Starting phenix.real_space_refine on Mon Mar 11 09:04:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhr_24467/03_2024/7rhr_24467_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhr_24467/03_2024/7rhr_24467.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhr_24467/03_2024/7rhr_24467.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhr_24467/03_2024/7rhr_24467.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhr_24467/03_2024/7rhr_24467_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhr_24467/03_2024/7rhr_24467_updated.pdb" } resolution = 3.0 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= 0.006 sd= 0.137 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 40 5.16 5 C 5121 2.51 5 N 1265 2.21 5 O 1394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 125": "NH1" <-> "NH2" Residue "A TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 291": "OD1" <-> "OD2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 380": "OD1" <-> "OD2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 451": "OD1" <-> "OD2" Residue "A PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A ASP 766": "OD1" <-> "OD2" Residue "A GLU 774": "OE1" <-> "OE2" Residue "A TYR 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 862": "OD1" <-> "OD2" Residue "A ASP 899": "OD1" <-> "OD2" Residue "A ASP 901": "OD1" <-> "OD2" Residue "A PHE 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 944": "OD1" <-> "OD2" Residue "A GLU 948": "OE1" <-> "OE2" Residue "A TYR 960": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A TYR 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1084": "OE1" <-> "OE2" Residue "A PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1102": "NH1" <-> "NH2" Residue "A ARG 1103": "NH1" <-> "NH2" Residue "A PHE 1112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1139": "NH1" <-> "NH2" Residue "A PHE 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1167": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7820 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7680 Classifications: {'peptide': 974} Link IDs: {'PTRANS': 41, 'TRANS': 932} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 112 Unusual residues: {'CLR': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.72, per 1000 atoms: 0.60 Number of scatterers: 7820 At special positions: 0 Unit cell: (79.5, 81.62, 138.86, 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 40 16.00 O 1394 8.00 N 1265 7.00 C 5121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 193 " - pdb=" SG CYS A 216 " distance=2.04 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 317 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 294 " 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 BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1503 " - " ASN A 302 " " NAG A1504 " - " ASN A 339 " " NAG B 1 " - " ASN A 989 " Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.4 seconds 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1828 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 3 sheets defined 55.6% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 90 through 107 removed outlier: 4.116A pdb=" N PHE A 102 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARG A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 125 through 136 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 189 through 192 No H-bonds generated for 'chain 'A' and resid 189 through 192' Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 221 through 224 Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 266 through 275 Processing helix chain 'A' and resid 309 through 313 Processing helix chain 'A' and resid 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 379 through 400 Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 429 through 447 Processing helix chain 'A' and resid 457 through 480 Processing helix chain 'A' and resid 493 through 517 removed outlier: 4.180A pdb=" N ASP A 503 " --> pdb=" O GLY A 499 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASP A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 554 removed outlier: 5.490A pdb=" N ALA A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N SER A 537 " --> pdb=" O ARG A 533 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET A 551 " --> pdb=" O THR A 547 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU A 554 " --> pdb=" O PHE A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 580 Processing helix chain 'A' and resid 582 through 594 removed outlier: 3.836A pdb=" N GLU A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 734 Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 737 through 757 removed outlier: 4.295A pdb=" N VAL A 741 " --> pdb=" O PRO A 737 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 742 " --> pdb=" O LYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 776 through 787 Processing helix chain 'A' and resid 807 through 814 Processing helix chain 'A' and resid 834 through 854 Processing helix chain 'A' and resid 868 through 878 Processing helix chain 'A' and resid 888 through 890 No H-bonds generated for 'chain 'A' and resid 888 through 890' Processing helix chain 'A' and resid 909 through 919 Processing helix chain 'A' and resid 921 through 926 Processing helix chain 'A' and resid 973 through 991 Processing helix chain 'A' and resid 1002 through 1005 No H-bonds generated for 'chain 'A' and resid 1002 through 1005' Processing helix chain 'A' and resid 1009 through 1011 No H-bonds generated for 'chain 'A' and resid 1009 through 1011' Processing helix chain 'A' and resid 1013 through 1036 Processing helix chain 'A' and resid 1039 through 1063 Processing helix chain 'A' and resid 1069 through 1095 removed outlier: 3.950A pdb=" N VAL A1079 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY A1080 " --> pdb=" O ILE A1076 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU A1084 " --> pdb=" O GLY A1080 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N PHE A1085 " --> pdb=" O ILE A1081 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR A1086 " --> pdb=" O GLY A1082 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS A1088 " --> pdb=" O GLU A1084 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL A1089 " --> pdb=" O PHE A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1111 Processing helix chain 'A' and resid 1113 through 1129 removed outlier: 3.537A pdb=" N VAL A1126 " --> pdb=" O THR A1122 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N MET A1128 " --> pdb=" O LEU A1124 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU A1129 " --> pdb=" O GLY A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1158 Processing helix chain 'A' and resid 1160 through 1166 removed outlier: 3.619A pdb=" N PHE A1166 " --> pdb=" O VAL A1162 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 407 through 412 removed outlier: 3.669A pdb=" N ASN A 144 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 180 through 182 Processing sheet with id= C, first strand: chain 'A' and resid 961 through 968 382 hydrogen bonds defined for protein. 1131 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: 2.15 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2384 1.34 - 1.46: 1327 1.46 - 1.58: 4236 1.58 - 1.70: 1 1.70 - 1.82: 65 Bond restraints: 8013 Sorted by residual: bond pdb=" CA ASP A 223 " pdb=" C ASP A 223 " ideal model delta sigma weight residual 1.522 1.488 0.034 1.38e-02 5.25e+03 6.06e+00 bond pdb=" CB PRO A 732 " pdb=" CG PRO A 732 " ideal model delta sigma weight residual 1.492 1.614 -0.122 5.00e-02 4.00e+02 5.91e+00 bond pdb=" CA ASN A 144 " pdb=" CB ASN A 144 " ideal model delta sigma weight residual 1.526 1.543 -0.016 9.30e-03 1.16e+04 3.12e+00 bond pdb=" CB VAL A 159 " pdb=" CG2 VAL A 159 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.75e+00 bond pdb=" C10 CLR A1502 " pdb=" C9 CLR A1502 " ideal model delta sigma weight residual 1.551 1.520 0.031 2.00e-02 2.50e+03 2.44e+00 ... (remaining 8008 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.85: 172 105.85 - 112.92: 4397 112.92 - 120.00: 