Starting phenix.real_space_refine on Fri Jul 19 14:16:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8js9_36617/07_2024/8js9_36617.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8js9_36617/07_2024/8js9_36617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8js9_36617/07_2024/8js9_36617.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8js9_36617/07_2024/8js9_36617.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8js9_36617/07_2024/8js9_36617.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8js9_36617/07_2024/8js9_36617.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.098 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 47 5.16 5 C 5283 2.51 5 N 1360 2.21 5 O 1487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 146": "OE1" <-> "OE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A ASP 227": "OD1" <-> "OD2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A ASP 680": "OD1" <-> "OD2" Residue "A PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 907": "OD1" <-> "OD2" Residue "B GLU 920": "OE1" <-> "OE2" Residue "B GLU 961": "OE1" <-> "OE2" Residue "B GLU 982": "OE1" <-> "OE2" Residue "B ASP 1009": "OD1" <-> "OD2" Residue "B ASP 1076": "OD1" <-> "OD2" Residue "B GLU 1081": "OE1" <-> "OE2" Residue "B PHE 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1118": "OD1" <-> "OD2" Residue "B GLU 1156": "OE1" <-> "OE2" Residue "B GLU 1203": "OE1" <-> "OE2" Residue "B ASP 1246": "OD1" <-> "OD2" Residue "B PHE 1249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1289": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8177 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4674 Classifications: {'peptide': 592} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 576} Chain breaks: 1 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: 5.13, per 1000 atoms: 0.63 Number of scatterers: 8177 At special positions: 0 Unit cell: (83, 81.34, 148.57, 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 47 16.00 O 1487 8.00 N 1360 7.00 C 5283 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 801 " - " ASN A 498 " " NAG A 802 " - " ASN A 548 " " NAG E 1 " - " ASN A 573 " Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 1.6 seconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1866 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 7 sheets defined 43.6% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 137 through 160 Processing helix chain 'A' and resid 162 through 183 removed outlier: 3.586A pdb=" N ASP A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 198 Proline residue: A 191 - end of helix removed outlier: 3.982A pdb=" N LYS A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 removed outlier: 3.536A pdb=" N LEU A 207 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.729A pdb=" N PHE A 220 " --> pdb=" O MET A 216 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 250 removed outlier: 3.504A pdb=" N SER A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 270 Processing helix chain 'A' and resid 271 through 281 removed outlier: 3.727A pdb=" N ILE A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 297 through 315 removed outlier: 4.269A pdb=" N MET A 301 " --> pdb=" O CYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.812A pdb=" N VAL A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 357 through 364 removed outlier: 3.548A pdb=" N PHE A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 386 removed outlier: 3.906A pdb=" N ALA A 370 " --> pdb=" O LYS A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 439 removed outlier: 3.507A pdb=" N PHE A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 483 Proline residue: A 469 - end of helix Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 592 through 605 removed outlier: 3.789A pdb=" N MET A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 619 removed outlier: 4.238A pdb=" N GLY A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 642 removed outlier: 3.565A pdb=" N MET A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 676 removed outlier: 3.767A pdb=" N ILE A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 706 Processing helix chain 'A' and resid 712 through 731 removed outlier: 3.510A pdb=" N ILE A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 933 removed outlier: 3.819A pdb=" N VAL B 933 " --> pdb=" O ASN B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 958 removed outlier: 3.667A pdb=" N ASN B 957 " --> pdb=" O SER B 954 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 958 " --> pdb=" O LYS B 955 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 954 through 958' Processing helix chain 'B' and resid 1080 through 1092 Processing helix chain 'B' and resid 1210 through 1214 removed outlier: 3.846A 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 496 removed outlier: 6.129A pdb=" N GLY A 509 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG A 491 " --> pdb=" O GLY A 509 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N TYR A 511 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU A 493 " --> pdb=" O TYR A 511 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASN A 513 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A 495 " --> pdb=" O ASN A 513 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU A 502 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N SER A 525 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLN A 504 " --> pdb=" O SER A 525 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N GLU A 527 " --> pdb=" O GLN A 504 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N HIS A 506 " --> pdb=" O GLU A 527 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 520 through 527 current: chain 'B' and resid 1142 through 1145 Processing sheet with id=AA2, first strand: chain 'B' and resid 877 through 884 removed outlier: 3.549A pdb=" N ASP B 887 " --> pdb=" O LYS B 884 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 887 through 890 current: chain 'B' and resid 914 through 917 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 914 through 917 current: chain 'B' and resid 1015 through 1021 removed outlier: 4.271A pdb=" N ASP B1037 " --> pdb=" O ILE B1029 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE B1031 " --> pdb=" O LEU B1035 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU B1035 " --> pdb=" O ILE B1031 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 897 through 900 removed outlier: 7.572A pdb=" N LYS B1052 " --> pdb=" O ILE B 968 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE B 968 " --> pdb=" O LYS B1052 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE B 964 " --> pdb=" O LYS B1056 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ASP B1058 " --> pdb=" O TYR B 962 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR B 962 " --> pdb=" O ASP B1058 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 976 " --> pdb=" O ILE B 964 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ASN B 966 " --> pdb=" O TRP B 974 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N TRP B 974 " --> pdb=" O ASN B 966 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1112 through 1115 Processing sheet with id=AA5, first strand: chain 'B' and resid 1122 through 1125 Processing sheet with id=AA6, first strand: chain 'B' and resid 1159 through 1164 removed outlier: 3.931A pdb=" N LYS B1159 " --> pdb=" O VAL B1185 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1189 through 1190 current: chain 'B' and resid 1232 through 1240 removed outlier: 27.213A pdb=" N ASN B1233 " --> pdb=" O LEU B1254 " (cutoff:3.500A) removed outlier: 23.621A pdb=" N LEU B1254 " --> pdb=" O ASN B1233 " (cutoff:3.500A) removed outlier: 15.861A pdb=" N CYS B1235 " --> pdb=" O PHE B1252 " (cutoff:3.500A) removed outlier: 11.185A pdb=" N PHE B1252 " --> pdb=" O CYS B1235 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N MET B1237 " --> pdb=" O ILE B1250 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY B1248 " --> pdb=" O LEU B1239 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1192 through 1194 377 hydrogen bonds defined for protein. 1086 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: 2.53 Time building geometry restraints manager: 3.58 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: 2574 1.34 - 1.46: 1944 1.46 - 1.58: 3777 1.58 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 8371 Sorted by residual: bond pdb=" C1 NAG A 802 " pdb=" O5 NAG A 802 " ideal model delta sigma weight residual 1.406 1.498 -0.092 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C1 NAG A 801 " pdb=" O5 NAG A 801 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.30e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" C5 NAG A 802 " pdb=" O5 NAG A 802 " ideal model delta sigma weight residual 1.413 1.439 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" CA THR A 500 " pdb=" CB THR A 500 " ideal model delta sigma weight residual 1.527 1.558 -0.031 2.48e-02 1.63e+03 1.52e+00 ... (remaining 8366 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.32: 145 106.32 - 113.25: 4445 113.25 - 120.18: 3001 120.18 - 127.11: 3650 127.11 - 134.04: 78 Bond angle restraints: 11319 Sorted by residual: angle pdb=" C LYS A 621 " pdb=" N ILE A 622 " pdb=" CA ILE A 622 " ideal model delta sigma weight residual 122.63 117.75 4.88 1.19e+00 7.06e-01 1.68e+01 angle pdb=" N LYS B1026 " pdb=" CA LYS B1026 " pdb=" C LYS B1026 " ideal model delta sigma weight residual 107.73 113.65 -5.92 1.61e+00 3.86e-01 1.35e+01 angle pdb=" CA PRO A 343 " pdb=" N PRO A 343 " pdb=" CD PRO A 343 " ideal model delta sigma weight residual 112.00 107.36 4.64 1.40e+00 5.10e-01 1.10e+01 angle pdb=" C SER A 272 " pdb=" N ILE A 273 " pdb=" CA ILE A 273 " ideal model delta sigma weight residual 120.33 122.65 -2.32 8.00e-01 1.56e+00 8.38e+00 angle pdb=" N ARG A 444 " pdb=" CA ARG A 444 " pdb=" C ARG A 444 " ideal model delta sigma weight residual 113.18 109.48 3.70 1.33e+00 5.65e-01 7.75e+00 ... (remaining 11314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.61: 4570 22.61 - 45.22: 333 45.22 - 67.83: 31 67.83 - 90.44: 11 90.44 - 113.05: 3 Dihedral angle restraints: 4948 sinusoidal: 2025 harmonic: 2923 Sorted by residual: dihedral pdb=" CA VAL B1144 " pdb=" C VAL B1144 " pdb=" N THR B1145 " pdb=" CA THR B1145 " ideal model delta harmonic sigma weight residual 180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" C2 NAG A 802 " pdb=" C1 NAG A 802 " pdb=" O5 NAG A 802 " pdb=" C5 NAG A 802 " ideal model delta sinusoidal sigma weight residual -62.96 50.09 -113.05 1 3.00e+01 1.11e-03 1.48e+01 dihedral pdb=" C1 NAG A 802 " pdb=" C5 NAG A 802 " pdb=" O5 NAG A 802 " pdb=" C6 NAG A 802 " ideal model delta sinusoidal sigma weight residual 171.16 -81.82 -107.02 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 4945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1137 0.081 - 0.161: 104 0.161 - 0.242: 1 0.242 - 0.323: 0 0.323 - 0.403: 1 Chirality restraints: 1243 Sorted by residual: chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 548 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 498 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CA ILE B 983 " pdb=" N ILE B 983 " pdb=" C ILE B 983 " pdb=" CB ILE B 983 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 1240 not shown) Planarity restraints: 1429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B1117 " -0.004 2.00e-02 2.50e+03 1.16e-02 2.34e+00 pdb=" CG PHE B1117 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE B1117 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B1117 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE B1117 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B1117 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B1117 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 342 " -0.025 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO A 343 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 343 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 343 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 609 " 0.023 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO A 610 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 610 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 610 " 0.020 5.00e-02 4.00e+02 ... (remaining 1426 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 127 2.69 - 3.24: 7788 3.24 - 3.79: 12821 3.79 - 4.35: 17377 4.35 - 4.90: 29401 Nonbonded interactions: 67514 Sorted by model distance: nonbonded pdb=" OD2 ASP A 227 " pdb=" OG1 THR A 684 " model vdw 2.136 2.440 nonbonded pdb=" OH TYR A 279 " pdb=" O PRO A 355 " model vdw 2.214 2.440 nonbonded pdb=" OH TYR A 152 " pdb=" O GLU A 282 " model vdw 2.254 2.440 nonbonded pdb=" OD1 ASN B1216 " pdb=" ND2 ASN B1242 " model vdw 2.262 2.520 nonbonded pdb=" NE2 GLN A 323 " pdb=" O TYR A 328 " model vdw 2.274 2.520 ... (remaining 67509 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: 1.860 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.910 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 : 0.004 0.092 8371 Z= 0.247 Angle : 0.550 7.461 11319 Z= 0.311 Chirality : 0.044 0.403 1243 Planarity : 0.003 0.037 1426 Dihedral : 15.239 113.055 3082 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.23 % Allowed : 11.26 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.68 (0.27), residues: 1006 helix: 1.75 (0.26), residues: 405 sheet: 0.67 (0.43), residues: 158 loop : -0.87 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 333 HIS 0.003 0.000 HIS B1253 PHE 0.024 0.002 PHE B1117 TYR 0.015 0.001 TYR A 306 ARG 0.003 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 1.002 Fit side-chains REVERT: A 286 GLN cc_start: 0.7784 (tt0) cc_final: 0.7375 (tm-30) REVERT: A 568 ASN cc_start: 0.8391 (t0) cc_final: 0.7918 (t0) REVERT: B 905 TYR cc_start: 0.8057 (m-80) cc_final: 0.7832 (m-80) REVERT: B 1118 ASP cc_start: 0.7198 (t70) cc_final: 0.6825 (t70) outliers start: 2 outliers final: 1 residues processed: 110 average time/residue: 0.2469 time to fit residues: 35.8930 Evaluate side-chains 110 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 942 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 960 ASN B1006 ASN B1022 ASN B1240 GLN B1270 