 Planarity : 0.004 0.045 2056 Dihedral : 4.254 58.248 1530 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.07 % 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: 0.31 (0.23), residues: 1363 helix: 1.90 (0.18), residues: 814 sheet: -0.23 (1.81), residues: 10 loop : -2.65 (0.25), residues: 539 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 36 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue VAL 591 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue ILE 617 is missing expected H atoms. Skipping. Residue ILE 618 is missing expected H atoms. Skipping. Residue ALA 619 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue LEU 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LYS 640 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue ILE 678 is missing expected H atoms. Skipping. Residue LEU 719 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 824 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 828 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue TYR 834 is missing expected H atoms. Skipping. Residue TYR 837 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 839 is missing expected H atoms. Skipping. Residue TYR 840 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue ALA 844 is missing expected H atoms. Skipping. Residue LYS 849 is missing expected H atoms. Skipping. Residue ALA 850 is missing expected H atoms. Skipping. Residue THR 852 is missing expected H atoms. Skipping. Residue THR 887 is missing expected H atoms. Skipping. Residue SER 889 is missing expected H atoms. Skipping. Residue SER 890 is missing expected H atoms. Skipping. Residue TYR 891 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 894 is missing expected H atoms. Skipping. Residue VAL 895 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue TYR 972 is missing expected H atoms. Skipping. Residue SER 977 is missing expected H atoms. Skipping. Residue SER 1092 is missing expected H atoms. Skipping. Residue THR 1180 is missing expected H atoms. Skipping. Residue SER 1183 is missing expected H atoms. Skipping. Residue LYS 1185 is missing expected H atoms. Skipping. Residue LEU 1186 is missing expected H atoms. Skipping. Residue ALA 1189 is missing expected H atoms. Skipping. Residue LYS 1191 is missing expected H atoms. Skipping. Residue SER 1198 is missing expected H atoms. Skipping. Residue THR 1199 is missing expected H atoms. Skipping. Residue SER 1213 is missing expected H atoms. Skipping. Residue ILE 1216 is missing expected H atoms. Skipping. Residue ILE 1225 is missing expected H atoms. Skipping. Residue SER 1286 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Residue MET 1318 is missing expected H atoms. Skipping. Residue SER 1331 is missing expected H atoms. Skipping. Residue TYR 1363 is missing expected H atoms. Skipping. Residue LYS 1422 is missing expected H atoms. Skipping. Residue THR 1425 is missing expected H atoms. Skipping. Residue SER 1427 is missing expected H atoms. Skipping. Residue ILE 1433 is missing expected H atoms. Skipping. Residue LYS 1464 is missing expected H atoms. Skipping. Residue LYS 1626 is missing expected H atoms. Skipping. Residue ILE 1629 is missing expected H atoms. Skipping. Residue THR 1630 is missing expected H atoms. Skipping. Residue LYS 1634 is missing expected H atoms. Skipping. Residue ALA 1657 is missing expected H atoms. Skipping. Residue TYR 1663 is missing expected H atoms. Skipping. Residue LEU 1664 is missing expected H atoms. Skipping. Residue LYS 1711 is missing expected H atoms. Skipping. Residue LYS 1759 is missing expected H atoms. Skipping. Residue ILE 1761 is missing expected H atoms. Skipping. Residue THR 1841 is missing expected H atoms. Skipping. Residue TYR 1862 is missing expected H atoms. Skipping. Residue SER 1911 is missing expected H atoms. Skipping. Residue LYS 1939 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 102 average time/residue: 0.4425 time to fit residues: 66.9064 Evaluate side-chains 94 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 1.640 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2190 time to fit residues: 4.6545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 ASN A 571 GLN A 631 HIS ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1839 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 12120 Z= 0.188 Angle : 0.497 10.108 16291 Z= 0.258 Chirality : 0.055 1.695 1708 Planarity : 0.003 0.038 2056 Dihedral : 4.087 57.512 1530 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.07 % 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: 0.45 (0.24), residues: 1363 helix: 1.95 (0.18), residues: 822 sheet: 0.17 (1.94), residues: 10 loop : -2.57 (0.25), residues: 531 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 36 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue VAL 591 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue ILE 617 is missing expected H atoms. Skipping. Residue ILE 618 is missing expected H atoms. Skipping. Residue ALA 619 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue LEU 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LYS 640 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue ILE 678 is missing expected H atoms. Skipping. Residue LEU 719 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 824 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 828 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue TYR 834 is missing expected H atoms. Skipping. Residue TYR 837 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 839 is missing expected H atoms. Skipping. Residue TYR 840 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue ALA 844 is missing expected H atoms. Skipping. Residue LYS 849 is missing expected H atoms. Skipping. Residue ALA 850 is missing expected H atoms. Skipping. Residue THR 852 is missing expected H atoms. Skipping. Residue THR 