2816 120.00 - 127.08: 3439 127.08 - 134.15: 92 Bond angle restraints: 10916 Sorted by residual: angle pdb=" CA PRO A 732 " pdb=" N PRO A 732 " pdb=" CD PRO A 732 " ideal model delta sigma weight residual 112.00 103.07 8.93 1.40e+00 5.10e-01 4.07e+01 angle pdb=" N PHE A1004 " pdb=" CA PHE A1004 " pdb=" C PHE A1004 " ideal model delta sigma weight residual 114.75 107.40 7.35 1.26e+00 6.30e-01 3.41e+01 angle pdb=" N ASN A 907 " pdb=" CA ASN A 907 " pdb=" C ASN A 907 " ideal model delta sigma weight residual 114.04 108.06 5.98 1.24e+00 6.50e-01 2.32e+01 angle pdb=" C TYR A 237 " pdb=" N LEU A 238 " pdb=" CA LEU A 238 " ideal model delta sigma weight residual 120.49 114.92 5.57 1.42e+00 4.96e-01 1.54e+01 angle pdb=" CA ARG A 932 " pdb=" CB ARG A 932 " pdb=" CG ARG A 932 " ideal model delta sigma weight residual 114.10 107.41 6.69 2.00e+00 2.50e-01 1.12e+01 ... (remaining 10911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4606 17.76 - 35.52: 272 35.52 - 53.28: 37 53.28 - 71.04: 13 71.04 - 88.80: 7 Dihedral angle restraints: 4935 sinusoidal: 2097 harmonic: 2838 Sorted by residual: dihedral pdb=" CA ARG A 932 " pdb=" C ARG A 932 " pdb=" N PRO A 933 " pdb=" CA PRO A 933 " ideal model delta harmonic sigma weight residual -180.00 -103.48 -76.52 0 5.00e+00 4.00e-02 2.34e+02 dihedral pdb=" CA LYS A 828 " pdb=" C LYS A 828 " pdb=" N GLN A 829 " pdb=" CA GLN A 829 " ideal model delta harmonic sigma weight residual -180.00 -150.91 -29.09 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA ASN A 882 " pdb=" C ASN A 882 " pdb=" N SER A 883 " pdb=" CA SER A 883 " ideal model delta harmonic sigma weight residual -180.00 -157.54 -22.46 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 4932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 920 0.050 - 0.101: 296 0.101 - 0.151: 52 0.151 - 0.201: 6 0.201 - 0.252: 3 Chirality restraints: 1277 Sorted by residual: chirality pdb=" C13 CLR A1502 " pdb=" C12 CLR A1502 " pdb=" C14 CLR A1502 " pdb=" C17 CLR A1502 " both_signs ideal model delta sigma weight residual False -2.93 -2.68 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C13 CLR A1505 " pdb=" C12 CLR A1505 " pdb=" C14 CLR A1505 " pdb=" C17 CLR A1505 " both_signs ideal model delta sigma weight residual False -2.93 -2.72 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C13 CLR A1501 " pdb=" C12 CLR A1501 " pdb=" C14 CLR A1501 " pdb=" C17 CLR A1501 " both_signs ideal model delta sigma weight residual False -2.93 -2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1274 not shown) Planarity restraints: 1350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 932 " 0.067 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO A 933 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO A 933 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 933 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 731 " 0.039 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO A 732 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 732 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 732 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 912 " 0.014 2.00e-02 2.50e+03 1.26e-02 3.15e+00 pdb=" CG TYR A 912 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 912 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 912 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 912 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 912 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 912 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 912 " 0.000 2.00e-02 2.50e+03 ... (remaining 1347 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 115 2.69 - 3.24: 7673 3.24 - 3.79: 11855 3.79 - 4.35: 16428 4.35 - 4.90: 27318 Nonbonded interactions: 63389 Sorted by model distance: nonbonded pdb=" OH TYR A 442 " pdb=" OD1 ASP A1117 " model vdw 2.131 2.440 nonbonded pdb=" NE2 GLN A 150 " pdb=" OE1 GLN A 407 " model vdw 2.172 2.520 nonbonded pdb=" NH2 ARG A 134 " pdb=" OE2 GLU A 140 " model vdw 2.191 2.520 nonbonded pdb=" NH2 ARG A 431 " pdb=" O MET A1128 " model vdw 2.235 2.520 nonbonded pdb=" OG1 THR A 880 " pdb=" O ASP A 884 " model vdw 2.315 2.440 ... (remaining 63384 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.210 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 24.450 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:11.