Starting phenix.real_space_refine on Wed Feb 14 22:27:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fap_31504/02_2024/7fap_31504_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fap_31504/02_2024/7fap_31504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fap_31504/02_2024/7fap_31504.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fap_31504/02_2024/7fap_31504.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fap_31504/02_2024/7fap_31504_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fap_31504/02_2024/7fap_31504_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 6578 2.51 5 N 1771 2.21 5 O 2031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 110": "OE1" <-> "OE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A GLU 573": "OE1" <-> "OE2" Residue "A GLU 595": "OE1" <-> "OE2" Residue "A GLU 615": "OE1" <-> "OE2" Residue "A GLU 672": "OE1" <-> "OE2" Residue "A TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 774": "OE1" <-> "OE2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A ASP 814": "OD1" <-> "OD2" Residue "A ARG 846": "NH1" <-> "NH2" Residue "A GLU 865": "OE1" <-> "OE2" Residue "A TYR 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1027": "OE1" <-> "OE2" Residue "A GLU 1635": "OE1" <-> "OE2" Residue "A TYR 1655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1660": "OD1" <-> "OD2" Residue "A GLU 1725": "OE1" <-> "OE2" Residue "A GLU 1763": "OE1" <-> "OE2" Residue "A GLU 1764": "OE1" <-> "OE2" Residue "A PHE 1774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1800": "OE1" <-> "OE2" Residue "A GLU 1957": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10445 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1236, 10265 Classifications: {'peptide': 1236} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 11} Link IDs: {'PTRANS': 33, 'TRANS': 1202} Chain breaks: 33 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 180 Unusual residues: {'ASG': 6, 'BDP': 6} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 12 Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" C1 BDP B 1 " occ=0.22 ... (11 atoms not shown) pdb=" O6B BDP B 1 " occ=0.22 residue: pdb=" C1 ASG B 2 " occ=0.34 ... (16 atoms not shown) pdb=" S ASG B 2 " occ=0.34 residue: pdb=" C1 BDP B 3 " occ=0.33 ... (10 atoms not shown) pdb=" O6B BDP B 3 " occ=0.33 residue: pdb=" C1 ASG B 4 " occ=0.29 ... (16 atoms not shown) pdb=" S ASG B 4 " occ=0.29 residue: pdb=" C1 BDP B 5 " occ=0.44 ... (10 atoms not shown) pdb=" O6B BDP B 5 " occ=0.44 residue: pdb=" C1 ASG B 6 " occ=0.51 ... (16 atoms not shown) pdb=" S ASG B 6 " occ=0.51 residue: pdb=" C1 BDP B 7 " occ=0.67 ... (10 atoms not shown) pdb=" O6B BDP B 7 " occ=0.67 residue: pdb=" C1 ASG B 8 " occ=0.62 ... (16 atoms not shown) pdb=" S ASG B 8 " occ=0.62 residue: pdb=" C1 BDP B 9 " occ=0.68 ... (10 atoms not shown) pdb=" O6B BDP B 9 " occ=0.68 residue: pdb=" C1 ASG B 10 " occ=0.62 ... (16 atoms not shown) pdb=" S ASG B 10 " occ=0.62 residue: pdb=" C1 BDP B 11 " occ=0.61 ... (9 atoms not shown) pdb=" O6B BDP B 11 " occ=0.61 residue: pdb=" C1 ASG B 12 " occ=0.31 ... (16 atoms not shown) pdb=" S ASG B 12 " occ=0.31 Time building chain proxies: 5.80, per 1000 atoms: 0.56 Number of scatterers: 10445 At special positions: 0 Unit cell: (105.444, 144.072, 107.532, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 2031 8.00 N 1771 7.00 C 6578 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 769 " - pdb=" SG CYS A 901 " distance=2.03 Simple disulfide: pdb=" SG CYS A 855 " - pdb=" SG CYS A 868 " distance=2.05 Simple disulfide: pdb=" SG CYS A 966 " - pdb=" SG CYS A1090 " distance=2.03 Simple disulfide: pdb=" SG CYS A1088 " - pdb=" SG CYS A1193 " distance=2.04 Simple disulfide: pdb=" SG CYS A1578 " - pdb=" SG CYS A1614 " distance=2.03 Simple disulfide: pdb=" SG CYS A1802 " - pdb=" SG CYS A1904 " distance=2.39 Simple disulfide: pdb=" SG CYS A1816 " - pdb=" SG CYS A1833 " 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 " " BDP B 11 " - " ASG B 12 " 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: 4.30 Conformation dependent library (CDL) restraints added in 1.7 seconds 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2356 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 0 sheets defined 56.