Starting phenix.real_space_refine on Fri Jul 19 14:43:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k77_36935/07_2024/8k77_36935.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k77_36935/07_2024/8k77_36935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k77_36935/07_2024/8k77_36935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k77_36935/07_2024/8k77_36935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k77_36935/07_2024/8k77_36935.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k77_36935/07_2024/8k77_36935.cif" } resolution = 3.11 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= 1.097 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 5294 2.51 5 N 1362 2.21 5 O 1489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 147": "OE1" <-> "OE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A ASP 479": "OD1" <-> "OD2" Residue "A ASP 528": "OD1" <-> "OD2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "B ASP 902": "OD1" <-> "OD2" Residue "B TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 961": "OE1" <-> "OE2" Residue "B TYR 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1086": "OD1" <-> "OD2" Residue "B ASP 1089": "OD1" <-> "OD2" Residue "B ASP 1099": "OD1" <-> "OD2" Residue "B TYR 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1171": "OD1" <-> "OD2" Residue "B TYR 1181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1190": "OE1" <-> "OE2" Residue "B TYR 1191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1283": "OE1" <-> "OE2" Residue "B PHE 1284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1293": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8192 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: "C" 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'NAG': 2, 'VLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.33, per 1000 atoms: 0.65 Number of scatterers: 8192 At special positions: 0 Unit cell: (84.66, 83.83, 146.08, 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 1489 8.00 N 1362 7.00 C 5294 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 C 1 " - " NAG C 2 " BETA1-6 " NAG C 1 " - " FUC C 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 C 1 " - " ASN A 573 " Time building additional restraints: 3.43 Conformation dependent library (CDL) restraints added in 1.8 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: 26 helices and 5 sheets defined 43.5% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 137 through 160 Processing helix chain 'A' and resid 162 through 183 removed outlier: 3.700A pdb=" N ASP A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 197 Proline residue: A 191 - end of helix removed outlier: 4.108A pdb=" N LYS A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 removed outlier: 4.435A pdb=" N VAL A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 220 " --> pdb=" O MET A 216 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 250 Processing helix chain 'A' and resid 255 through 271 removed outlier: 4.491A pdb=" N GLY A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.568A pdb=" N ILE A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 284 No H-bonds generated for 'chain 'A' and resid 283 through 284' Processing helix chain 'A' and resid 285 through 288 removed outlier: 3.711A pdb=" N LYS A 288 " --> pdb=" O ALA A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 285 through 288' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.826A pdb=" N MET A 301 " --> pdb=" O CYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.725A 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: 3.669A pdb=" N PHE A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 386 Processing helix chain 'A' and resid 419 through 439 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 593 through 619 removed outlier: 3.729A pdb=" N VAL A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 608 " --> pdb=" O GLY A 604 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 609 " --> pdb=" O THR A 605 " (cutoff:3.500A) Proline residue: A 610 - end of helix removed outlier: 3.530A pdb=" N ILE A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 642 removed outlier: 3.836A pdb=" N MET A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 676 removed outlier: 3.791A pdb=" N ILE A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 