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.0459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8371 Z= 0.207 Angle : 0.485 10.986 11319 Z= 0.260 Chirality : 0.043 0.343 1243 Planarity : 0.003 0.033 1426 Dihedral : 6.410 81.251 1206 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.48 % Allowed : 11.49 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.84 (0.27), residues: 1006 helix: 1.95 (0.26), residues: 408 sheet: 0.56 (0.41), residues: 163 loop : -0.80 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 333 HIS 0.002 0.001 HIS A 494 PHE 0.021 0.001 PHE A 497 TYR 0.015 0.001 TYR A 306 ARG 0.002 0.000 ARG B1061 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 0.939 Fit side-chains REVERT: A 318 TYR cc_start: 0.7744 (m-80) cc_final: 0.7537 (m-80) REVERT: A 513 ASN cc_start: 0.8689 (t0) cc_final: 0.8188 (t0) REVERT: A 533 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: B 905 TYR cc_start: 0.8055 (m-80) cc_final: 0.7837 (m-80) outliers start: 13 outliers final: 6 residues processed: 125 average time/residue: 0.2259 time to fit residues: 37.6945 Evaluate side-chains 116 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1203 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 81 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 988 GLN B1270 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8371 Z= 0.157 Angle : 0.443 9.238 11319 Z= 0.238 Chirality : 0.041 0.174 1243 Planarity : 0.003 0.032 1426 Dihedral : 5.032 36.983 1205 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.25 % Allowed : 11.72 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.96 (0.27), residues: 1006 helix: 2.11 (0.26), residues: 412 sheet: 0.58 (0.41), residues: 163 loop : -0.81 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 333 HIS 0.001 0.000 HIS A 331 PHE 0.018 0.001 PHE B1117 TYR 0.012 0.001 TYR A 306 ARG 0.002 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 0.890 Fit side-chains REVERT: A 245 PHE cc_start: 0.8362 (m-80) cc_final: 0.8073 (m-80) REVERT: A 444 ARG cc_start: 0.6059 (ttt180) cc_final: 0.5575 (ttp-110) REVERT: A 491 ARG cc_start: 0.7516 (tmm-80) cc_final: 0.7315 (tpp80) REVERT: A 513 ASN cc_start: 0.8826 (t0) cc_final: 0.8619 (t0) REVERT: A 533 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: A 655 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7900 (tp) REVERT: B 905 TYR cc_start: 0.8065 (m-80) cc_final: 0.7842 (m-80) REVERT: B 920 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7146 (mm-30) outliers start: 11 outliers final: 7 residues processed: 124 average time/residue: 0.2245 time to fit residues: 37.4636 Evaluate side-chains 119 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain B residue 923 THR 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 1203 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 0.0170 chunk 97 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN B1022 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8371 Z= 0.232 Angle : 0.471 5.274 11319 Z= 0.255 Chirality : 0.043 0.162 1243 Planarity : 0.003 0.032 1426 Dihedral : 4.890 39.875 1205 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.59 % Allowed : 12.06 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.95 (0.27), residues: 1006 helix: 2.06 (0.26), residues: 409 sheet: 0.40 (0.42), residues: 152 loop : -0.64 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 333 HIS 0.003 0.001 HIS B1253 PHE 0.017 0.001 PHE A 497 TYR 0.016 0.001 TYR A 306 ARG 0.002 0.000 ARG B1061 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 0.893 Fit side-chains REVERT: A 444 ARG cc_start: 0.6092 (ttt180) cc_final: 0.5597 (ttp-110) REVERT: A 513 ASN cc_start: 0.8848 (t0) cc_final: 0.8588 (t0) REVERT: A 533 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: B 905 TYR cc_start: 0.8108 (m-80) cc_final: 0.7812 (m-80) REVERT: B 925 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7028 (tt0) outliers start: 14 outliers final: 7 residues processed: 122 average time/residue: 0.2139 time to fit residues: 35.4174 Evaluate side-chains 116 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 925 GLU Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1020 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN B 988 GLN B1245 ASN ** B1265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8371 Z= 0.259 Angle : 0.488 5.354 11319 Z= 0.264 Chirality : 0.043 0.154 1243 Planarity : 0.003 0.031 1426 Dihedral : 4.862 41.049 1205 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.71 % Allowed : 13.08 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.86 (0.27), residues: 1006 helix: 2.00 (0.26), residues: 408 sheet: 0.38 (0.41), residues: 163 loop : -0.74 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 333 HIS 0.002 0.001 HIS B1253 PHE 0.032 0.002 PHE A 497 TYR 0.016 0.001 TYR A 306 ARG 0.003 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 0.943 Fit side-chains REVERT: A 444 ARG cc_start: 0.6040 (ttt180) cc_final: 0.5582 (ttp-110) REVERT: A 513 ASN cc_start: 0.8867 (t0) cc_final: 0.8194 (t0) REVERT: A 533 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: A 568 ASN cc_start: 0.8406 (t0) cc_final: 0.8085 (t0) REVERT: B 905 TYR cc_start: 0.8170 (m-80) cc_final: 0.7877 (m-80) REVERT: B 925 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6699 (tt0) outliers start: 15 outliers final: 8 residues processed: 125 average time/residue: 0.2240 time to fit residues: 37.4383 Evaluate side-chains 117 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 925 GLU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN B 988 GLN ** B1265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8371 Z= 0.189 Angle : 0.449 5.300 11319 Z= 0.245 Chirality : 0.042 0.150 1243 Planarity : 0.003 0.030 1426 Dihedral : 4.704 41.961 1205 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.28 % Allowed : 13.31 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.96 (0.27), residues: 1006 helix: 2.11 (0.26), residues: 409 sheet: 0.44 (0.40), residues: 163 loop : -0.74 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 333 HIS 0.001 0.000 HIS B1253 PHE 0.024 0.001 PHE A 497 TYR 0.013 0.001 TYR A 306 ARG 0.002 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 444 ARG cc_start: 0.6042 (ttt180) cc_final: 0.5590 (ttp-110) REVERT: A 513 ASN cc_start: 0.8861 (t0) cc_final: 0.8642 (t0) REVERT: A 533 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: A 568 ASN cc_start: 0.8408 (t0) cc_final: 0.8089 (t0) REVERT: B 905 TYR cc_start: 0.8167 (m-80) cc_final: 0.7895 (m-80) REVERT: B 925 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6529 (tp30) outliers start: 20 outliers final: 12 residues processed: 122 average time/residue: 0.2272 time to fit residues: 37.1285 Evaluate side-chains 120 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 925 GLU 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 1024 LEU Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 60 optimal weight: 0.5980 chunk 59 optimal weight: 0.4980 chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN B 988 GLN B1245 ASN ** B1265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8371 Z= 0.150 Angle : 0.432 5.773 11319 Z= 0.235 Chirality : 0.041 0.148 1243 Planarity : 0.003 0.030 1426 Dihedral : 4.529 41.875 1205 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.05 % Allowed : 13.08 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.27), residues: 1006 helix: 2.22 (0.26), residues: 411 sheet: 0.47 (0.40), residues: 164 loop : -0.79 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 333 HIS 0.001 0.000 HIS A 331 PHE 0.022 0.001 PHE A 497 TYR 0.011 0.001 TYR A 306 ARG 0.002 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 0.924 Fit side-chains REVERT: A 444 ARG cc_start: 0.6029 (ttt180) cc_final: 0.5588 (ttp-110) REVERT: A 479 ASP cc_start: 0.8051 (t0) cc_final: 0.7829 (t0) REVERT: A 513 ASN cc_start: 0.8856 (t0) cc_final: 0.8646 (t0) REVERT: A 533 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: A 568 ASN cc_start: 0.8423 (t0) cc_final: 0.8098 (t0) REVERT: B 905 TYR cc_start: 0.8122 (m-80) cc_final: 0.7862 (m-80) REVERT: B 925 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7044 (tt0) REVERT: B 942 SER cc_start: 0.9083 (OUTLIER) cc_final: 0.8876 (p) outliers start: 18 outliers final: 14 residues processed: 122 average time/residue: 0.2226 time to fit residues: 36.8521 Evaluate side-chains 125 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 925 GLU 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 1024 LEU Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 61 optimal weight: 7.9990 chunk 66 optimal weight: 0.0270 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 0.0040 chunk 85 optimal weight: 3.9990 overall best weight: 0.2850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN B 988 GLN ** B1265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8371 Z= 0.115 Angle : 0.408 5.546 11319 Z= 0.223 Chirality : 0.040 0.158 1243 Planarity : 0.002 0.030 1426 Dihedral : 4.292 40.358 1205 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.48 % Allowed : 14.11 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.20 (0.27), residues: 1006 helix: 2.38 (0.26), residues: 410 sheet: 0.53 (0.41), residues: 162 loop : -0.68 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 333 HIS 0.001 0.000 HIS A 474 PHE 0.020 0.001 PHE A 497 TYR 0.008 0.001 TYR B1149 ARG 0.003 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.922 Fit side-chains REVERT: A 444 ARG cc_start: 0.6019 (ttt180) cc_final: 0.5570 (ttp-110) REVERT: A 479 ASP cc_start: 0.8036 (t0) cc_final: 0.7791 (t0) REVERT: A 513 ASN cc_start: 0.8833 (t0) cc_final: 0.8633 (t0) REVERT: A 533 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: A 568 ASN cc_start: 0.8432 (t0) cc_final: 0.8085 (t0) REVERT: A 680 ASP cc_start: 0.8029 (p0) cc_final: 0.7733 (t0) REVERT: B 905 TYR cc_start: 0.8102 (m-80) cc_final: 0.7830 (m-80) REVERT: B 925 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6467 (tp30) REVERT: B 937 MET cc_start: 0.3365 (tpp) cc_final: 0.2758 (tpp) outliers start: 13 outliers final: 10 residues processed: 132 average time/residue: 0.2212 time to fit residues: 39.2568 Evaluate side-chains 122 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 925 GLU Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1024 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1022 ASN B1188 ASN ** B1265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8371 Z= 0.222 Angle : 0.461 5.324 11319 Z= 0.250 Chirality : 0.043 0.166 1243 Planarity : 0.003 0.030 1426 Dihedral : 4.446 40.926 1205 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.93 % Allowed : 13.65 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.06 (0.27), residues: 1006 helix: 2.27 (0.26), residues: 409 sheet: 0.58 (0.40), residues: 162 loop : -0.81 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 467 HIS 0.002 0.000 HIS B1253 PHE 0.021 0.001 PHE A 497 TYR 0.016 0.001 TYR A 306 ARG 0.003 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 0.938 Fit side-chains REVERT: A 444 ARG cc_start: 0.6067 (ttt180) cc_final: 0.5590 (ttp-110) REVERT: A 479 ASP cc_start: 0.8076 (t0) cc_final: 0.7870 (t0) REVERT: A 513 ASN cc_start: 0.8861 (t0) cc_final: 0.8629 (t0) REVERT: A 533 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: A 568 ASN cc_start: 0.8432 (t0) cc_final: 0.8102 (t0) REVERT: B 905 TYR cc_start: 0.8172 (m-80) cc_final: 0.7936 (m-80) REVERT: B 925 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6610 (mt-10) outliers start: 17 outliers final: 13 residues processed: 127 average time/residue: 0.2235 time to fit residues: 38.4367 Evaluate side-chains 125 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain B residue 925 GLU 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 1024 LEU Chi-restraints excluded: chain B residue 1225 SER Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 GLN B1245 ASN ** B1265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8371 Z= 0.263 Angle : 0.486 6.573 11319 Z= 0.264 Chirality : 0.044 0.170 1243 Planarity : 0.003 0.030 1426 Dihedral : 4.616 42.983 1205 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.82 % Allowed : 14.45 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.27), residues: 1006 helix: 2.06 (0.26), residues: 411 sheet: 0.52 (0.41), residues: 162 loop : -0.84 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 333 HIS 0.002 0.001 HIS A 331 PHE 0.021 0.001 PHE A 497 TYR 0.017 0.001 TYR A 306 ARG 0.003 0.000 ARG A 145 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 1.022 Fit side-chains REVERT: A 444 ARG cc_start: 0.6109 (ttt180) cc_final: 0.5649 (ttp-110) REVERT: A 513 ASN cc_start: 0.8892 (t0) cc_final: 0.8632 (t0) REVERT: A 533 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: B 905 TYR cc_start: 0.8165 (m-80) cc_final: 0.7917 (m-80) REVERT: B 925 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6607 (mt-10) outliers start: 16 outliers final: 11 residues processed: 127 average time/residue: 0.2223 time to fit residues: 38.0849 Evaluate side-chains 123 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 925 GLU 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 1024 LEU Chi-restraints excluded: chain B residue 1225 SER Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 GLN B1188 ASN ** B1265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.165437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.123861 restraints weight = 8964.875| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.28 r_work: 0.3107 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8371 Z= 0.208 Angle : 0.466 6.626 11319 Z= 0.255 Chirality : 0.043 0.175 1243 Planarity : 0.003 0.030 1426 Dihedral : 4.565 43.846 1205 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.59 % Allowed : 14.90 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.27), residues: 1006 helix: 2.08 (0.26), residues: 411 sheet: 0.49 (0.40), residues: 162 loop : -0.84 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B1266 HIS 0.002 0.000 HIS B1253 PHE 0.021 0.001 PHE A 497 TYR 0.014 0.001 TYR A 306 ARG 0.006 0.000 ARG B1269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2254.80 seconds wall clock time: 40 minutes 45.08 seconds (2445.08 seconds total)