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.571A pdb=" N LYS A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 107 through 111' Processing helix chain 'A' and resid 119 through 139 removed outlier: 4.051A pdb=" N PHE A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 166 removed outlier: 3.743A pdb=" N ASN A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 191 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 218 through 225 removed outlier: 3.506A pdb=" N TRP A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 320 through 337 removed outlier: 4.269A pdb=" N LYS A 333 " --> pdb=" O CYS A 329 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LYS A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TRP A 335 " --> pdb=" O CYS A 331 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LYS A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' Processing helix chain 'A' and resid 582 through 585 No H-bonds generated for 'chain 'A' and resid 582 through 585' Processing helix chain 'A' and resid 599 through 601 No H-bonds generated for 'chain 'A' and resid 599 through 601' Processing helix chain 'A' and resid 609 through 626 Processing helix chain 'A' and resid 632 through 635 Processing helix chain 'A' and resid 640 through 658 Processing helix chain 'A' and resid 668 through 682 Processing helix chain 'A' and resid 704 through 722 removed outlier: 5.747A pdb=" N LYS A 715 " --> pdb=" O ASN A 711 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR A 716 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE A 717 " --> pdb=" O ASN A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 781 Proline residue: A 778 - end of helix Processing helix chain 'A' and resid 801 through 812 removed outlier: 3.902A pdb=" N TYR A 808 " --> pdb=" O LYS A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 846 Processing helix chain 'A' and resid 873 through 883 Processing helix chain 'A' and resid 888 through 895 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 951 through 953 No H-bonds generated for 'chain 'A' and resid 951 through 953' Processing helix chain 'A' and resid 962 through 965 No H-bonds generated for 'chain 'A' and resid 962 through 965' Processing helix chain 'A' and resid 1017 through 1040 removed outlier: 3.898A pdb=" N GLN A1034 " --> pdb=" O ASN A1030 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR A1035 " --> pdb=" O LYS A1031 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU A1038 " --> pdb=" O GLN A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1117 removed outlier: 3.538A pdb=" N ASP A1107 " --> pdb=" O ASP A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1147 removed outlier: 3.945A pdb=" N PHE A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU A1143 " --> pdb=" O SER A1139 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR A1144 " --> pdb=" O CYS A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1170 Processing helix chain 'A' and resid 1178 through 1198 removed outlier: 3.856A pdb=" N LYS A1185 " --> pdb=" O ILE A1181 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N CYS A1193 " --> pdb=" O ALA A1189 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS A1194 " --> pdb=" O GLU A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1260 No H-bonds generated for 'chain 'A' and resid 1258 through 1260' Processing helix chain 'A' and resid 1296 through 1307 Processing helix chain 'A' and resid 1338 through 1352 Processing helix chain 'A' and resid 1365 through 1374 Processing helix chain 'A' and resid 1396 through 1419 Processing helix chain 'A' and resid 1450 through 1467 Processing helix chain 'A' and resid 1483 through 1502 removed outlier: 4.163A pdb=" N GLN A1499 " --> pdb=" O SER A1495 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU A1500 " --> pdb=" O GLU A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1537 No H-bonds generated for 'chain 'A' and resid 1535 through 1537' Processing helix chain 'A' and resid 1541 through 1546 Processing helix chain 'A' and resid 1608 through 1611 No H-bonds generated for 'chain 'A' and resid 1608 through 1611' Processing helix chain 'A' and resid 1617 through 1624 removed outlier: 3.806A pdb=" N ILE A1621 " --> pdb=" O GLU A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1658 removed outlier: 4.273A pdb=" N ALA A1657 " --> pdb=" O LYS A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1663 through 1683 Processing helix chain 'A' and resid 1693 through 1705 removed outlier: 3.650A pdb=" N TYR