887 is missing expected H atoms. Skipping. Residue SER 889 is missing expected H atoms. Skipping. Residue SER 890 is missing expected H atoms. Skipping. Residue TYR 891 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 894 is missing expected H atoms. Skipping. Residue VAL 895 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue TYR 972 is missing expected H atoms. Skipping. Residue SER 977 is missing expected H atoms. Skipping. Residue SER 1092 is missing expected H atoms. Skipping. Residue THR 1180 is missing expected H atoms. Skipping. Residue SER 1183 is missing expected H atoms. Skipping. Residue LYS 1185 is missing expected H atoms. Skipping. Residue LEU 1186 is missing expected H atoms. Skipping. Residue ALA 1189 is missing expected H atoms. Skipping. Residue LYS 1191 is missing expected H atoms. Skipping. Residue SER 1198 is missing expected H atoms. Skipping. Residue THR 1199 is missing expected H atoms. Skipping. Residue SER 1213 is missing expected H atoms. Skipping. Residue ILE 1216 is missing expected H atoms. Skipping. Residue ILE 1225 is missing expected H atoms. Skipping. Residue SER 1286 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Residue MET 1318 is missing expected H atoms. Skipping. Residue SER 1331 is missing expected H atoms. Skipping. Residue TYR 1363 is missing expected H atoms. Skipping. Residue LYS 1422 is missing expected H atoms. Skipping. Residue THR 1425 is missing expected H atoms. Skipping. Residue SER 1427 is missing expected H atoms. Skipping. Residue ILE 1433 is missing expected H atoms. Skipping. Residue LYS 1464 is missing expected H atoms. Skipping. Residue LYS 1626 is missing expected H atoms. Skipping. Residue ILE 1629 is missing expected H atoms. Skipping. Residue THR 1630 is missing expected H atoms. Skipping. Residue LYS 1634 is missing expected H atoms. Skipping. Residue ALA 1657 is missing expected H atoms. Skipping. Residue TYR 1663 is missing expected H atoms. Skipping. Residue LEU 1664 is missing expected H atoms. Skipping. Residue LYS 1711 is missing expected H atoms. Skipping. Residue LYS 1759 is missing expected H atoms. Skipping. Residue ILE 1761 is missing expected H atoms. Skipping. Residue THR 1841 is missing expected H atoms. Skipping. Residue TYR 1862 is missing expected H atoms. Skipping. Residue SER 1911 is missing expected H atoms. Skipping. Residue LYS 1939 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 100 average time/residue: 0.3959 time to fit residues: 60.9316 Evaluate side-chains 96 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 1.662 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2517 time to fit residues: 4.1033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 61 optimal weight: 0.0070 chunk 86 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1150 ASN A1443 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 12120 Z= 0.202 Angle : 0.487 9.758 16291 Z= 0.257 Chirality : 0.055 1.694 1708 Planarity : 0.003 0.042 2056 Dihedral : 4.088 53.645 1530 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.24), residues: 1363 helix: 1.97 (0.19), residues: 822 sheet: 0.36 (2.01), residues: 10 loop : -2.62 (0.25), residues: 531 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 36 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue VAL 591 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue ILE 617 is missing expected H atoms. Skipping. Residue ILE 618 is missing expected H atoms. Skipping. Residue ALA 619 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue LEU 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LYS 640 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue ILE 678 is missing expected H atoms. Skipping. Residue LEU 719 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 824 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 828 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue TYR 834 is missing expected H atoms. Skipping. Residue TYR 837 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 839 is missing expected H atoms. Skipping. Residue TYR 840 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue ALA 844 is missing expected H atoms. Skipping. Residue LYS 849 is missing expected H atoms. Skipping. Residue ALA 850 is missing expected H atoms. Skipping. Residue THR 852 is missing expected H atoms. Skipping. Residue THR 887 is missing expected H atoms. Skipping. Residue SER 889 is missing expected H atoms. Skipping. Residue SER 890 is missing expected H atoms. Skipping. Residue TYR 891 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 894 is missing expected H atoms. Skipping. Residue VAL 895 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue TYR 972 is missing expected H atoms. Skipping. Residue SER 977 is missing expected H atoms. Skipping. Residue SER 1092 is missing expected H atoms. Skipping. Residue THR 1180 is missing expected H atoms. Skipping. Residue SER 1183 is missing expected H atoms. Skipping. Residue LYS 1185 is missing expected H atoms. Skipping. Residue LEU 1186 is missing expected H atoms. Skipping. Residue ALA 1189 is missing expected H atoms. Skipping. Residue LYS 1191 is missing expected H atoms. Skipping. Residue SER 1198 is missing expected H atoms. Skipping. Residue THR 1199 is missing expected H atoms. Skipping. Residue SER 1213 is missing expected H atoms. Skipping. Residue ILE 1216 is missing expected H atoms. Skipping. Residue ILE 1225 is missing expected H atoms. Skipping. Residue SER 1286 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Residue MET 1318 is missing expected H atoms. Skipping. Residue SER 1331 is missing expected H atoms. Skipping. Residue TYR 1363 is missing expected H atoms. Skipping. Residue LYS 1422 is missing expected H atoms. Skipping. Residue THR 1425 is missing expected H atoms. Skipping. Residue SER 1427 is missing expected H atoms. Skipping. Residue