707 Processing helix chain 'A' and resid 712 through 731 removed outlier: 4.000A pdb=" N ILE A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 933 removed outlier: 3.888A pdb=" N VAL B 933 " --> pdb=" O ASN B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 958 removed outlier: 3.639A pdb=" N LEU B 958 " --> pdb=" O LYS B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 1080 through 1092 Processing helix chain 'B' and resid 1265 through 1273 Processing sheet with id=AA1, first strand: chain 'A' and resid 485 through 492 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 485 through 492 current: chain 'A' and resid 514 through 527 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 514 through 527 current: chain 'B' and resid 1142 through 1144 Processing sheet with id=AA2, first strand: chain 'B' and resid 877 through 884 removed outlier: 3.720A 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: 3.856A pdb=" N ASP B1037 " --> pdb=" O ILE B1029 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE B1031 " --> pdb=" O LEU B1035 " (cutoff:3.500A) removed outlier: 5.471A 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: 7.659A pdb=" N MET B1054 " --> pdb=" O CYS B 967 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS B 967 " --> pdb=" O MET B1054 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LYS B1056 " --> pdb=" O ILE B 965 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE B 965 " --> pdb=" O LYS B1056 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N THR B 963 " --> pdb=" O LEU B 978 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU B 978 " --> pdb=" O THR B 963 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP B 974 " --> pdb=" O CYS B 967 " (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 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1134 through 1137 current: chain 'B' and resid 1179 through 1186 removed outlier: 5.618A pdb=" N ILE B1182 " --> pdb=" O LEU B1193 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1189 through 1194 current: chain 'B' and resid 1232 through 1240 removed outlier: 27.341A pdb=" N ASN B1233 " --> pdb=" O LEU B1254 " (cutoff:3.500A) removed outlier: 23.656A pdb=" N LEU B1254 " --> pdb=" O ASN B1233 " (cutoff:3.500A) removed outlier: 15.969A pdb=" N CYS B1235 " --> pdb=" O PHE B1252 " (cutoff:3.500A) removed outlier: 11.261A pdb=" N PHE B1252 " --> pdb=" O CYS B1235 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N MET B1237 " --> pdb=" O ILE B1250 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 1071 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: 2.44 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.18: 2 1.18 - 1.34: 2535 1.34 - 1.49: 2386 1.49 - 1.65: 3387 1.65 - 1.81: 76 Bond restraints: 8386 Sorted by residual: bond pdb=" CG PRO A 343 " pdb=" CD PRO A 343 " ideal model delta sigma weight residual 1.503 1.158 0.345 3.40e-02 8.65e+02 1.03e+02 bond pdb=" CB PRO A 343 " pdb=" CG PRO A 343 " ideal model delta sigma weight residual 1.492 1.021 0.471 5.00e-02 4.00e+02 8.89e+01 bond pdb=" C6 VLX A 803 " pdb=" N1 VLX A 803 " ideal model delta sigma weight residual 1.351 1.500 -0.149 2.00e-02 2.50e+03 5.54e+01 bond pdb=" C9 VLX A 803 " pdb=" N2 VLX A 803 " ideal model delta sigma weight residual 1.339 1.448 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" N PRO A 343 " pdb=" CA PRO A 343 " ideal model delta sigma weight residual 1.471 1.525 -0.054 1.32e-02 5.74e+03 1.67e+01 ... (remaining 8381 not shown) Histogram of bond angle deviations from ideal: 75.32 - 96.25: 2 96.25 - 117.17: 5864 117.17 - 138.10: 5472 138.10 - 159.03: 0 159.03 - 179.95: 1 Bond angle restraints: 11339 Sorted by residual: angle pdb=" CB PRO A 343 " pdb=" CG PRO A 343 " pdb=" CD PRO A 343 " ideal model delta sigma weight residual 106.10 179.95 -73.85 3.20e+00 9.77e-02 5.33e+02 angle pdb=" N PRO A 343 " pdb=" CD PRO A 343 " pdb=" CG PRO A 343 " ideal model delta sigma weight residual 103.20 76.47 26.73 1.50e+00 4.44e-01 3.18e+02 angle pdb=" CA PRO A 343 " pdb=" CB PRO A 343 " pdb=" CG PRO A 343 " ideal model delta sigma weight residual 104.50 75.32 29.18 1.90e+00 2.77e-01 2.36e+02 angle pdb=" CA PRO A 343 " pdb=" N PRO A 343 " pdb=" CD PRO A 343 " ideal model delta sigma weight residual 112.00 101.62 10.38 1.40e+00 5.10e-01 5.50e+01 angle pdb=" N