A1697 " --> pdb=" O GLU A1693 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU A1704 " --> pdb=" O SER A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1717 through 1725 Processing helix chain 'A' and resid 1746 through 1762 Processing helix chain 'A' and resid 1789 through 1815 Processing helix chain 'A' and resid 1831 through 1861 removed outlier: 3.652A pdb=" N LYS A1835 " --> pdb=" O ILE A1831 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA A1836 " --> pdb=" O GLU A1832 " (cutoff:3.500A) Proline residue: A1846 - end of helix Processing helix chain 'A' and resid 1883 through 1889 removed outlier: 3.945A pdb=" N LYS A1889 " --> pdb=" O ASP A1885 " (cutoff:3.500A) Processing helix chain 'A' and resid 1910 through 1913 No H-bonds generated for 'chain 'A' and resid 1910 through 1913' Processing helix chain 'A' and resid 1954 through 1970 455 hydrogen bonds defined for protein. 1362 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1785 1.31 - 1.44: 2833 1.44 - 1.57: 5932 1.57 - 1.70: 23 1.70 - 1.83: 74 Bond restraints: 10647 Sorted by residual: bond pdb=" OSC ASG B 2 " pdb=" S ASG B 2 " ideal model delta sigma weight residual 1.457 1.654 -0.197 2.00e-02 2.50e+03 9.73e+01 bond pdb=" OSC ASG B 12 " pdb=" S ASG B 12 " ideal model delta sigma weight residual 1.457 1.654 -0.197 2.00e-02 2.50e+03 9.69e+01 bond pdb=" OSC ASG B 6 " pdb=" S ASG B 6 " ideal model delta sigma weight residual 1.457 1.653 -0.196 2.00e-02 2.50e+03 9.61e+01 bond pdb=" OSC ASG B 10 " pdb=" S ASG B 10 " ideal model delta sigma weight residual 1.457 1.653 -0.196 2.00e-02 2.50e+03 9.60e+01 bond pdb=" OSC ASG B 4 " pdb=" S ASG B 4 " ideal model delta sigma weight residual 1.457 1.652 -0.195 2.00e-02 2.50e+03 9.51e+01 ... (remaining 10642 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.68: 226 106.68 - 113.61: 5757 113.61 - 120.54: 4525 120.54 - 127.47: 3676 127.47 - 134.41: 120 Bond angle restraints: 14304 Sorted by residual: angle pdb=" N ILE A 900 " pdb=" CA ILE A 900 " pdb=" C ILE A 900 " ideal model delta sigma weight residual 113.47 107.50 5.97 1.01e+00 9.80e-01 3.49e+01 angle pdb=" CA GLY A1151 " pdb=" C GLY A1151 " pdb=" O GLY A1151 " ideal model delta sigma weight residual 122.52 117.89 4.63 7.90e-01 1.60e+00 3.43e+01 angle pdb=" C SER A 871 " pdb=" N ASP A 872 " pdb=" CA ASP A 872 " ideal model delta sigma weight residual 122.11 131.43 -9.32 1.59e+00 3.96e-01 3.43e+01 angle pdb=" CA GLY A1784 " pdb=" C GLY A1784 " pdb=" O GLY A1784 " ideal model delta sigma weight residual 122.52 117.94 4.58 7.90e-01 1.60e+00 3.36e+01 angle pdb=" N ILE A1683 " pdb=" CA ILE A1683 " pdb=" C ILE A1683 " ideal model delta sigma weight residual 110.72 104.97 5.75 1.01e+00 9.80e-01 3.24e+01 ... (remaining 14299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.89: 6073 25.89 - 51.78: 374 51.78 - 77.67: 101 77.67 - 103.56: 44 103.56 - 129.45: 22 Dihedral angle restraints: 6614 sinusoidal: 2989 harmonic: 3625 Sorted by residual: dihedral pdb=" CB CYS A1578 " pdb=" SG CYS A1578 " pdb=" SG CYS A1614 " pdb=" CB CYS A1614 " ideal model delta sinusoidal sigma weight residual 93.00 163.50 -70.50 1 1.00e+01 1.00e-02 6.40e+01 dihedral pdb=" CB CYS A1816 " pdb=" SG CYS A1816 " pdb=" SG CYS A1833 " pdb=" CB CYS A1833 " ideal model delta sinusoidal sigma weight residual -86.00 -143.16 57.16 1 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" C THR A1695 " pdb=" N THR A1695 " pdb=" CA THR A1695 " pdb=" CB THR A1695 " ideal model delta harmonic sigma weight residual -122.00 -133.34 11.34 0 2.50e+00 1.60e-01 2.06e+01 ... (remaining 6611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 1450 0.179 - 0.358: 48 0.358 - 0.537: 3 0.537 - 0.716: 0 0.716 - 0.895: 1 Chirality restraints: 1502 Sorted by residual: chirality pdb=" C1 ASG B 8 " pdb=" O4 BDP B 7 " pdb=" C2 ASG B 8 " pdb=" O5 ASG B 8 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-02 2.50e+03 2.00e+03 chirality pdb=" C1 BDP B 9 " pdb=" O3 ASG B 8 " pdb=" C2 BDP B 9 " pdb=" O5 BDP B 9 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 5.35e+00 chirality pdb=" C3 BDP B 11 " pdb=" C2 BDP B 11 " pdb=" C4 BDP B 11 " pdb=" O3 BDP B 11 " both_signs ideal model delta sigma weight residual False 2.44 1.99 0.45 2.00e-01 2.50e+01 5.09e+00 ... (remaining 1499 not shown) Planarity restraints: 1799 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1149 " -0.024 2.00e-02 2.50e+03 4.83e-02 