Starting phenix.real_space_refine on Sat Dec 28 09:03:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8js9_36617/12_2024/8js9_36617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8js9_36617/12_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/cci-nas-00/data/ceres_data/8js9_36617/12_2024/8js9_36617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8js9_36617/12_2024/8js9_36617.map" model { file = "/net/cci-nas-00/data/ceres_data/8js9_36617/12_2024/8js9_36617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8js9_36617/12_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. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.40, per 1000 atoms: 0.66 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 - 3.00 Amino acid : True - 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: 2.27 Conformation dependent library (CDL) restraints added in 971.3 milliseconds 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: 2.43 Time building geometry restraints manager: 2.55 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: 0.00 - 1.49: 11065 1.49 - 2.98: 215 2.98 - 4.48: 28 4.48 - 5.97: 7 5.97 - 7.46: 4 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 3.040 nonbonded pdb=" OH TYR A 279 " pdb=" O PRO A 355 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR A 152 " pdb=" O GLU A 282 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASN B1216 " pdb=" ND2 ASN B1242 " model vdw 2.262 3.120 nonbonded pdb=" NE2 GLN A 323 " pdb=" O TYR A 328 " model vdw 2.274 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 1.930 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.440 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.710 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.831 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: 0.2787 time to fit residues: 40.3493 Evaluate side-chains 110 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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: 0.9980 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 612 ASN B 960 ASN B1006 ASN B1240 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.0572 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= 0.232 Angle : 0.506 10.465 11319 Z= 0.272 Chirality : 0.044 0.377 1243 Planarity : 0.003 0.033 1426 Dihedral : 6.517 83.977 1206 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.37 % Allowed : 11.26 % Favored : 87.37 % 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: 0.77 (0.27), residues: 1006 helix: 1.87 (0.26), residues: 408 sheet: 0.51 (0.41), residues: 163 loop : -0.82 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 333 HIS 0.003 0.001 HIS B1253 PHE 0.021 0.001 PHE A 497 TYR 0.015 0.001 TYR A 306 ARG 0.003 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 126 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.887 Fit side-chains REVERT: A 227 ASP cc_start: 0.8737 (m-30) cc_final: 0.8387 (m-30) REVERT: A 318 TYR cc_start: 0.7764 (m-80) cc_final: 0.7562 (m-80) REVERT: A 513 ASN cc_start: 0.8641 (t0) cc_final: 0.8167 (t0) REVERT: A 533 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.7526 (mp0) REVERT: A 568 ASN cc_start: 0.8398 (t0) cc_final: 0.7911 (t0) REVERT: B 905 TYR cc_start: 0.8049 (m-80) cc_final: 0.7837 (m-80) REVERT: B 920 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7340 (mm-30) outliers start: 12 outliers final: 7 residues processed: 122 average time/residue: 0.2540 time to fit residues: 41.0007 Evaluate side-chains 117 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET 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: 4.9990 chunk 76 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 25 optimal weight: 0.0040 chunk 91 optimal weight: 0.0040 chunk 99 optimal weight: 0.2980 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 0.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 988 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8371 Z= 0.131 Angle : 0.437 9.545 11319 Z= 0.236 Chirality : 0.041 0.177 1243 Planarity : 0.003 0.032 1426 Dihedral : 4.994 36.852 1205 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.59 % Allowed : 11.15 % Favored : 87.26 % 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: 0.56 (0.41), residues: 163 loop : -0.80 (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 494 PHE 0.018 0.001 PHE B1117 TYR 0.010 0.001 TYR A 306 ARG 0.003 0.000 ARG A 334 *********************** 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 135 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.995 Fit side-chains REVERT: A 142 ARG cc_start: 0.7240 (ttm170) cc_final: 0.6653 (mtt180) REVERT: A 227 ASP cc_start: 0.8666 (m-30) cc_final: 