PRO A 343 " pdb=" CA PRO A 343 " pdb=" C PRO A 343 " ideal model delta sigma weight residual 113.84 120.10 -6.26 1.30e+00 5.92e-01 2.32e+01 ... (remaining 11334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 4257 16.65 - 33.31: 502 33.31 - 49.96: 161 49.96 - 66.62: 34 66.62 - 83.27: 15 Dihedral angle restraints: 4969 sinusoidal: 2046 harmonic: 2923 Sorted by residual: dihedral pdb=" CA ASP A 528 " pdb=" CB ASP A 528 " pdb=" CG ASP A 528 " pdb=" OD1 ASP A 528 " ideal model delta sinusoidal sigma weight residual -30.00 -84.32 54.32 1 2.00e+01 2.50e-03 1.00e+01 dihedral pdb=" CA ASP A 620 " pdb=" CB ASP A 620 " pdb=" CG ASP A 620 " pdb=" OD1 ASP A 620 " ideal model delta sinusoidal sigma weight residual -30.00 -84.03 54.03 1 2.00e+01 2.50e-03 9.90e+00 dihedral pdb=" CG ARG B 996 " pdb=" CD ARG B 996 " pdb=" NE ARG B 996 " pdb=" CZ ARG B 996 " ideal model delta sinusoidal sigma weight residual 90.00 132.49 -42.49 2 1.50e+01 4.44e-03 9.73e+00 ... (remaining 4966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1217 0.113 - 0.226: 26 0.226 - 0.338: 1 0.338 - 0.451: 0 0.451 - 0.564: 1 Chirality restraints: 1245 Sorted by residual: 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 -1.84 -0.56 2.00e-01 2.50e+01 7.94e+00 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 -2.12 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.53e+00 ... (remaining 1242 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 440 " -0.070 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO A 441 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO A 441 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 441 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 342 " -0.071 5.00e-02 4.00e+02 9.80e-02 1.54e+01 pdb=" N PRO A 343 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 343 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 343 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 343 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C PRO A 343 " -0.044 2.00e-02 2.50e+03 pdb=" O PRO A 343 " 0.016 2.00e-02 2.50e+03 pdb=" N SER A 344 " 0.015 2.00e-02 2.50e+03 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 223 2.71 - 3.26: 8033 3.26 - 3.80: 13167 3.80 - 4.35: 16905 4.35 - 4.90: 28823 Nonbonded interactions: 67151 Sorted by model distance: nonbonded pdb=" O GLY B1129 " pdb=" OG SER B1207 " model vdw 2.160 2.440 nonbonded pdb=" OH TYR A 279 " pdb=" O PRO A 355 " model vdw 2.180 2.440 nonbonded pdb=" OH TYR B 934 " pdb=" O GLU B 939 " model vdw 2.206 2.440 nonbonded pdb=" NH2 ARG B 903 " pdb=" OH TYR B 905 " model vdw 2.234 2.520 nonbonded pdb=" OG1 THR B1195 " pdb=" O ILE B1205 " model vdw 2.263 2.440 ... (remaining 67146 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.300 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 : 0.008 0.471 8386 Z= 0.545 Angle : 0.987 73.852 11339 Z= 0.450 Chirality : 0.047 0.564 1245 Planarity : 0.005 0.106 1428 Dihedral : 16.518 83.272 3103 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 19.11 % Favored : 80.89 % 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: 0.80 (0.27), residues: 1006 helix: 1.90 (0.26), residues: 407 sheet: 0.20 (0.33), residues: 243 loop : -0.79 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 467 HIS 0.003 0.001 HIS A 494 PHE 0.019 0.001 PHE A 342 TYR 0.016 0.001 TYR A 306 ARG 0.014 0.001 ARG B 903 *********************** 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 105 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2508 time to fit residues: 35.1372 Evaluate side-chains 105 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 0.0270 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 91 optimal weight: 6.