2.33e+01 pdb=" C PHE A1149 " 0.083 2.00e-02 2.50e+03 pdb=" O PHE A1149 " -0.032 2.00e-02 2.50e+03 pdb=" N ASN A1150 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 ASG B 8 " 0.043 2.00e-02 2.50e+03 3.60e-02 1.62e+01 pdb=" C7 ASG B 8 " -0.012 2.00e-02 2.50e+03 pdb=" C8 ASG B 8 " 0.033 2.00e-02 2.50e+03 pdb=" N2 ASG B 8 " -0.058 2.00e-02 2.50e+03 pdb=" O7 ASG B 8 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 64 " 0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO A 65 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 65 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 65 " 0.044 5.00e-02 4.00e+02 ... (remaining 1796 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 688 2.74 - 3.28: 10921 3.28 - 3.82: 17205 3.82 - 4.36: 20817 4.36 - 4.90: 33957 Nonbonded interactions: 83588 Sorted by model distance: nonbonded pdb=" OH TYR A 993 " pdb=" OD1 ASP A1019 " model vdw 2.195 2.440 nonbonded pdb=" O CYS A 588 " pdb=" OH TYR A 653 " model vdw 2.198 2.440 nonbonded pdb=" O ASP A1688 " pdb=" OD1 ASP A1688 " model vdw 2.205 3.040 nonbonded pdb=" O GLY A1893 " pdb=" OG SER A1903 " model vdw 2.245 2.440 nonbonded pdb=" O TYR A 574 " pdb=" OG1 THR A 577 " model vdw 2.249 2.440 ... (remaining 83583 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.22 max=1.00 mean=0.99 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: 1.940 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: 7.910 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 30.060 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 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 : 0.011 0.197 10647 Z= 0.774 Angle : 1.048 10.278 14304 Z= 0.647 Chirality : 0.073 0.895 1502 Planarity : 0.005 0.081 1799 Dihedral : 20.810 129.454 4237 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.31 % Favored : 94.61 % Rotamer: Outliers : 0.80 % Allowed : 3.04 % Favored : 96.16 % Cbeta Deviations : 0.08 % 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: -1.03 (0.24), residues: 1168 helix: 0.30 (0.19), residues: 715 sheet: None (None), residues: 0 loop : -2.32 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A1501 HIS 0.006 0.001 HIS A1666 PHE 0.018 0.002 PHE A 158 TYR 0.017 0.001 TYR A 328 ARG 0.005 0.000 ARG A1720 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1041 MET cc_start: 0.6177 (mtm) cc_final: 0.5940 (mtp) REVERT: A 1338 PHE cc_start: 0.5419 (t80) cc_final: 0.4725 (t80) REVERT: A 1415 LYS cc_start: 0.7013 (tttt) cc_final: 0.6653 (tptt) REVERT: A 1778 MET cc_start: 0.6737 (mmm) cc_final: 0.5885 (mmm) REVERT: A 1952 LYS cc_start: 0.4018 (OUTLIER) cc_final: 0.2759 (mmmt) outliers start: 9 outliers final: 1 residues processed: 149 average time/residue: 0.2745 time to fit residues: 55.4647 Evaluate side-chains 102 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 1952 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.0270 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 0.0980 chunk 111 optimal weight: 0.6980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 622 HIS A 870 GLN ** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1454 GLN A1627 ASN ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10647 Z= 0.196 Angle : 0.608 10.170 14304 Z= 0.298 Chirality : 0.043 0.397 1502 Planarity : 0.004 0.051 1799 Dihedral : 19.796 119.066 1593 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.70 % Allowed : 8.57 % Favored : 89.73 % 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: -0.49 (0.24), residues: 1168 helix: 0.63 (0.19), residues: 716 sheet: None (None), residues: 0 loop : -1.91 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1501 HIS 0.004 0.001 HIS A1666 PHE 0.019 0.002 PHE A 158 TYR 0.034 0.001 TYR A1663 ARG 0.003 0.000 ARG A 846 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 1.261 Fit side-chains REVERT: A 49 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.7974 (t0) REVERT: A 286 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6409 (t80) REVERT: A 328 TYR cc_start: 0.5905 (OUTLIER) cc_final: 0.4530 (t80) REVERT: A 1041 MET cc_start: 0.6129 (mtm) cc_final: 0.5916 (mtp) REVERT: A 1415 LYS cc_start: 0.7211 (tttt) cc_final: 0.6791 (tptt) REVERT: A 1511 LYS cc_start: 0.8029 (ttmt) cc_final: 0.7547 (ttmm) REVERT: A 1654 GLN cc_start: 0.7799 (tm-30) cc_final: 0.7446 (tt0) REVERT: A 1778 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.6334 (mtp) REVERT: A 1861 ILE cc_start: 0.8482 (pt) cc_final: 0.8254 (pt) outliers start: 19 outliers final: 9 residues processed: 121 average time/residue: 0.2619 time to fit residues: 44.0428 Evaluate side-chains 104 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 328 TYR Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1591 TYR Chi-restraints excluded: chain A residue 1688 ASP Chi-restraints excluded: chain A residue 1778 MET Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1803 GLU Chi-restraints excluded: chain A residue 1915 THR Chi-restraints excluded: chain A residue 1974 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A1030 ASN ** A1538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1654 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10647 Z= 0.285 Angle : 0.627 8.994 14304 Z= 0.308 Chirality : 0.044 0.418 1502 Planarity : 0.004 0.041 1799 Dihedral : 18.124 116.216 1588 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.50 % Allowed : 11.52 % Favored : 85.98 % 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: -0.64 (0.24), residues: 1168 helix: 0.54 (0.19), residues: 712 sheet: None (None), residues: 0 loop : -1.99 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 558 HIS 0.006 0.001 HIS A1666 PHE 0.023 0.002 PHE A 158 TYR 0.026 0.002 TYR A1663 ARG 0.005 0.000 ARG A1720 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 93 time to evaluate : 1.132 Fit side-chains REVERT: A 286 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.6600 (t80) REVERT: A 328 TYR cc_start: 0.5939 (OUTLIER) cc_final: 0.4700 (t80) REVERT: A 1415 LYS cc_start: 0.7296 (tttt) cc_final: 0.6886 (tptt) REVERT: A 1778 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6087 (mmm) outliers start: 28 outliers final: 17 residues processed: 111 average time/residue: 0.2423 time to fit residues: 38.4159 Evaluate side-chains 107 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 328 TYR Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1591 TYR Chi-restraints excluded: chain A residue 1627 ASN Chi-restraints excluded: chain A residue 1656 HIS Chi-restraints excluded: chain A residue 1688 ASP Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1778 MET Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1803 GLU Chi-restraints excluded: chain A residue 1915 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 112 optimal weight: 0.0980 chunk 118 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 956 GLN A1034 GLN ** A1538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10647 Z= 0.199 Angle : 0.575 9.375 14304 Z= 0.279 Chirality : 0.042 0.412 1502 Planarity : 0.003 0.036 1799 Dihedral : 17.104 112.959 1588 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.96 % Allowed : 14.11 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.24), residues: 1168 helix: 0.69 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -1.92 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.005 0.001 HIS A1666 PHE 0.020 0.002 PHE A1535 TYR 0.031 0.001 TYR A1663 ARG 0.004 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 1.209 Fit side-chains REVERT: A 286 PHE cc_start: 0.7346 (OUTLIER) cc_final: 0.6794 (t80) REVERT: A 328 TYR cc_start: 0.6058 (OUTLIER) cc_final: 0.4818 (t80) REVERT: A 1415 LYS cc_start: 0.7255 (tttt) cc_final: 0.6845 (tptt) REVERT: A 1778 MET cc_start: 0.7100 (mmm) cc_final: 0.6109 (mmm) REVERT: A 1952 LYS cc_start: 0.3949 (OUTLIER) cc_final: 0.2070 (mmtp) REVERT: A 1953 MET cc_start: 0.7428 (tmm) cc_final: 0.7193 (tmm) outliers start: 22 outliers final: 12 residues processed: 105 average time/residue: 0.2564 time to fit residues: 38.0144 Evaluate side-chains 101 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 328 TYR Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1265 VAL Chi-restraints excluded: chain A residue 1591 TYR Chi-restraints excluded: chain A residue 1688 ASP Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1803 GLU Chi-restraints excluded: chain A residue 1952 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 88 optimal weight: 0.1980 chunk 49 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1332 ASN ** A1538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1654 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10647 Z= 0.229 Angle : 0.581 10.487 14304 Z= 0.282 Chirality : 0.042 0.400 1502 Planarity : 0.003 0.037 1799 Dihedral : 16.190 109.761 1588 