0.8443 (m-30) REVERT: A 245 PHE cc_start: 0.8335 (m-80) cc_final: 0.8030 (m-80) REVERT: A 444 ARG cc_start: 0.6028 (ttt180) cc_final: 0.5551 (ttp-110) REVERT: A 491 ARG cc_start: 0.7510 (tmm-80) cc_final: 0.7307 (tpp80) REVERT: A 513 ASN cc_start: 0.8760 (t0) cc_final: 0.8506 (t0) REVERT: A 533 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: A 568 ASN cc_start: 0.8376 (t0) cc_final: 0.8056 (t0) REVERT: A 655 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7934 (tp) REVERT: A 680 ASP cc_start: 0.7976 (p0) cc_final: 0.7686 (t0) REVERT: B 905 TYR cc_start: 0.8039 (m-80) cc_final: 0.7822 (m-80) REVERT: B 1082 LYS cc_start: 0.7489 (tptm) cc_final: 0.7218 (tmmt) REVERT: B 1118 ASP cc_start: 0.7160 (t0) cc_final: 0.6795 (t70) outliers start: 14 outliers final: 8 residues processed: 131 average time/residue: 0.2406 time to fit residues: 41.9255 Evaluate side-chains 124 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 909 ILE Chi-restraints excluded: chain B residue 923 THR 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 1203 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 0.3980 chunk 97 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8371 Z= 0.221 Angle : 0.464 5.274 11319 Z= 0.252 Chirality : 0.042 0.164 1243 Planarity : 0.003 0.032 1426 Dihedral : 4.736 35.148 1205 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.93 % Allowed : 11.38 % Favored : 86.69 % 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: 0.91 (0.27), residues: 1006 helix: 2.10 (0.26), residues: 410 sheet: 0.47 (0.41), residues: 163 loop : -0.82 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 333 HIS 0.002 0.000 HIS B1253 PHE 0.016 0.001 PHE A 497 TYR 0.015 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 127 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.904 Fit side-chains REVERT: A 227 ASP cc_start: 0.8693 (m-30) cc_final: 0.8391 (m-30) REVERT: A 245 PHE cc_start: 0.8400 (m-80) cc_final: 0.8146 (m-80) REVERT: A 444 ARG cc_start: 0.6064 (ttt180) cc_final: 0.5584 (ttp-110) REVERT: A 513 ASN cc_start: 0.8767 (t0) cc_final: 0.8483 (t0) REVERT: A 533 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: A 568 ASN cc_start: 0.8400 (t0) cc_final: 0.8101 (t0) REVERT: A 680 ASP cc_start: 0.8037 (p0) cc_final: 0.7708 (t0) REVERT: B 925 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6969 (mt-10) REVERT: B 1118 ASP cc_start: 0.7195 (t0) cc_final: 0.6851 (t70) outliers start: 17 outliers final: 9 residues processed: 125 average time/residue: 0.2365 time to fit residues: 39.2884 Evaluate side-chains 120 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 942 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1203 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8371 Z= 0.235 Angle : 0.473 5.294 11319 Z= 0.257 Chirality : 0.043 0.158 1243 Planarity : 0.003 0.031 1426 Dihedral : 4.681 37.414 1205 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.48 % Allowed : 12.63 % Favored : 85.89 % 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: 0.91 (0.27), residues: 1006 helix: 2.12 (0.26), residues: 406 sheet: 0.35 (0.40), residues: 163 loop : -0.75 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 333 HIS 0.003 0.001 HIS B1253 PHE 0.016 0.001 PHE A 497 TYR 0.015 0.001 TYR A 306 ARG 0.002 0.000 ARG B1179 *********************** 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 to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.864 Fit side-chains REVERT: A 227 ASP cc_start: 0.8713 (m-30) cc_final: 0.8338 (m-30) REVERT: A 245 PHE cc_start: 0.8422 (m-80) cc_final: 0.8218 (m-10) REVERT: A 444 ARG cc_start: 0.6045 (ttt180) cc_final: 0.5565 (ttp-110) REVERT: A 513 ASN cc_start: 0.8823 (t0) cc_final: 0.8545 (t0) REVERT: A 533 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: A 568 ASN cc_start: 0.8413 (t0) cc_final: 0.8103 (t0) REVERT: A 680 ASP cc_start: 0.8036 (p0) cc_final: 0.7671 (t0) REVERT: B 925 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6560 (mt-10) REVERT: B 1023 ARG cc_start: 0.7224 (mmm-85) cc_final: 0.7011 (mmm-85) REVERT: B 1118 ASP cc_start: 0.7158 (t0) cc_final: 0.6811 (t70) outliers start: 13 outliers final: 7 residues processed: 125 average time/residue: 0.2379 time to fit residues: 39.7743 Evaluate side-chains 118 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 914 ILE 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 1203 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 B1188 ASN B1245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1255 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= 0.195 Angle : 0.455 5.272 11319 Z= 0.248 Chirality : 0.042 0.153 1243 Planarity : 0.003 