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS A 434 ASN ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 ASN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 ASN B 988 GLN B1003 GLN B1093 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.0611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8386 Z= 0.165 Angle : 0.461 5.566 11339 Z= 0.249 Chirality : 0.043 0.383 1245 Planarity : 0.003 0.058 1428 Dihedral : 5.667 59.538 1226 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.50 % Allowed : 16.61 % Favored : 80.89 % 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: 2.42 (0.26), residues: 412 sheet: 0.26 (0.33), residues: 237 loop : -0.78 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 467 HIS 0.005 0.001 HIS A 494 PHE 0.011 0.001 PHE A 459 TYR 0.013 0.001 TYR A 306 ARG 0.002 0.000 ARG B1175 *********************** 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 134 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.6350 (mtt) cc_final: 0.5091 (ttm) REVERT: A 442 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7362 (mt-10) REVERT: A 523 SER cc_start: 0.8729 (m) cc_final: 0.8298 (p) REVERT: B 1058 ASP cc_start: 0.7519 (m-30) cc_final: 0.7260 (m-30) REVERT: B 1085 LYS cc_start: 0.7662 (tppp) cc_final: 0.7174 (tppt) REVERT: B 1246 ASP cc_start: 0.7717 (p0) cc_final: 0.7298 (p0) outliers start: 22 outliers final: 13 residues processed: 128 average time/residue: 0.2178 time to fit residues: 37.7578 Evaluate side-chains 121 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 988 GLN Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1093 ASN Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1146 THR Chi-restraints excluded: chain B residue 1209 LEU 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: 9.9990 chunk 62 optimal weight: 0.0370 chunk 25 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 GLN B1003 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8386 Z= 0.314 Angle : 0.530 5.542 11339 Z= 0.285 Chirality : 0.045 0.322 1245 Planarity : 0.003 0.042 1428 Dihedral : 5.722 50.480 1226 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.53 % Allowed : 17.63 % Favored : 78.84 % 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: 2.29 (0.26), residues: 409 sheet: 0.17 (0.33), residues: 236 loop : -0.88 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 467 HIS 0.004 0.001 HIS A 494 PHE 0.013 0.002 PHE A 499 TYR 0.022 0.002 TYR A 306 ARG 0.002 0.000 ARG A 491 *********************** 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 134 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 103 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.6501 (mtt) cc_final: 0.5243 (ttm) REVERT: A 442 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7519 (mt-10) REVERT: A 523 SER cc_start: 0.8799 (m) cc_final: 0.8346 (p) REVERT: A 741 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7978 (tp) REVERT: B 1058 ASP cc_start: 0.7518 (m-30) cc_final: 0.7263 (m-30) REVERT: B 1085 LYS cc_start: 0.7664 (tppp) cc_final: 0.7223 (tppt) outliers start: 31 outliers final: 19 residues processed: 128 average time/residue: 0.2331 time to fit residues: 39.9854 Evaluate side-chains 116 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1146 THR 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: 0.3980 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 0.0040 chunk 97 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8386 Z= 0.177 Angle : 0.461 6.806 11339 Z= 0.250 Chirality : 0.042 0.306 1245 Planarity : 0.003 0.034 1428 Dihedral : 5.266 52.198 1226 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.07 % Allowed : 17.75 % Favored : 79.18 % 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: 1.14 (0.27), residues: 1006 helix: 2.40 (0.26), residues: 412 sheet: 0.26 (0.33), residues: 236 loop : -0.86 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 467 HIS 0.004 0.001 HIS A 494 PHE 0.011 0.001 PHE A 459 TYR 0.014 0.001 TYR A 306 ARG 0.002 0.000 ARG B1175 *********************** 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 129 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 102 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6510 (mtt) cc_final: 0.5206 (ttm) REVERT: A 442 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7516 (mt-10) REVERT: A 523 SER cc_start: 0.8817 (m) cc_final: 0.8354 (p) REVERT: B 1058 ASP cc_start: 0.7536 (m-30) cc_final: 0.7271 (m-30) REVERT: B 1085 LYS cc_start: 0.7668 (tppp) cc_final: 0.7185 (tppt) outliers start: 27 outliers final: 20 residues processed: 123 average time/residue: 0.2444 time to fit residues: 39.7217 Evaluate side-chains 120 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1146 THR Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1226 LYS Chi-restraints excluded: chain B residue 1270 GLN Chi-restraints excluded: chain B residue 1294 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 87 optimal weight: 0.0770 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN B 988 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8386 Z= 0.176 Angle : 0.446 5.537 11339 Z= 0.242 Chirality : 0.042 0.296 1245 Planarity : 0.003 0.029 1428 Dihedral : 4.953 51.733 1226 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.64 % Allowed : 17.86 % Favored : 78.50 % 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: 1.20 (0.27), residues: 1006 helix: 2.49 (0.26), residues: 411 sheet: 0.29 (0.33), residues: 236 loop : -0.87 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 467 HIS 0.004 0.001 HIS A 494 PHE 0.011 0.001 PHE A 459 TYR 0.014 0.001 TYR A 306 ARG 0.003 0.000 ARG B1064 *********************** 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 141 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 109 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6546 (mtt) cc_final: 0.5061 (ttm) REVERT: A 442 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7491 (mt-10) REVERT: A 513 ASN cc_start: 0.7977 (t0) cc_final: 0.7770 (m110) REVERT: A 523 SER cc_start: 0.8797 (m) cc_final: 0.8347 (p) REVERT: B 1058 ASP cc_start: 0.7571 (m-30) cc_final: 0.7291 (m-30) REVERT: B 1085 LYS cc_start: 0.7678 (tppp) cc_final: 0.7411 (tppt) outliers start: 32 outliers final: 24 residues processed: 133 average time/residue: 0.2246 time to fit residues: 40.3970 Evaluate side-chains 129 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1226 LYS Chi-restraints excluded: chain B residue 1270 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 94 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 988 GLN B1003 GLN B1233 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8386 Z= 0.190 Angle : 0.456 5.296 11339 Z= 0.246 Chirality : 0.042 0.296 1245 Planarity : 0.003 0.029 1428 Dihedral : 4.884 51.710 1226 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.64 % Allowed : 18.32 % Favored : 78.04 % 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: 1.22 (0.27), residues: 1006 helix: 2.50 (0.26), residues: 411 sheet: 0.36 (0.33), residues: 231 loop : -0.89 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 467 HIS 0.003 0.001 HIS A 367 PHE 0.012 0.001 PHE A 499 TYR 0.015 0.001 TYR A 306 ARG 0.002 0.000 ARG B1064 *********************** 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 141 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 109 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8111 (mp) REVERT: A 197 MET cc_start: 0.6530 (mtt) cc_final: 0.5051 (ttm) REVERT: A 442 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7547 (mt-10) REVERT: A 513 ASN cc_start: 0.8017 (t0) cc_final: 0.7736 (m110) REVERT: A 523 SER cc_start: 0.8784 (m) cc_final: 0.8335 (p) REVERT: B 1058 ASP cc_start: 0.7631 (m-30) cc_final: 0.7365 (m-30) REVERT: B 1085 LYS cc_start: 0.7675 (tppp) cc_final: 0.7413 (tppt) REVERT: B 1210 GLU cc_start: 0.7330 (mp0) cc_final: 0.7126 (mp0) outliers start: 32 outliers final: 25 residues processed: 133 average time/residue: 0.2182 time to fit residues: 39.4024 Evaluate side-chains 132 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 106 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1146 THR Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1226 LYS Chi-restraints excluded: chain B residue 1270 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN B 988 GLN B1003 GLN B1196 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8386 Z= 0.266 Angle : 0.509 7.327 11339 Z= 0.272 Chirality : 0.044 0.288 1245 Planarity : 0.003 0.028 1428 Dihedral : 5.279 50.590 1226 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.55 % Allowed : 17.86 % Favored : 77.59 % 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: 0.99 (0.27), residues: 1006 helix: 2.28 (0.26), residues: 411 sheet: 0.19 (0.35), residues: 206 loop : -0.85 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 333 HIS 0.003 0.001 HIS A 494 PHE 0.014 0.001 PHE A 459 TYR 0.020 0.002 TYR A 306 ARG 0.002 0.000 ARG A 163 *********************** 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 151 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 111 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7566 (mt-10) REVERT: A 449 MET cc_start: 0.6784 (mtp) cc_final: 0.6511 (mtp) REVERT: A 513 ASN cc_start: 0.8038 (t0) cc_final: 0.7760 (m110) REVERT: A 523 SER cc_start: 0.8771 (m) cc_final: 0.8345 (p) REVERT: A 533 GLU cc_start: 0.8175 (tp30) cc_final: 0.7934 (tp30) REVERT: A 741 LEU cc_start: 0.8407 (mt) cc_final: 0.8158 (tp) REVERT: A 742 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.6911 (tm-30) REVERT: B 1058 ASP cc_start: 0.7616 (m-30) cc_final: 0.7329 (m-30) REVERT: B 1085 LYS cc_start: 0.7727 (tppp) cc_final: 0.7474 (tppt) REVERT: B 1210 GLU cc_start: 0.7334 (mp0) cc_final: 0.7079 (mp0) outliers start: 40 outliers final: 29 residues processed: 141 average time/residue: 0.2153 time to fit residues: 41.3990 Evaluate side-chains 138 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 108 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 742 GLN Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 988 GLN Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1164 LYS Chi-restraints excluded: chain B residue 1180 VAL Chi-restraints excluded: chain B residue 1226 LYS Chi-restraints excluded: chain B residue 1270 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.0670 chunk 61 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8386 Z= 0.177 Angle : 0.464 6.755 11339 Z= 0.249 Chirality : 0.042 0.275 1245 Planarity : 0.003 0.029 1428 Dihedral : 4.979 50.827 1226 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.64 % Allowed : 19.34 % Favored : 77.02 % 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: 1.12 (0.27), residues: 1006 helix: 2.42 (0.26), residues: 411 sheet: 0.24 (0.35), residues: 206 loop : -0.82 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 467 HIS 0.004 0.001 HIS A 494 PHE 0.014 0.001 PHE A 499 TYR 0.014 0.001 TYR A 306 ARG 0.003 0.000 ARG B1064 *********************** 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 146 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 114 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6601 (mtt) cc_final: 0.5046 (ttm) REVERT: A 442 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7564 (mt-10) REVERT: A 449 MET cc_start: 0.6792 (mtp) cc_final: 0.6537 (mtp) REVERT: A 513 ASN cc_start: 0.8021 (t0) cc_final: 0.7762 (m110) REVERT: A 523 SER cc_start: 0.8742 (m) cc_final: 0.8339 (p) REVERT: A 533 GLU cc_start: 0.8159 (tp30) cc_final: 0.7922 (tp30) REVERT: A 741 LEU cc_start: 0.8273 (mt) cc_final: 0.8030 (tp) REVERT: A 742 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.6823 (tm-30) REVERT: B 1058 ASP cc_start: 0.7620 (m-30) cc_final: 0.7339 (m-30) REVERT: B 1064 ARG cc_start: 0.6548 (mtt180) cc_final: 0.5988 (ttt180) REVERT: B 1085 LYS cc_start: 0.7699 (tppp) cc_final: 0.7468 (tppt) REVERT: B 1209 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8104 (pp) REVERT: B 1210 GLU cc_start: 0.7306 (mp0) cc_final: 0.7067 (mp0) REVERT: B 1246 ASP cc_start: 0.8071 (p0) cc_final: 0.7863 (m-30) outliers start: 32 outliers final: 26 residues processed: 137 average time/residue: 0.2189 time to fit residues: 40.1793 Evaluate side-chains 138 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 110 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 742 GLN Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1164 LYS Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1226 LYS Chi-restraints excluded: chain B residue 1254 LEU Chi-restraints excluded: chain B residue 1270 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.0970 chunk 85 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8386 Z= 0.180 Angle : 0.457 6.753 11339 Z= 0.246 Chirality : 0.042 0.275 1245 Planarity : 0.003 0.028 1428 Dihedral : 4.794 49.351 1226 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.53 % Allowed : 19.57 % Favored : 76.91 % 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: 1.19 (0.27), residues: 1006 helix: 2.46 (0.26), residues: 411 sheet: 0.30 (0.35), residues: 203 loop : -0.77 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 467 HIS 0.004 0.001 HIS A 494 PHE 0.013 0.001 PHE A 499 TYR 0.014 0.001 TYR A 595 ARG 0.002 0.000 ARG A 491 *********************** 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 141 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 110 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7553 (mt-10) REVERT: A 449 MET cc_start: 0.6811 (mtp) cc_final: 0.6567 (mtp) REVERT: A 513 ASN cc_start: 0.8039 (t0) cc_final: 0.7813 (m110) REVERT: A 523 SER cc_start: 0.8737 (m) cc_final: 0.8337 (p) REVERT: A 533 GLU cc_start: 0.8164 (tp30) cc_final: 0.7942 (tp30) REVERT: A 741 LEU cc_start: 0.8331 (mt) cc_final: 0.8072 (tp) REVERT: A 742 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.6847 (tm-30) REVERT: B 1058 ASP cc_start: 0.7590 (m-30) cc_final: 0.7291 (m-30) REVERT: B 1064 ARG cc_start: 0.6630 (mtt180) cc_final: 0.5952 (ttt180) REVERT: B 1209 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8063 (pp) REVERT: B 1210 GLU cc_start: 0.7353 (mp0) cc_final: 0.7132 (mp0) REVERT: B 1246 ASP cc_start: 0.8140 (p0) cc_final: 0.7839 (m-30) outliers start: 31 outliers final: 28 residues processed: 131 average time/residue: 0.2359 time to fit residues: 41.9687 Evaluate side-chains 137 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 107 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 742 GLN Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1164 LYS Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1226 LYS Chi-restraints excluded: chain B residue 1254 LEU Chi-restraints excluded: chain B residue 1270 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 92 optimal weight: 0.1980 chunk 80 optimal weight: 0.0370 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 GLN B1003 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8386 Z= 0.180 Angle : 0.462 7.391 11339 Z= 0.247 Chirality : 0.042 0.267 1245 Planarity : 0.003 0.028 1428 Dihedral : 4.751 48.960 1226 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.75 % Allowed : 19.57 % Favored : 76.68 % 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: 1.21 (0.27), residues: 1006 helix: 2.46 (0.26), residues: 410 sheet: 0.35 (0.35), residues: 203 loop : -0.75 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 467 HIS 0.004 0.001 HIS A 494 PHE 0.013 0.001 PHE A 499 TYR 0.014 0.001 TYR A 306 ARG 0.002 0.000 ARG A 491 ********************** 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 143 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 110 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 MET cc_start: 0.4337 (mmp) cc_final: 0.4083 (mmp) REVERT: A 442 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7587 (mt-10) REVERT: A 449 MET cc_start: 0.6783 (mtp) cc_final: 0.6538 (mtp) REVERT: A 513 ASN cc_start: 0.8060 (t0) cc_final: 0.7832 (m110) REVERT: A 523 SER cc_start: 0.8734 (m) cc_final: 0.8345 (p) REVERT: A 533 GLU cc_start: 0.8168 (tp30) cc_final: 0.7952 (tp30) REVERT: A 741 LEU cc_start: 0.8321 (mt) cc_final: 0.8088 (tp) REVERT: A 742 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.6707 (tm-30) REVERT: B 1058 ASP cc_start: 0.7589 (m-30) cc_final: 0.7270 (m-30) REVERT: B 1064 ARG cc_start: 0.6612 (mtt180) cc_final: 0.5997 (ttt180) REVERT: B 1246 ASP cc_start: 0.8135 (p0) cc_final: 0.7747 (m-30) outliers start: 33 outliers final: 29 residues processed: 132 average time/residue: 0.2267 time to fit residues: 40.1445 Evaluate side-chains 140 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 522 LYS Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 742 GLN Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 988 GLN Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1164 LYS Chi-restraints excluded: chain B residue 1226 LYS Chi-restraints excluded: chain B residue 1254 LEU Chi-restraints excluded: chain B residue 1270 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 80 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 GLN B1003 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.199366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.154009 restraints weight = 8931.791| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.25 r_work: 0.3556 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 8386 Z= 0.212 Angle : 0.869 59.151 11339 Z= 0.525 Chirality : 0.043 0.345 1245 Planarity : 0.003 0.028 1428 Dihedral : 4.764 48.961 1226 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.19 % Allowed : 20.14 % Favored : 76.68 % Cbeta Deviations : 0.11 % 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: 2.47 (0.26), residues: 410 sheet: 0.31 (0.36), residues: 203 loop : -0.76 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 467 HIS 0.004 0.001 HIS A 494 PHE 0.012 0.001 PHE A 499 TYR 0.014 0.001 TYR A 306 ARG 0.001 0.000 ARG A 491 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2076.21 seconds wall clock time: 37 minutes 31.99 seconds (2251.99 seconds total)