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.04 % Allowed : 14.02 % Favored : 82.95 % 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: -0.37 (0.24), residues: 1168 helix: 0.72 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -1.87 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 558 HIS 0.006 0.001 HIS A1666 PHE 0.021 0.002 PHE A 158 TYR 0.028 0.001 TYR A1663 ARG 0.005 0.000 ARG A1720 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 89 time to evaluate : 1.179 Fit side-chains REVERT: A 286 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.7099 (t80) REVERT: A 328 TYR cc_start: 0.6101 (OUTLIER) cc_final: 0.5011 (t80) REVERT: A 1415 LYS cc_start: 0.7273 (tttt) cc_final: 0.6879 (tptt) REVERT: A 1778 MET cc_start: 0.7109 (mmm) cc_final: 0.6120 (mmm) REVERT: A 1952 LYS cc_start: 0.4068 (OUTLIER) cc_final: 0.2063 (mmtp) outliers start: 34 outliers final: 20 residues processed: 114 average time/residue: 0.2411 time to fit residues: 39.2582 Evaluate side-chains 106 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 83 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 328 TYR Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1591 TYR Chi-restraints excluded: chain A residue 1627 ASN Chi-restraints excluded: chain A residue 1656 HIS Chi-restraints excluded: chain A residue 1688 ASP Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1803 GLU Chi-restraints excluded: chain A residue 1809 PHE Chi-restraints excluded: chain A residue 1915 THR Chi-restraints excluded: chain A residue 1952 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN A 576 ASN ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1454 GLN ** A1538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10647 Z= 0.296 Angle : 0.643 8.606 14304 Z= 0.309 Chirality : 0.046 0.408 1502 Planarity : 0.004 0.039 1799 Dihedral : 15.073 103.409 1588 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.95 % Allowed : 15.54 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.24), residues: 1168 helix: 0.59 (0.19), residues: 714 sheet: None (None), residues: 0 loop : -1.79 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 240 HIS 0.006 0.001 HIS A1666 PHE 0.025 0.002 PHE A 158 TYR 0.028 0.002 TYR A1663 ARG 0.006 0.001 ARG A1720 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 86 time to evaluate : 1.497 Fit side-chains REVERT: A 286 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.7134 (t80) REVERT: A 328 TYR cc_start: 0.6116 (OUTLIER) cc_final: 0.5025 (t80) REVERT: A 1030 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8102 (t0) REVERT: A 1415 LYS cc_start: 0.7280 (tttt) cc_final: 0.6886 (tptt) REVERT: A 1778 MET cc_start: 0.7110 (mmm) cc_final: 0.6137 (mmm) REVERT: A 1952 LYS cc_start: 0.3983 (OUTLIER) cc_final: 0.2004 (mmtp) outliers start: 33 outliers final: 23 residues processed: 111 average time/residue: 0.2364 time to fit residues: 37.6998 Evaluate side-chains 107 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 80 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 328 TYR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 993 TYR Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1030 ASN Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1193 CYS Chi-restraints excluded: chain A residue 1265 VAL Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1591 TYR Chi-restraints excluded: chain A residue 1627 ASN Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1656 HIS Chi-restraints excluded: chain A residue 1688 ASP Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1803 GLU Chi-restraints excluded: chain A residue 1809 PHE Chi-restraints excluded: chain A residue 1915 THR Chi-restraints excluded: chain A residue 1952 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 chunk 74 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1454 GLN ** A1538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10647 Z= 0.249 Angle : 0.603 8.525 14304 Z= 0.291 Chirality : 0.043 0.402 1502 Planarity : 0.003 0.038 1799 Dihedral : 14.521 102.038 1588 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.12 % Allowed : 15.89 % Favored : 80.98 % 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: -0.45 (0.24), residues: 1168 helix: 0.62 (0.19), residues: 719 sheet: None (None), residues: 0 loop : -1.81 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 282 HIS 0.006 0.001 HIS A1666 PHE 0.020 0.002 PHE A 158 TYR 0.026 0.001 TYR A1663 ARG 0.004 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 84 time to evaluate : 1.199 Fit side-chains revert: symmetry clash REVERT: A 286 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.7224 (t80) REVERT: A 1030 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.8109 (t0) REVERT: A 1415 LYS cc_start: 0.7276 (tttt) cc_final: 0.6883 (tptt) REVERT: A 1778 MET cc_start: 0.7083 (mmm) cc_final: 0.6148 (mmm) REVERT: A 1952 LYS cc_start: 0.4081 (OUTLIER) cc_final: 0.2033 (mmtp) outliers start: 35 outliers final: 24 residues processed: 110 average time/residue: 0.2372 time to fit residues: 37.5074 Evaluate side-chains 109 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 82 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 328 TYR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 993 TYR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1030 ASN Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1193 CYS Chi-restraints excluded: chain A residue 1265 VAL Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1591 TYR Chi-restraints excluded: chain A residue 1627 ASN Chi-restraints excluded: chain A residue 1688 ASP Chi-restraints excluded: chain A residue 1693 GLU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1803 GLU Chi-restraints excluded: chain A residue 1916 VAL Chi-restraints excluded: chain A residue 1952 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 0.0770 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1454 GLN ** A1538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10647 Z= 0.237 Angle : 0.608 8.915 14304 Z= 0.292 Chirality : 0.043 0.399 1502 Planarity : 0.003 0.038 1799 Dihedral : 13.972 100.420 1588 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.86 % Allowed : 16.25 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.24), residues: 1168 helix: 0.66 (0.19), residues: 721 sheet: None (None), residues: 0 loop : -1.79 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 558 HIS 0.006 0.001 HIS A1666 PHE 0.021 0.002 PHE A 158 TYR 0.023 0.001 TYR A1663 ARG 0.005 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 87 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: A 286 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.7218 (t80) REVERT: A 607 ARG cc_start: 0.6855 (mmm160) cc_final: 0.6597 (mmm160) REVERT: A 1030 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.8122 (t0) REVERT: A 1415 LYS cc_start: 0.7279 (tttt) cc_final: 0.6881 (tptt) REVERT: A 1778 MET cc_start: 0.7034 (mmm) cc_final: 0.6051 (mmm) REVERT: A 1952 LYS cc_start: 0.4046 (OUTLIER) cc_final: 0.2025 (mmtp) outliers start: 32 outliers final: 25 residues processed: 110 average time/residue: 0.2505 time to fit residues: 39.2830 Evaluate side-chains 109 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 81 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 328 TYR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 993 TYR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1030 ASN Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1193 CYS Chi-restraints excluded: chain A residue 1265 VAL Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1591 TYR Chi-restraints excluded: chain A residue 1627 ASN Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1656 HIS Chi-restraints excluded: chain A residue 1688 ASP Chi-restraints excluded: chain A residue 1693 GLU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1803 GLU Chi-restraints excluded: chain A residue 1809 PHE Chi-restraints excluded: chain A residue 1916 VAL Chi-restraints excluded: chain A residue 1952 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.0980 chunk 110 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1454 GLN ** A1538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 10647 Z= 0.224 Angle : 0.594 8.855 14304 Z= 0.284 Chirality : 0.042 0.398 1502 Planarity : 0.003 0.038 1799 Dihedral : 13.241 98.713 1588 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.86 % Allowed : 17.14 % Favored : 80.00 % 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: -0.33 (0.24), residues: 1168 helix: 0.73 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -1.80 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 558 HIS 0.007 0.001 HIS A1666 PHE 0.019 0.002 PHE A 158 TYR 0.028 0.001 TYR A1663 ARG 0.004 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 88 