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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 : 0.006 0.122 8013 Z= 0.401 Angle : 0.838 8.980 10916 Z= 0.480 Chirality : 0.050 0.252 1277 Planarity : 0.005 0.101 1347 Dihedral : 11.889 88.803 3098 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.05 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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 (0.27), residues: 970 helix: 0.41 (0.22), residues: 563 sheet: 0.63 (0.77), residues: 47 loop : -1.49 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 268 HIS 0.006 0.001 HIS A 813 PHE 0.029 0.003 PHE A 249 TYR 0.031 0.002 TYR A 912 ARG 0.011 0.001 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.908 Fit side-chains REVERT: A 107 ARG cc_start: 0.7263 (pmt170) cc_final: 0.6571 (mmt180) REVERT: A 395 GLN cc_start: 0.7629 (mt0) cc_final: 0.7238 (tt0) REVERT: A 738 LYS cc_start: 0.7101 (mttt) cc_final: 0.6386 (tmtt) REVERT: A 785 PHE cc_start: 0.7810 (m-10) cc_final: 0.7451 (t80) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 1.2474 time to fit residues: 154.6925 Evaluate side-chains 93 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 76 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 245 GLN A1000 ASN A1009 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8013 Z= 0.201 Angle : 0.587 6.542 10916 Z= 0.296 Chirality : 0.042 0.151 1277 Planarity : 0.005 0.089 1347 Dihedral : 6.604 71.715 1326 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.85 % Favored : 95.05 % Rotamer: Outliers : 1.81 % Allowed : 7.61 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 0.14 (0.27), residues: 970 helix: 0.84 (0.22), residues: 567 sheet: 0.68 (0.76), residues: 47 loop : -1.16 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 327 HIS 0.003 0.001 HIS A1015 PHE 0.022 0.002 PHE A 78 TYR 0.017 0.002 TYR A 912 ARG 0.004 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.867 Fit side-chains REVERT: A 107 ARG cc_start: 0.7292 (pmt170) cc_final: 0.6518 (mmt-90) REVERT: A 395 GLN cc_start: 0.7537 (mt0) cc_final: 0.7165 (tt0) REVERT: A 738 LYS cc_start: 0.7019 (mttt) cc_final: 0.6461 (tmtt) REVERT: A 785 PHE cc_start: 0.7672 (m-10) cc_final: 0.7383 (t80) REVERT: A 956 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7290 (mp0) outliers start: 15 outliers final: 8 residues processed: 109 average time/residue: 1.0813 time to fit residues: 126.0227 Evaluate side-chains 106 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 846 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8013 Z= 0.274 Angle : 0.600 6.812 10916 Z= 0.304 Chirality : 0.043 0.142 1277 Planarity : 0.005 0.094 1347 Dihedral : 6.262 71.158 1326 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.74 % Favored : 95.15 % Rotamer: Outliers : 2.90 % Allowed : 10.27 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 0.14 (0.27), residues: 970 helix: 0.83 (0.22), residues: 567 sheet: 0.84 (0.76), residues: 47 loop : -1.17 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 327 HIS 0.004 0.001 HIS A 398 PHE 0.019 0.002 PHE A 963 TYR 0.020 0.002 TYR A 990 ARG 0.006 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 0.872 Fit side-chains REVERT: A 86 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7305 (ttmt) REVERT: A 107 ARG cc_start: 0.7464 (pmt170) cc_final: 0.6578 (mmt-90) REVERT: A 191 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7013 (mt-10) REVERT: A 325 MET cc_start: 0.8972 (mtp) cc_final: 0.8596 (mtp) REVERT: A 395 GLN cc_start: 0.7569 (mt0) cc_final: 0.7195 (tt0) REVERT: A 738 LYS cc_start: 0.7003 (mttt) cc_final: 0.6443 (tmtt) REVERT: A 785 PHE cc_start: 0.7693 (m-10) cc_final: 0.7402 (t80) outliers start: 24 outliers final: 12 residues processed: 110 average