ILE 1433 is missing expected H atoms. Skipping. Residue LYS 1464 is missing expected H atoms. Skipping. Residue LYS 1626 is missing expected H atoms. Skipping. Residue ILE 1629 is missing expected H atoms. Skipping. Residue THR 1630 is missing expected H atoms. Skipping. Residue LYS 1634 is missing expected H atoms. Skipping. Residue ALA 1657 is missing expected H atoms. Skipping. Residue TYR 1663 is missing expected H atoms. Skipping. Residue LEU 1664 is missing expected H atoms. Skipping. Residue LYS 1711 is missing expected H atoms. Skipping. Residue LYS 1759 is missing expected H atoms. Skipping. Residue ILE 1761 is missing expected H atoms. Skipping. Residue THR 1841 is missing expected H atoms. Skipping. Residue TYR 1862 is missing expected H atoms. Skipping. Residue SER 1911 is missing expected H atoms. Skipping. Residue LYS 1939 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 107 average time/residue: 0.4050 time to fit residues: 66.0918 Evaluate side-chains 101 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 1.722 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3002 time to fit residues: 8.3132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 56 optimal weight: 0.0980 chunk 117 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1150 ASN ** A1666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1703 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 12120 Z= 0.204 Angle : 0.497 10.032 16291 Z= 0.263 Chirality : 0.055 1.696 1708 Planarity : 0.003 0.043 2056 Dihedral : 4.158 54.435 1530 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.07 % 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: 0.35 (0.24), residues: 1363 helix: 1.91 (0.19), residues: 814 sheet: 0.35 (2.02), residues: 10 loop : -2.62 (0.25), residues: 539 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 36 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue VAL 591 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue ILE 617 is missing expected H atoms. Skipping. Residue ILE 618 is missing expected H atoms. Skipping. Residue ALA 619 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue LEU 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LYS 640 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue ILE 678 is missing expected H atoms. Skipping. Residue LEU 719 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 824 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 828 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue TYR 834 is missing expected H atoms. Skipping. Residue TYR 837 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 839 is missing expected H atoms. Skipping. Residue TYR 840 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue ALA 844 is missing expected H atoms. Skipping. Residue LYS 849 is missing expected H atoms. Skipping. Residue ALA 850 is missing expected H atoms. Skipping. Residue THR 852 is missing expected H atoms. Skipping. Residue THR 887 is missing expected H atoms. Skipping. Residue SER 889 is missing expected H atoms. Skipping. Residue SER 890 is missing expected H atoms. Skipping. Residue TYR 891 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 894 is missing expected H atoms. Skipping. Residue VAL 895 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue TYR 972 is missing expected H atoms. Skipping. Residue SER 977 is missing expected H atoms. Skipping. Residue SER 1092 is missing expected H atoms. Skipping. Residue THR 1180 is missing expected H atoms. Skipping. Residue SER 1183 is missing expected H atoms. Skipping. Residue LYS 1185 is missing expected H atoms. Skipping. Residue LEU 1186 is missing expected H atoms. Skipping. Residue ALA 1189 is missing expected H atoms. Skipping. Residue LYS 1191 is missing expected H atoms. Skipping. Residue SER 1198 is missing expected H atoms. Skipping. Residue THR 1199 is missing expected H atoms. Skipping. Residue SER 1213 is missing expected H atoms. Skipping. Residue ILE 1216 is missing expected H atoms. Skipping. Residue ILE 1225 is missing expected H atoms. Skipping. Residue SER 1286 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Residue MET 1318 is missing expected H atoms. Skipping. Residue SER 1331 is missing expected H atoms. Skipping. Residue TYR 1363 is missing expected H atoms. Skipping. Residue LYS 1422 is missing expected H atoms. Skipping. Residue THR 1425 is missing expected H atoms. Skipping. Residue SER 1427 is missing expected H atoms. Skipping. Residue ILE 1433 is missing expected H atoms. Skipping. Residue LYS 1464 is missing expected H atoms. Skipping. Residue LYS 1626 is missing expected H atoms. Skipping. Residue ILE 1629 is missing expected H atoms. Skipping. Residue THR 1630 is missing expected H atoms. Skipping. Residue LYS 1634 is missing expected H atoms. Skipping. Residue ALA 1657 is missing expected H atoms. Skipping. Residue TYR 1663 is missing expected H atoms. Skipping. Residue LEU 1664 is missing expected H atoms. Skipping. Residue LYS 1711 is missing expected H atoms. Skipping. Residue LYS 1759 is missing expected H atoms. Skipping. Residue ILE 1761 is missing expected H atoms. Skipping. Residue THR 1841 is missing expected H atoms. Skipping. Residue TYR 1862 is missing expected H atoms. Skipping. Residue SER 1911 is missing expected H atoms. Skipping. Residue LYS 1939 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 97 average time/residue: 0.3884 time to fit residues: 58.7922 Evaluate side-chains 96 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 1.859 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2261 time to fit residues: 5.9517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 137 optimal weight: 0.2980 chunk 114 optimal weight: 0.2980 chunk 63 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.3639 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: