Starting phenix.real_space_refine on Thu Jul 18 23:08:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlg_36396/07_2024/8jlg_36396.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlg_36396/07_2024/8jlg_36396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlg_36396/07_2024/8jlg_36396.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlg_36396/07_2024/8jlg_36396.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlg_36396/07_2024/8jlg_36396.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlg_36396/07_2024/8jlg_36396.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.038 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 15 5.16 5 C 2829 2.51 5 N 738 2.21 5 O 844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 961": "OE1" <-> "OE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1076": "OD1" <-> "OD2" Residue "B TYR 1112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1156": "OE1" <-> "OE2" Residue "B PHE 1249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1256": "OD1" <-> "OD2" Residue "B GLU 1283": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4426 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 923 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain: "B" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3437 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 411} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" 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 Time building chain proxies: 3.80, per 1000 atoms: 0.86 Number of scatterers: 4426 At special positions: 0 Unit cell: (83.83, 82.17, 92.13, 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 15 16.00 O 844 8.00 N 738 7.00 C 2829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 601 " - " ASN A 498 " " NAG A 602 " - " ASN A 548 " " NAG E 1 " - " ASN A 573 " Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 833.1 milliseconds 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1000 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 9 sheets defined 7.7% alpha, 48.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 480 through 484 removed outlier: 3.758A pdb=" N THR A 484 " --> pdb=" O ALA A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 933 removed outlier: 3.692A pdb=" N VAL B 933 " --> pdb=" O ASN B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 958 removed outlier: 3.544A pdb=" N LEU B 958 " --> pdb=" O LYS B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 1080 through 1091 Processing helix chain 'B' and resid 1210 through 1214 removed outlier: 4.012A pdb=" N VAL B1214 " --> pdb=" O ILE B1211 " (cutoff:3.500A) Processing helix chain 'B' and resid 1265 through 1273 Processing sheet with id=AA1, first strand: chain 'A' and resid 485 through 493 removed outlier: 6.189A pdb=" N GLY A 509 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG A 491 " --> pdb=" O GLY A 509 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR A 511 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU A 493 " --> pdb=" O TYR A 511 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR A 500 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU A 521 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLU A 502 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER A 523 " --> pdb=" O GLU A 502 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 515 through 527 current: chain 'A' and resid 550 through 552 Processing sheet with id=AA2, first strand: chain 'A' and resid 566 through 567 removed outlier: 5.939A pdb=" N PHE A 546 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N PHE A 545 " --> pdb=" O LYS A 522 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL A 524 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ARG A 547 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE A 526 " --> pdb=" O ARG A 547 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR A 500 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU A 521 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLU A 502 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER A 523 " --> pdb=" O GLU A 502 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 500 through 512 current: chain 'A' and resid 555 through 559 Processing sheet with id=AA3, first strand: chain 'B' and resid 887 through 890 removed outlier: 3.581A pdb=" N ASP B 887 " --> pdb=" O LYS B 884 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 879 " --> pdb=" O LEU B1074 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE B1072 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N TYR B 883 " --> pdb=" O LYS B1070 " (cutoff:3.500A) removed outlier: 12.393A pdb=" N LYS B1070 " --> pdb=" O TYR B 883 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 887 through 890 removed outlier: 3.581A pdb=" N ASP B 887 " --> pdb=" O LYS B 884 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 879 " --> pdb=" O LEU B1074 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE B1072 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N TYR B 883 " --> pdb=" O LYS B1070 " (cutoff:3.500A) removed outlier: 12.393A pdb=" N LYS B1070 " --> pdb=" O TYR B 883 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE B1069 " --> pdb=" O LYS B 948 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS B 948 " --> pdb=" O ILE B1069 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N TYR B1071 " --> pdb=" O TRP B 946 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TRP B 946 " --> pdb=" O TYR B1071 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE B 941 " --> pdb=" O ASN B1021 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP B1037 " --> pdb=" O ILE B1029 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE B1031 " --> pdb=" O LEU B1035 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LEU B1035 " --> pdb=" O ILE B1031 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 897 through 900 removed outlier: 7.303A pdb=" N LYS B1052 " --> pdb=" O ILE B 968 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE B 968 " --> pdb=" O LYS B1052 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE B 964 " --> pdb=" O LYS B1056 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASP B1058 " --> pdb=" O TYR B 962 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TYR B 962 " --> pdb=" O ASP B1058 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL B 976 " --> pdb=" O ILE B 964 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ASN B 966 " --> pdb=" O TRP B 974 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TRP B 974 " --> pdb=" O ASN B 966 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1112 through 1115 Processing sheet with id=AA7, first strand: chain 'B' and resid 1122 through 1125 Processing sheet with id=AA8, first strand: chain 'B' and resid 1159 through 1164 removed outlier: 3.986A pdb=" N LYS B1159 " --> pdb=" O VAL B1185 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP B1178 " --> pdb=" O MET B1223 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LYS B1226 " --> pdb=" O LYS B1234 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LYS B1234 " --> pdb=" O LYS B1226 " (cutoff:3.500A) removed outlier: 27.061A pdb=" N ASN B1233 " --> pdb=" O LEU B1254 " (cutoff:3.500A) removed outlier: 23.354A pdb=" N LEU B1254 " --> pdb=" O ASN B1233 " (cutoff:3.500A) removed outlier: 15.632A pdb=" N CYS B1235 " --> pdb=" O PHE B1252 " (cutoff:3.500A) removed outlier: 10.927A pdb=" N PHE B1252 " --> pdb=" O CYS B1235 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N MET B1237 " --> pdb=" O ILE B1250 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B1248 " --> pdb=" O LEU B1239 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1159 through 1164 removed outlier: 3.986A pdb=" N LYS B1159 " --> pdb=" O VAL B1185 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE B1182 " --> pdb=" O LEU B1193 " (cutoff:3.500A) 155 hydrogen bonds defined for protein. 402 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: 1.43 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 764 1.32 - 1.45: 1415 1.45 - 1.58: 2317 1.58 - 1.71: 0 1.71 - 1.84: 23 Bond restraints: 4519 Sorted by residual: bond pdb=" C ILE B1161 " pdb=" N ILE B1162 " ideal model delta sigma weight residual 1.330 1.277 0.054 1.26e-02 6.30e+03 1.81e+01 bond pdb=" CA SER B1281 " pdb=" CB SER B1281 " ideal model delta sigma weight residual 1.531 1.466 0.064 1.52e-02 4.33e+03 1.79e+01 bond pdb=" C TYR B1001 " pdb=" O TYR B1001 " ideal model delta sigma weight residual 1.236 1.187 0.048 1.20e-02 6.94e+03 1.62e+01 bond pdb=" C ILE B1029 " pdb=" O ILE B1029 " ideal model delta sigma weight residual 1.236 1.199 0.037 1.02e-02 9.61e+03 1.31e+01 bond pdb=" C GLY B 981 " pdb=" O GLY B 981 " ideal model delta sigma weight residual 1.236 1.190 0.045 1.31e-02 5.83e+03 1.21e+01 ... (remaining 4514 not shown) Histogram of bond angle deviations from ideal: 96.21 - 103.81: 27 103.81 - 111.41: 1689 111.41 - 119.01: 1943 119.01 - 126.62: 2409 126.62 - 134.22: 38 Bond angle restraints: 6106 Sorted by residual: angle pdb=" CA ASP B1256 " pdb=" CB ASP B1256 " pdb=" CG ASP B1256 " ideal model delta sigma weight residual 112.60 116.45 -3.85 1.00e+00 1.00e+00 1.48e+01 angle pdb=" C PRO B1119 " pdb=" N ASN B1120 " pdb=" CA ASN B1120 " ideal model delta sigma weight residual 122.65 116.95 5.70 1.60e+00 3.91e-01 1.27e+01 angle pdb=" OD1 ASN B1103 " pdb=" CG ASN B1103 " pdb=" ND2 ASN B1103 " ideal model delta sigma weight residual 122.60 126.09 -3.49 1.00e+00 1.00e+00 1.22e+01 angle pdb=" N PRO B1119 " pdb=" CA PRO B1119 " pdb=" CB PRO B1119 " ideal model delta sigma weight residual 102.17 105.77 -3.60 1.05e+00 9.07e-01 1.17e+01 angle pdb=" N ASN B1120 " pdb=" CA ASN B1120 " pdb=" CB ASN B1120 " ideal model delta sigma weight residual 110.56 115.28 -4.72 1.46e+00 4.69e-01 1.04e+01 ... (remaining 6101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.70: 2606 22.70 - 45.39: 112 45.39 - 68.08: 21 68.08 - 90.77: 3 90.77 - 113.47: 3 Dihedral angle restraints: 2745 sinusoidal: 1182 harmonic: 1563 Sorted by residual: dihedral pdb=" CA GLU A 532 " pdb=" C GLU A 532 " pdb=" N GLU A 533 " pdb=" CA GLU A 533 " ideal model delta harmonic sigma weight residual -180.00 -158.39 -21.61 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA PHE A 499 " pdb=" C PHE A 499 " pdb=" N THR A 500 " pdb=" CA THR A 500 " ideal model delta harmonic sigma weight residual 180.00 160.62 19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" C1 NAG A 602 " pdb=" C5 NAG A 602 " pdb=" O5 NAG A 602 " pdb=" C4 NAG A 602 " ideal model delta sinusoidal sigma weight residual -64.11 49.36 -113.47 1 3.00e+01 1.11e-03 1.49e+01 ... (remaining 2742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 637 0.151 - 0.301: 33 0.301 - 0.451: 3 0.451 - 0.602: 0 0.602 - 0.752: 1 Chirality restraints: 674 Sorted by residual: chirality pdb=" C1 FUC E 3 " pdb=" O6 NAG E 1 " pdb=" C2 FUC E 3 " pdb=" O5 FUC E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.32e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.62e+01 chirality pdb=" C1 NAG A 602 " pdb=" ND2 ASN A 548 " pdb=" C2 NAG A 602 " pdb=" O5 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.41e+01 ... (remaining 671 not shown) Planarity restraints: 778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 573 " -0.037 2.00e-02 2.50e+03 4.07e-02 2.07e+01 pdb=" CG ASN A 573 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 573 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 573 " 0.065 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 999 " 0.036 2.00e-02 2.50e+03 3.11e-02 1.69e+01 pdb=" CG PHE B 999 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE B 999 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 999 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 PHE B 999 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 PHE B 999 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 999 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 576 " 0.036 2.00e-02 2.50e+03 2.95e-02 1.53e+01 pdb=" CG PHE A 576 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 576 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE A 576 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 576 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 PHE A 576 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 576 " 0.003 2.00e-02 2.50e+03 ... (remaining 775 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 493 2.75 - 3.29: 4092 3.29 - 3.83: 7101 3.83 - 4.36: 9176 4.36 - 4.90: 15739 Nonbonded interactions: 36601 Sorted by model distance: nonbonded pdb=" OD1 ASN B1216 " pdb=" ND2 ASN B1242 " model vdw 2.213 2.520 nonbonded pdb=" O TRP B1266 " pdb=" NE2 GLN B1270 " model vdw 2.215 2.520 nonbonded pdb=" NH2 ARG A 570 " pdb=" O7 NAG A 602 " model vdw 2.262 2.520 nonbonded pdb=" OH TYR B 980 " pdb=" O ILE B1148 " model vdw 2.272 2.440 nonbonded pdb=" ND2 ASN B 918 " pdb=" O ASP B1062 " model vdw 2.304 2.520 ... (remaining 36596 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: 1.200 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 19.640 Find NCS groups from input model: 0.040 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:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 0.090 4519 Z= 0.724 Angle : 1.114 7.277 6106 Z= 0.685 Chirality : 0.085 0.752 674 Planarity : 0.009 0.103 775 Dihedral : 13.811 113.467 1745 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.01 (0.35), residues: 527 helix: 1.04 (1.04), residues: 23 sheet: -0.34 (0.33), residues: 233 loop : -1.07 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.009 TRP B1282 HIS 0.008 0.004 HIS A 506 PHE 0.055 0.012 PHE B 999 TYR 0.040 0.010 TYR B1122 ARG 0.027 0.003 ARG B1175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.487 Fit side-chains REVERT: B 1000 LYS cc_start: 0.8796 (mtpp) cc_final: 0.8354 (mttp) REVERT: B 1052 LYS cc_start: 0.7817 (mttt) cc_final: 0.7607 (ttmt) REVERT: B 1118 ASP cc_start: 0.6869 (t70) cc_final: 0.6535 (t70) REVERT: B 1130 ILE cc_start: 0.7908 (mp) cc_final: 0.7637 (tp) REVERT: B 1266 TRP cc_start: 0.6567 (t60) cc_final: 0.6314 (t60) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 1.1226 time to fit residues: 107.4440 Evaluate side-chains 64 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 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 504 GLN B 988 GLN B1188 ASN B1265 ASN ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4519 Z= 0.182 Angle : 0.519 10.515 6106 Z= 0.282 Chirality : 0.049 0.357 674 Planarity : 0.003 0.027 775 Dihedral : 8.981 85.654 687 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.84 % Allowed : 11.07 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.72 (0.35), residues: 527 helix: 1.41 (1.03), residues: 23 sheet: -0.15 (0.34), residues: 224 loop : -0.86 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 974 HIS 0.002 0.001 HIS A 506 PHE 0.016 0.001 PHE A 497 TYR 0.012 0.001 TYR B1149 ARG 0.003 0.000 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: B 982 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8370 (mt-10) REVERT: B 1000 LYS cc_start: 0.8681 (mtpp) cc_final: 0.8268 (mttp) REVERT: B 1052 LYS cc_start: 0.7811 (mttt) cc_final: 0.7599 (ttmt) REVERT: B 1118 ASP cc_start: 0.6662 (t70) cc_final: 0.6346 (t70) REVERT: B 1130 ILE cc_start: 0.7788 (mp) cc_final: 0.7556 (tp) REVERT: B 1190 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6697 (tp30) REVERT: B 1266 TRP cc_start: 0.6552 (t60) cc_final: 0.6258 (t60) outliers start: 9 outliers final: 4 residues processed: 79 average time/residue: 1.2132 time to fit residues: 99.5980 Evaluate side-chains 69 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1190 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B 988 GLN ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 4519 Z= 0.387 Angle : 0.617 11.632 6106 Z= 0.326 Chirality : 0.052 0.343 674 Planarity : 0.004 0.038 775 Dihedral : 8.324 76.072 687 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.69 % Allowed : 12.91 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.90 (0.34), residues: 527 helix: 1.06 (1.01), residues: 23 sheet: 0.53 (0.42), residues: 142 loop : -1.26 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 974 HIS 0.002 0.001 HIS A 494 PHE 0.015 0.002 PHE A 497 TYR 0.015 0.002 TYR B 962 ARG 0.005 0.001 ARG B1179 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 0.523 Fit side-chains REVERT: A 497 PHE cc_start: 0.7847 (t80) cc_final: 0.7494 (t80) REVERT: A 517 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8410 (pt) REVERT: A 532 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7524 (tt0) REVERT: B 1118 ASP cc_start: 0.6823 (t70) cc_final: 0.6528 (t70) REVERT: B 1130 ILE cc_start: 0.7840 (mp) cc_final: 0.7581 (tp) REVERT: B 1190 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6576 (tp30) outliers start: 18 outliers final: 10 residues processed: 74 average time/residue: 1.1590 time to fit residues: 89.2521 Evaluate side-chains 71 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 942 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1190 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B 988 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4519 Z= 0.221 Angle : 0.542 12.020 6106 Z= 0.286 Chirality : 0.048 0.235 674 Planarity : 0.003 0.024 775 Dihedral : 7.032 55.826 687 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.28 % Allowed : 16.80 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.82 (0.35), residues: 527 helix: 1.24 (1.04), residues: 23 sheet: 0.49 (0.42), residues: 148 loop : -1.20 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 974 HIS 0.001 0.000 HIS A 494 PHE 0.013 0.001 PHE A 497 TYR 0.011 0.001 TYR B1149 ARG 0.003 0.000 ARG B1179 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 0.525 Fit side-chains REVERT: A 497 PHE cc_start: 0.7684 (t80) cc_final: 0.7338 (t80) REVERT: A 517 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8229 (pp) REVERT: B 982 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8394 (mt-10) REVERT: B 1052 LYS cc_start: 0.7725 (mttt) cc_final: 0.7468 (ttmt) REVERT: B 1118 ASP cc_start: 0.6733 (t70) cc_final: 0.6456 (t70) REVERT: B 1130 ILE cc_start: 0.7814 (mp) cc_final: 0.7540 (tp) REVERT: B 1190 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6641 (tp30) REVERT: B 1266 TRP cc_start: 0.6576 (t60) cc_final: 0.6234 (t60) outliers start: 16 outliers final: 7 residues processed: 72 average time/residue: 1.1804 time to fit residues: 88.4966 Evaluate side-chains 68 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain B residue 1190 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 0.0770 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B 988 GLN B1270 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4519 Z= 0.163 Angle : 0.478 8.550 6106 Z= 0.261 Chirality : 0.046 0.175 674 Planarity : 0.002 0.023 775 Dihedral : 5.662 40.937 687 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.25 % Allowed : 18.65 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.62 (0.35), residues: 527 helix: 1.61 (1.07), residues: 23 sheet: 0.41 (0.43), residues: 136 loop : -0.91 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 985 HIS 0.001 0.000 HIS A 494 PHE 0.012 0.001 PHE B 941 TYR 0.010 0.001 TYR B1149 ARG 0.003 0.000 ARG B1179 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.508 Fit side-chains REVERT: A 497 PHE cc_start: 0.7653 (t80) cc_final: 0.7348 (t80) REVERT: A 532 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7514 (tt0) REVERT: B 1118 ASP cc_start: 0.6747 (t70) cc_final: 0.6478 (t70) REVERT: B 1130 ILE cc_start: 0.7794 (mp) cc_final: 0.7524 (tp) REVERT: B 1190 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6616 (tp30) REVERT: B 1210 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: B 1266 TRP cc_start: 0.6480 (t60) cc_final: 0.6128 (t60) outliers start: 11 outliers final: 7 residues processed: 69 average time/residue: 1.1011 time to fit residues: 79.3141 Evaluate side-chains 68 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1190 GLU Chi-restraints excluded: chain B residue 1210 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B 988 GLN B1270 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4519 Z= 0.278 Angle : 0.530 9.314 6106 Z= 0.287 Chirality : 0.048 0.161 674 Planarity : 0.003 0.028 775 Dihedral : 5.468 36.696 687 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.89 % Allowed : 17.42 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.87 (0.34), residues: 527 helix: 1.35 (1.03), residues: 23 sheet: 0.36 (0.40), residues: 154 loop : -1.22 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B1266 HIS 0.002 0.001 HIS A 494 PHE 0.014 0.002 PHE A 531 TYR 0.012 0.001 TYR B 962 ARG 0.003 0.000 ARG B1179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 61 time to evaluate : 0.517 Fit side-chains REVERT: A 497 PHE cc_start: 0.7448 (t80) cc_final: 0.6999 (t80) REVERT: A 517 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8232 (pp) REVERT: A 532 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7475 (tt0) REVERT: B 1118 ASP cc_start: 0.6803 (t70) cc_final: 0.6539 (t70) REVERT: B 1130 ILE cc_start: 0.7794 (mp) cc_final: 0.7490 (tp) REVERT: B 1190 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6612 (tp30) REVERT: B 1266 TRP cc_start: 0.6566 (t60) cc_final: 0.6211 (t60) outliers start: 19 outliers final: 12 residues processed: 73 average time/residue: 1.0062 time to fit residues: 76.8713 Evaluate side-chains 74 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain B residue 1190 GLU Chi-restraints excluded: chain B residue 1247 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 0.0050 chunk 28 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B 988 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4519 Z= 0.226 Angle : 0.502 10.658 6106 Z= 0.272 Chirality : 0.047 0.168 674 Planarity : 0.003 0.024 775 Dihedral : 5.261 34.860 687 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.51 % Allowed : 17.01 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.34), residues: 527 helix: 1.29 (1.03), residues: 23 sheet: 0.32 (0.42), residues: 142 loop : -1.02 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 974 HIS 0.002 0.001 HIS A 494 PHE 0.013 0.002 PHE B1055 TYR 0.011 0.001 TYR B1149 ARG 0.004 0.000 ARG B1179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 512 PHE cc_start: 0.6926 (t80) cc_final: 0.6671 (t80) REVERT: A 517 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8238 (pp) REVERT: A 532 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: B 1118 ASP cc_start: 0.6801 (t70) cc_final: 0.6542 (t70) REVERT: B 1130 ILE cc_start: 0.7784 (mp) cc_final: 0.7507 (tp) REVERT: B 1190 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6639 (tp30) REVERT: B 1203 GLU cc_start: 0.8893 (mp0) cc_final: 0.8600 (mt-10) REVERT: B 1225 SER cc_start: 0.8265 (OUTLIER) cc_final: 0.7963 (m) REVERT: B 1266 TRP cc_start: 0.6536 (t60) cc_final: 0.6139 (t60) outliers start: 22 outliers final: 14 residues processed: 76 average time/residue: 1.0148 time to fit residues: 80.6981 Evaluate side-chains 77 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 59 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 942 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain B residue 1190 GLU Chi-restraints excluded: chain B residue 1225 SER Chi-restraints excluded: chain B residue 1247 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B 988 GLN B1270 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4519 Z= 0.279 Angle : 0.536 11.493 6106 Z= 0.289 Chirality : 0.048 0.161 674 Planarity : 0.003 0.024 775 Dihedral : 5.258 34.258 687 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.30 % Allowed : 18.03 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.83 (0.34), residues: 527 helix: 1.19 (1.02), residues: 23 sheet: 0.31 (0.42), residues: 142 loop : -1.08 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 974 HIS 0.002 0.001 HIS A 494 PHE 0.015 0.002 PHE B1055 TYR 0.012 0.001 TYR B1149 ARG 0.003 0.000 ARG B1179 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 58 time to evaluate : 0.478 Fit side-chains REVERT: A 497 PHE cc_start: 0.7402 (t80) cc_final: 0.7129 (t80) REVERT: A 517 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8427 (pt) REVERT: B 1023 ARG cc_start: 0.6854 (mmm-85) cc_final: 0.6565 (mmt90) REVERT: B 1118 ASP cc_start: 0.6825 (t70) cc_final: 0.6569 (t70) REVERT: B 1130 ILE cc_start: 0.7826 (mp) cc_final: 0.7496 (tp) REVERT: B 1190 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6592 (tp30) REVERT: B 1203 GLU cc_start: 0.8880 (mp0) cc_final: 0.8577 (mt-10) REVERT: B 1225 SER cc_start: 0.8235 (OUTLIER) cc_final: 0.7945 (m) REVERT: B 1266 TRP cc_start: 0.6411 (t60) cc_final: 0.5997 (t60) outliers start: 21 outliers final: 14 residues processed: 72 average time/residue: 1.1134 time to fit residues: 83.6682 Evaluate side-chains 74 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 57 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 942 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain B residue 1190 GLU Chi-restraints excluded: chain B residue 1225 SER Chi-restraints excluded: chain B residue 1247 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B 988 GLN B1270 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4519 Z= 0.270 Angle : 0.530 11.801 6106 Z= 0.286 Chirality : 0.048 0.161 674 Planarity : 0.003 0.024 775 Dihedral : 5.206 32.708 687 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.10 % Allowed : 18.03 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.80 (0.34), residues: 527 helix: 1.25 (1.04), residues: 23 sheet: 0.30 (0.42), residues: 141 loop : -1.05 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B1266 HIS 0.001 0.001 HIS A 494 PHE 0.013 0.002 PHE B 941 TYR 0.012 0.001 TYR B1149 ARG 0.003 0.000 ARG B1179 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 58 time to evaluate : 0.486 Fit side-chains REVERT: A 497 PHE cc_start: 0.7377 (t80) cc_final: 0.7101 (t80) REVERT: A 517 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8437 (pt) REVERT: B 1023 ARG cc_start: 0.6850 (mmm-85) cc_final: 0.6562 (mmt90) REVERT: B 1118 ASP cc_start: 0.6823 (t70) cc_final: 0.6571 (t70) REVERT: B 1130 ILE cc_start: 0.7837 (mp) cc_final: 0.7525 (tp) REVERT: B 1190 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6605 (tp30) REVERT: B 1203 GLU cc_start: 0.8876 (mp0) cc_final: 0.8572 (mt-10) REVERT: B 1225 SER cc_start: 0.8249 (OUTLIER) cc_final: 0.7962 (m) REVERT: B 1266 TRP cc_start: 0.6495 (t60) cc_final: 0.6105 (t60) outliers start: 20 outliers final: 15 residues processed: 71 average time/residue: 1.1655 time to fit residues: 86.2379 Evaluate side-chains 75 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 942 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain B residue 1190 GLU Chi-restraints excluded: chain B residue 1225 SER Chi-restraints excluded: chain B residue 1247 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B1270 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4519 Z= 0.177 Angle : 0.485 12.428 6106 Z= 0.263 Chirality : 0.046 0.166 674 Planarity : 0.002 0.023 775 Dihedral : 4.944 30.789 687 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.69 % Allowed : 18.44 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.65 (0.35), residues: 527 helix: 1.39 (1.04), residues: 23 sheet: 0.42 (0.44), residues: 131 loop : -0.92 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1266 HIS 0.001 0.000 HIS A 494 PHE 0.014 0.001 PHE B 941 TYR 0.010 0.001 TYR B1149 ARG 0.004 0.000 ARG B1179 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 58 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 517 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8428 (pt) REVERT: A 532 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7500 (tt0) REVERT: B 1023 ARG cc_start: 0.6849 (mmm-85) cc_final: 0.6567 (mmt90) REVERT: B 1118 ASP cc_start: 0.6746 (t70) cc_final: 0.6498 (t70) REVERT: B 1130 ILE cc_start: 0.7820 (mp) cc_final: 0.7500 (tp) REVERT: B 1190 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6667 (tp30) REVERT: B 1203 GLU cc_start: 0.8854 (mp0) cc_final: 0.8556 (mt-10) REVERT: B 1225 SER cc_start: 0.8226 (OUTLIER) cc_final: 0.7952 (m) REVERT: B 1266 TRP cc_start: 0.6402 (t60) cc_final: 0.5987 (t60) outliers start: 18 outliers final: 12 residues processed: 71 average time/residue: 1.1309 time to fit residues: 83.7370 Evaluate side-chains 74 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 942 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1190 GLU Chi-restraints excluded: chain B residue 1225 SER Chi-restraints excluded: chain B residue 1247 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 0.0000 chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B1270 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.163446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.125926 restraints weight = 5061.723| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.45 r_work: 0.3283 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4519 Z= 0.232 Angle : 0.510 12.457 6106 Z= 0.275 Chirality : 0.047 0.163 674 Planarity : 0.003 0.029 775 Dihedral : 4.972 30.439 687 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.48 % Allowed : 18.65 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.69 (0.35), residues: 527 helix: 1.40 (1.05), residues: 23 sheet: 0.31 (0.42), residues: 141 loop : -0.95 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B1266 HIS 0.001 0.000 HIS A 494 PHE 0.013 0.002 PHE B1055 TYR 0.011 0.001 TYR B1149 ARG 0.005 0.000 ARG A 570 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2280.38 seconds wall clock time: 40 minutes 27.29 seconds (2427.29 seconds total)