0.030 1426 Dihedral : 4.582 37.501 1205 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.93 % Allowed : 12.29 % Favored : 85.78 % 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: 0.91 (0.27), residues: 1006 helix: 2.16 (0.26), residues: 408 sheet: 0.38 (0.40), residues: 163 loop : -0.83 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 333 HIS 0.002 0.000 HIS B1253 PHE 0.033 0.001 PHE A 497 TYR 0.013 0.001 TYR A 306 ARG 0.002 0.000 ARG B1179 *********************** 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 125 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.946 Fit side-chains REVERT: A 227 ASP cc_start: 0.8709 (m-30) cc_final: 0.8282 (m-30) REVERT: A 444 ARG cc_start: 0.6072 (ttt180) cc_final: 0.5585 (ttp-110) REVERT: A 513 ASN cc_start: 0.8807 (t0) cc_final: 0.8526 (t0) REVERT: A 533 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: A 568 ASN cc_start: 0.8410 (t0) cc_final: 0.8099 (t0) REVERT: A 680 ASP cc_start: 0.7995 (p0) cc_final: 0.7662 (t0) REVERT: B 925 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6150 (tp30) REVERT: B 1054 MET cc_start: 0.8302 (tpt) cc_final: 0.7310 (tpt) REVERT: B 1118 ASP cc_start: 0.7120 (t0) cc_final: 0.6774 (t70) outliers start: 17 outliers final: 10 residues processed: 123 average time/residue: 0.2450 time to fit residues: 39.9169 Evaluate side-chains 121 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 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 942 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1203 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 0.0370 overall best weight: 0.9262 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1344 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= 0.200 Angle : 0.456 5.486 11319 Z= 0.249 Chirality : 0.042 0.160 1243 Planarity : 0.003 0.030 1426 Dihedral : 4.545 38.078 1205 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.82 % Allowed : 13.08 % Favored : 85.10 % 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: 0.92 (0.27), residues: 1006 helix: 2.17 (0.26), residues: 408 sheet: 0.37 (0.40), residues: 163 loop : -0.83 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 333 HIS 0.002 0.000 HIS B1253 PHE 0.028 0.001 PHE A 497 TYR 0.013 0.001 TYR A 306 ARG 0.002 0.000 ARG B1179 *********************** 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 to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.895 Fit side-chains REVERT: A 227 ASP cc_start: 0.8720 (m-30) cc_final: 0.8300 (m-30) REVERT: A 444 ARG cc_start: 0.6048 (ttt180) cc_final: 0.5587 (ttp-110) REVERT: A 513 ASN cc_start: 0.8779 (t0) cc_final: 0.8528 (t0) REVERT: A 533 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: A 568 ASN cc_start: 0.8412 (t0) cc_final: 0.8105 (t0) REVERT: A 680 ASP cc_start: 0.7951 (p0) cc_final: 0.7640 (t0) REVERT: B 937 MET cc_start: 0.3133 (tpp) cc_final: 0.2606 (tpp) REVERT: B 942 SER cc_start: 0.9110 (OUTLIER) cc_final: 0.8866 (p) REVERT: B 1118 ASP cc_start: 0.7138 (t0) cc_final: 0.6790 (t70) outliers start: 16 outliers final: 10 residues processed: 123 average time/residue: 0.2388 time to fit residues: 39.2196 Evaluate side-chains 120 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 914 ILE Chi-restraints excluded: chain B residue 923 THR 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 1203 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.0370 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 0.0570 chunk 61 optimal weight: 2.9990 chunk 66 optimal weight: 0.0980 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 0.2980 chunk 85 optimal weight: 0.5980 overall best weight: 0.2176 ------------------------------------------------------------------------------- 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 B1003 GLN B1188 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8371 Z= 0.110 Angle : 0.411 5.370 11319 Z= 0.227 Chirality : 0.041 0.168 1243 Planarity : 0.003 0.029 1426 Dihedral : 4.284 36.120 1205 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.71 % Allowed : 13.42 % 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: 1.15 (0.27), residues: 1006 helix: 2.34 (0.26), residues: 409 sheet: 0.46 (0.40), residues: 164 loop : -0.67 (0.30), residues: 433 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 0.024 0.001 PHE A 497 TYR 0.008 0.001 TYR B1149 ARG 0.003 0.000 ARG B1179 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 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 133 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.906 Fit side-chains REVERT: A 444 ARG cc_start: 0.6064 (ttt180) cc_final: 0.5573 (ttp-110) REVERT: A 479 ASP cc_start: 