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: A 286 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.7213 (t80) REVERT: A 607 ARG cc_start: 0.6828 (mmm160) cc_final: 0.6562 (mmm160) REVERT: A 1415 LYS cc_start: 0.7277 (tttt) cc_final: 0.6878 (tptt) REVERT: A 1778 MET cc_start: 0.7068 (mmm) cc_final: 0.6117 (mmm) outliers start: 32 outliers final: 27 residues processed: 110 average time/residue: 0.2274 time to fit residues: 36.2479 Evaluate side-chains 113 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 85 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 328 TYR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 993 TYR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1193 CYS Chi-restraints excluded: chain A residue 1265 VAL Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1591 TYR Chi-restraints excluded: chain A residue 1621 ILE Chi-restraints excluded: chain A residue 1627 ASN Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1688 ASP Chi-restraints excluded: chain A residue 1689 LEU Chi-restraints excluded: chain A residue 1693 GLU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1803 GLU Chi-restraints excluded: chain A residue 1809 PHE Chi-restraints excluded: chain A residue 1916 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.0470 chunk 55 optimal weight: 0.1980 chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 112 optimal weight: 0.0980 chunk 97 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10647 Z= 0.174 Angle : 0.566 9.473 14304 Z= 0.271 Chirality : 0.041 0.391 1502 Planarity : 0.003 0.038 1799 Dihedral : 12.211 96.462 1588 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.41 % Allowed : 17.59 % Favored : 80.00 % 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: -0.09 (0.25), residues: 1168 helix: 0.94 (0.19), residues: 723 sheet: None (None), residues: 0 loop : -1.76 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1094 HIS 0.007 0.001 HIS A1666 PHE 0.027 0.002 PHE A1535 TYR 0.023 0.001 TYR A1663 ARG 0.004 0.000 ARG A 277 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 1.224 Fit side-chains revert: symmetry clash REVERT: A 286 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.7190 (t80) REVERT: A 607 ARG cc_start: 0.6894 (mmm160) cc_final: 0.6586 (mmm160) REVERT: A 1415 LYS cc_start: 0.7263 (tttt) cc_final: 0.6861 (tptt) REVERT: A 1778 MET cc_start: 0.7041 (mmm) cc_final: 0.6120 (mmm) outliers start: 27 outliers final: 24 residues processed: 110 average time/residue: 0.2275 time to fit residues: 36.4803 Evaluate side-chains 110 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 85 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 328 TYR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 993 TYR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1193 CYS Chi-restraints excluded: chain A residue 1265 VAL Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1591 TYR Chi-restraints excluded: chain A residue 1621 ILE Chi-restraints excluded: chain A residue 1688 ASP Chi-restraints excluded: chain A residue 1693 GLU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1803 GLU Chi-restraints excluded: chain A residue 1809 PHE Chi-restraints excluded: chain A residue 1916 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.0060 chunk 97 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.0020 chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1454 GLN A1666 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.129922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.112089 restraints weight = 21146.841| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 1.98 r_work: 0.3833 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10647 Z= 0.199 Angle : 0.583 9.948 14304 Z= 0.279 Chirality : 0.042 0.382 1502 Planarity : 0.003 0.039 1799 Dihedral : 11.801 94.263 1588 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.41 % Allowed : 18.04 % Favored : 79.55 % 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: -0.05 (0.25), residues: 1168 helix: 0.95 (0.19), residues: 725 sheet: None (None), residues: 0 loop : -1.73 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 616 HIS 0.011 0.001 HIS A1666 PHE 0.020 0.002 PHE A 158 TYR 0.028 0.001 TYR A1663 ARG 0.004 0.000 ARG A 277 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2334.82 seconds wall clock time: 43 minutes 39.88 seconds (2619.88 seconds total)