time/residue: 1.0429 time to fit residues: 122.9390 Evaluate side-chains 109 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.0050 chunk 66 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 846 GLN A1000 ASN A1101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8013 Z= 0.201 Angle : 0.539 7.167 10916 Z= 0.275 Chirality : 0.041 0.148 1277 Planarity : 0.005 0.086 1347 Dihedral : 5.851 68.607 1326 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.43 % Favored : 95.46 % Rotamer: Outliers : 2.78 % Allowed : 12.44 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.27), residues: 970 helix: 1.07 (0.22), residues: 568 sheet: 0.88 (0.77), residues: 47 loop : -0.96 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 327 HIS 0.002 0.001 HIS A 934 PHE 0.022 0.002 PHE A 78 TYR 0.018 0.001 TYR A 363 ARG 0.003 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 0.880 Fit side-chains REVERT: A 86 LYS cc_start: 0.7827 (ptmm) cc_final: 0.7306 (ttmt) REVERT: A 107 ARG cc_start: 0.7404 (pmt170) cc_final: 0.6343 (mmt-90) REVERT: A 253 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: A 325 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8557 (mtp) REVERT: A 395 GLN cc_start: 0.7542 (mt0) cc_final: 0.7171 (tt0) REVERT: A 574 ASN cc_start: 0.7857 (t0) cc_final: 0.7458 (m-40) REVERT: A 785 PHE cc_start: 0.7642 (m-10) cc_final: 0.7370 (t80) REVERT: A 905 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: A 953 ARG cc_start: 0.7968 (ptm160) cc_final: 0.7738 (ptm-80) outliers start: 23 outliers final: 12 residues processed: 113 average time/residue: 1.0757 time to fit residues: 130.0880 Evaluate side-chains 114 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 905 GLN Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 1 optimal weight: 3.9990 chunk 69 optimal weight: 0.0980 chunk 38 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 846 GLN A1000 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8013 Z= 0.167 Angle : 0.525 7.680 10916 Z= 0.268 Chirality : 0.040 0.147 1277 Planarity : 0.004 0.083 1347 Dihedral : 5.547 66.482 1326 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.43 % Favored : 95.46 % Rotamer: Outliers : 2.66 % Allowed : 13.41 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 0.72 (0.28), residues: 970 helix: 1.28 (0.22), residues: 568 sheet: 0.89 (0.75), residues: 47 loop : -0.86 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 327 HIS 0.003 0.001 HIS A 374 PHE 0.013 0.001 PHE A 963 TYR 0.013 0.001 TYR A 990 ARG 0.002 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.846 Fit side-chains REVERT: A 107 ARG cc_start: 0.7304 (pmt170) cc_final: 0.6481 (mpp-170) REVERT: A 235 MET cc_start: 0.7881 (mmm) cc_final: 0.7585 (mmt) REVERT: A 325 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8543 (mtp) REVERT: A 360 LYS cc_start: 0.7726 (tttm) cc_final: 0.7344 (ttpp) REVERT: A 395 GLN cc_start: 0.7497 (mt0) cc_final: 0.7144 (tt0) REVERT: A 785 PHE cc_start: 0.7642 (m-10) cc_final: 0.7406 (t80) REVERT: A 953 ARG cc_start: 0.7958 (ptm160) cc_final: 0.7726 (ptm-80) REVERT: A 1000 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.7869 (t0) outliers start: 22 outliers final: 14 residues processed: 111 average time/residue: 1.0444 time to fit residues: 124.3335 Evaluate side-chains 119 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 846 GLN A1000 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 8013 Z= 0.447 Angle : 0.686 7.985 10916 Z= 0.347 Chirality : 0.046 0.176 1277 Planarity : 0.006 0.102 1347 Dihedral : 6.002 72.111 1326 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.77 % Favored : 94.12 % Rotamer: Outliers : 3.50 % Allowed : 13.53 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 0.14 (0.27), residues: 970 helix: 0.77 (0.22), residues: 569 sheet: 0.60 (0.76), residues: 49 loop : -1.01 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 389 HIS 0.006 0.002 HIS A 398 PHE 0.030 0.002 PHE A 963 TYR 0.025 0.003 TYR A 990 ARG 0.008 0.001 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 100 time to evaluate : 0.886 Fit side-chains REVERT: A 107 ARG cc_start: 0.7505 (pmt170) cc_final: 0.6566 (mpp-170) REVERT: A 235 MET cc_start: 0.8084 (mmm) cc_final: 0.7813 (mmt) REVERT: A 360 LYS cc_start: 0.7769 (tttm) cc_final: 0.7356 (ttpp) REVERT: A 395 GLN cc_start: 0.7582 (mt0) cc_final: 0.7229 (tt0) REVERT: A 785 PHE cc_start: 0.7798 (m-10) cc_final: 0.7468 (t80) REVERT: A 905 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: A 932 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8042 (mmp-170) outliers start: 29 outliers final: 16 residues processed: 115 average time/residue: 1.0897 time to fit residues: 134.0554 Evaluate side-chains 115 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 905 GLN Chi-restraints excluded: chain A residue 932 ARG Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 0.5980 chunk 53 optimal weight: 0.3980 chunk 68 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 57 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 846 GLN A1038 ASN A1101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8013 Z= 0.173 Angle : 0.534 8.504 10916 Z= 0.273 Chirality : 0.040 0.154 1277 Planarity : 0.004 0.084 1347 Dihedral : 5.446 67.020 1326 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.92 % Favored : 95.98 % Rotamer: Outliers : 2.17 % Allowed : 15.70 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.28), residues: 970 helix: 1.22 (0.22), residues: 568 sheet: 0.90 (0.77), residues: 47 loop : -0.85 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 327 HIS 0.004 0.001 HIS A 374 PHE 0.012 0.001 PHE A 963 TYR 0.016 0.001 TYR A 990 ARG 0.002 0.000 ARG A1103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 0.890 Fit side-chains REVERT: A 107 ARG cc_start: 0.7328 (pmt170) cc_final: 0.6346 (mpp-170) REVERT: A 235 MET cc_start: 0.7933 (mmm) cc_final: 0.7669 (mmt) REVERT: A 360 LYS cc_start: 0.7726 (tttm) cc_final: 0.7326 (ttpp) REVERT: A 395 GLN cc_start: 0.7509 (mt0) cc_final: 0.7162 (tt0) REVERT: A 785 PHE cc_start: 0.7660 (m-10) cc_final: 0.7388 (t80) REVERT: A 905 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: A 956 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7234 (mp0) outliers start: 18 outliers final: 12 residues processed: 110 average time/residue: 1.0504 time to fit residues: 123.6428 Evaluate side-chains 113 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 905 GLN Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 63 optimal weight: 0.0570 chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN A1038 ASN A1101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8013 Z= 0.198 Angle : 0.537 9.068 10916 Z= 0.273 Chirality : 0.040 0.152 1277 Planarity : 0.005 0.086 1347 Dihedral : 5.276 66.558 1326 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.74 % Favored : 95.15 % Rotamer: Outliers : 2.90 % Allowed : 14.73 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 0.78 (0.28), residues: 970 helix: 1.31 (0.22), residues: 569 sheet: 0.87 (0.78), residues: 47 loop : -0.78 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 327 HIS 0.003 0.001 HIS A 279 PHE 0.025 0.001 PHE A 78 TYR 0.023 0.002 TYR A 363 ARG 0.003 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 0.923 Fit side-chains REVERT: A 107 ARG cc_start: 0.7328 (pmt170) cc_final: 0.6333 (mpp-170) REVERT: A 115 VAL cc_start: 0.7868 (t) cc_final: 0.7665 (t) REVERT: A 235 MET cc_start: 0.7913 (mmm) cc_final: 0.7642 (mmt) REVERT: A 325 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8565 (mtp) REVERT: A 360 LYS cc_start: 0.7722 (tttm) cc_final: 0.7327 (ttpp) REVERT: A 395 GLN cc_start: 0.7503 (mt0) cc_final: 0.7157 (tt0) REVERT: A 785 PHE cc_start: 0.7667 (m-10) cc_final: 0.7398 (t80) REVERT: A 905 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7828 (tm-30) outliers start: 24 outliers final: 16 residues processed: 116 average time/residue: 1.0796 time to fit residues: 134.0739 Evaluate side-chains 119 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 905 GLN Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.0020 chunk 89 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 846 GLN A1101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8013 Z= 0.177 Angle : 0.527 9.542 10916 Z= 0.268 Chirality : 0.040 0.149 1277 Planarity : 0.004 0.084 1347 Dihedral : 5.112 65.664 1326 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.23 % Favored : 95.67 % Rotamer: Outliers : 2.54 % Allowed : 14.98 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 0.91 (0.28), residues: 970 helix: 1.42 (0.22), residues: 569 sheet: 0.90 (0.78), residues: 47 loop : -0.74 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 327 HIS 0.002 0.001 HIS A 279 PHE 0.028 0.001 PHE A 78 TYR 0.016 0.001 TYR A 990 ARG 0.002 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 0.845 Fit side-chains REVERT: A 107 ARG cc_start: 0.7298 (pmt170) cc_final: 0.6291 (mpp-170) REVERT: A 115 VAL cc_start: 0.7814 (t) cc_final: 0.7599 (t) REVERT: A 235 MET cc_start: 0.7851 (mmm) cc_final: 0.7640 (mmt) REVERT: A 282 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8581 (mmm) REVERT: A 360 LYS cc_start: 0.7704 (tttm) cc_final: 0.7310 (ttpp) REVERT: A 395 GLN cc_start: 0.7537 (mt0) cc_final: 0.7146 (tt0) REVERT: A 785 PHE cc_start: 0.7615 (m-10) cc_final: 0.7386 (t80) REVERT: A 905 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7788 (tm-30) outliers start: 21 outliers final: 14 residues processed: 114 average time/residue: 1.0599 time to fit residues: 129.4448 Evaluate side-chains 117 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 905 GLN Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.0870 chunk 43 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN A1101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8013 Z= 0.193 Angle : 0.535 9.837 10916 Z= 0.271 Chirality : 0.040 0.152 1277 Planarity : 0.004 0.085 1347 Dihedral : 5.077 65.910 1326 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.85 % Favored : 95.05 % Rotamer: Outliers : 2.05 % Allowed : 15.70 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 0.94 (0.28), residues: 970 helix: 1.47 (0.22), residues: 568 sheet: 0.90 (0.79), residues: 47 loop : -0.78 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 327 HIS 0.003 0.001 HIS A 279 PHE 0.028 0.001 PHE A 78 TYR 0.027 0.002 TYR A 363 ARG 0.003 0.000 ARG A 284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 0.815 Fit side-chains REVERT: A 107 ARG cc_start: 0.7436 (pmt170) cc_final: 0.6459 (mpp-170) REVERT: A 115 VAL cc_start: 0.7837 (t) cc_final: 0.7618 (t) REVERT: A 235 MET cc_start: 0.7862 (mmm) cc_final: 0.7649 (mmt) REVERT: A 282 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8621 (mmm) REVERT: A 360 LYS cc_start: 0.7730 (tttm) cc_final: 0.7299 (ttpp) REVERT: A 395 GLN cc_start: 0.7545 (mt0) cc_final: 0.7152 (tt0) REVERT: A 785 PHE cc_start: 0.7616 (m-10) cc_final: 0.7382 (t80) outliers start: 17 outliers final: 14 residues processed: 112 average time/residue: 1.0358 time to fit residues: 124.4119 Evaluate side-chains 118 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN A 891 GLN A1101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.163232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.125655 restraints weight = 8649.618| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.94 r_work: 0.3015 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8013 Z= 0.214 Angle : 0.553 9.824 10916 Z= 0.279 Chirality : 0.041 0.154 1277 Planarity : 0.005 0.086 1347 Dihedral : 5.092 66.282 1326 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.43 % Favored : 95.46 % Rotamer: Outliers : 2.05 % Allowed : 15.82 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 0.90 (0.28), residues: 970 helix: 1.45 (0.22), residues: 568 sheet: 0.90 (0.79), residues: 47 loop : -0.82 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 327 HIS 0.003 0.001 HIS A 279 PHE 0.028 0.001 PHE A 78 TYR 0.018 0.001 TYR A 990 ARG 0.003 0.000 ARG A 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2814.94 seconds wall clock time: 50 minutes 58.45 seconds (3058.45 seconds total)