0.8033 (t0) cc_final: 0.7799 (t0) REVERT: A 513 ASN cc_start: 0.8778 (t0) cc_final: 0.8535 (t0) REVERT: A 533 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: A 568 ASN cc_start: 0.8403 (t0) cc_final: 0.8077 (t0) REVERT: B 925 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7026 (tt0) REVERT: B 937 MET cc_start: 0.3096 (tpp) cc_final: 0.2551 (tpp) REVERT: B 1118 ASP cc_start: 0.7071 (t0) cc_final: 0.6731 (t70) REVERT: B 1217 LEU cc_start: 0.8556 (mt) cc_final: 0.8353 (mm) outliers start: 15 outliers final: 10 residues processed: 129 average time/residue: 0.2340 time to fit residues: 40.3301 Evaluate side-chains 121 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 1203 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 59 optimal weight: 0.0770 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN B1188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8371 Z= 0.164 Angle : 0.436 5.622 11319 Z= 0.241 Chirality : 0.042 0.172 1243 Planarity : 0.003 0.029 1426 Dihedral : 4.286 35.925 1205 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.48 % Allowed : 13.42 % Favored : 85.10 % 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: 2.33 (0.26), residues: 409 sheet: 0.48 (0.40), residues: 164 loop : -0.72 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 467 HIS 0.002 0.000 HIS B1253 PHE 0.024 0.001 PHE A 497 TYR 0.012 0.001 TYR A 306 ARG 0.004 0.000 ARG A 682 *********************** 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 121 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.832 Fit side-chains REVERT: A 444 ARG cc_start: 0.6092 (ttt180) cc_final: 0.5596 (ttp-110) REVERT: A 513 ASN cc_start: 0.8787 (t0) cc_final: 0.8529 (t0) REVERT: A 533 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: A 568 ASN cc_start: 0.8372 (t0) cc_final: 0.8068 (t0) REVERT: B 925 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6857 (tt0) REVERT: B 937 MET cc_start: 0.3138 (tpp) cc_final: 0.2614 (tpp) outliers start: 13 outliers final: 10 residues processed: 118 average time/residue: 0.2610 time to fit residues: 40.5871 Evaluate side-chains 116 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 24 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 B1188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8371 Z= 0.188 Angle : 0.447 5.210 11319 Z= 0.246 Chirality : 0.042 0.177 1243 Planarity : 0.003 0.029 1426 Dihedral : 4.346 36.443 1205 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.37 % Allowed : 13.77 % 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: 1.09 (0.27), residues: 1006 helix: 2.31 (0.26), residues: 408 sheet: 0.48 (0.40), residues: 164 loop : -0.73 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 371 HIS 0.002 0.000 HIS B1253 PHE 0.023 0.001 PHE A 497 TYR 0.013 0.001 TYR A 306 ARG 0.002 0.000 ARG B1179 ********************** 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 122 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.918 Fit side-chains REVERT: A 444 ARG cc_start: 0.6096 (ttt180) cc_final: 0.5593 (ttp-110) REVERT: A 513 ASN cc_start: 0.8777 (t0) cc_final: 0.8518 (t0) REVERT: A 533 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: A 568 ASN cc_start: 0.8377 (t0) cc_final: 0.8070 (t0) REVERT: B 937 MET cc_start: 0.3207 (tpp) cc_final: 0.2668 (tpp) REVERT: B 1052 LYS cc_start: 0.8361 (ttmt) cc_final: 0.7465 (tttm) outliers start: 12 outliers final: 10 residues processed: 121 average time/residue: 0.2567 time to fit residues: 41.1207 Evaluate side-chains 113 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 926 VAL Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1024 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN B1188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.162794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.119433 restraints weight = 8968.518| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.38 r_work: 0.3125 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8371 Z= 0.178 Angle : 0.442 5.205 11319 Z= 0.244 Chirality : 0.042 0.181 1243 Planarity : 0.003 0.029 1426 Dihedral : 4.316 36.549 1205 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.48 % Allowed : 13.88 % Favored : 84.64 % 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: 1.10 (0.27), residues: 1006 helix: 2.28 (0.26), residues: 409 sheet: 0.53 (0.40), residues: 162 loop : -0.72 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 371 HIS 0.002 0.000 HIS B1253 PHE 0.023 0.001 PHE A 497 TYR 0.012 0.001 TYR A 306 ARG 0.003 0.000 ARG A 145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2251.69 seconds wall clock time: 41 minutes 39.33 seconds (2499.33 seconds total)