Starting phenix.real_space_refine on Tue Apr 29 00:21:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8js9_36617/04_2025/8js9_36617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8js9_36617/04_2025/8js9_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_36617/04_2025/8js9_36617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8js9_36617/04_2025/8js9_36617.map" model { file = "/net/cci-nas-00/data/ceres_data/8js9_36617/04_2025/8js9_36617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8js9_36617/04_2025/8js9_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-5669/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: 5.49, per 1000 atoms: 0.67 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: 2.43 Conformation dependent library (CDL) restraints added in 974.3 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: 0.93 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: 2.47 Time building geometry restraints manager: 2.81 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: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.070 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.590 ------------------------------------------------------------------------------- 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 8376 Z= 0.174 Angle : 0.561 9.465 11334 Z= 0.314 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00887 ( 3) link_NAG-ASN : angle 3.90661 ( 9) link_BETA1-4 : bond 0.01034 ( 1) link_BETA1-4 : angle 1.55102 ( 3) hydrogen bonds : bond 0.09981 ( 377) hydrogen bonds : angle 5.08301 ( 1086) link_BETA1-6 : bond 0.00459 ( 1) link_BETA1-6 : angle 1.40108 ( 3) covalent geometry : bond 0.00385 ( 8371) covalent geometry : angle 0.54961 (11319) *********************** 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 : 0.894 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: 0.2515 time to fit residues: 36.2521 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 : 1.086 ------------------------------------------------------------------------------- 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: 4.9990 chunk 26 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 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: 1.0582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.161324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.116958 restraints weight = 8943.428| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.30 r_work: 0.3137 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.0578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8376 Z= 0.154 Angle : 0.515 10.887 11334 Z= 0.273 Chirality : 0.044 0.364 1243 Planarity : 0.003 0.033 1426 Dihedral : 6.479 83.105 1206 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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: 0.78 (0.27), residues: 1006 helix: 1.88 (0.26), residues: 408 sheet: 0.52 (0.41), residues: 163 loop : -0.81 (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 A 262 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 3) link_NAG-ASN : angle 3.69669 ( 9) link_BETA1-4 : bond 0.00521 ( 1) link_BETA1-4 : angle 1.27364 ( 3) hydrogen bonds : bond 0.04601 ( 377) hydrogen bonds : angle 4.28454 ( 1086) link_BETA1-6 : bond 0.00426 ( 1) link_BETA1-6 : angle 1.33902 ( 3) covalent geometry : bond 0.00364 ( 8371) covalent geometry : angle 0.50416 (11319) *********************** 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 125 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.846 Fit side-chains REVERT: A 227 ASP cc_start: 0.8648 (m-30) cc_final: 0.8294 (m-30) REVERT: A 318 TYR cc_start: 0.7716 (m-80) cc_final: 0.7492 (m-80) REVERT: A 513 ASN cc_start: 0.8605 (t0) cc_final: 0.8133 (t0) REVERT: A 533 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: A 568 ASN cc_start: 0.8617 (t0) cc_final: 0.8112 (t0) REVERT: B 905 TYR cc_start: 0.7938 (m-80) cc_final: 0.7725 (m-80) REVERT: B 920 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7303 (mm-30) outliers start: 12 outliers final: 7 residues processed: 121 average time/residue: 0.2355 time to fit residues: 37.5917 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 : 0.846 ------------------------------------------------------------------------------- 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 95 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 chunk 5 optimal weight: 0.1980 chunk 52 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.176957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.136034 restraints weight = 8927.026| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.40 r_work: 0.3193 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8376 Z= 0.117 Angle : 0.465 9.558 11334 Z= 0.247 Chirality : 0.042 0.173 1243 Planarity : 0.003 0.032 1426 Dihedral : 5.098 38.204 1205 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.48 % Allowed : 11.60 % Favored : 86.92 % 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: 0.94 (0.27), residues: 1006 helix: 2.08 (0.26), residues: 408 sheet: 0.51 (0.41), residues: 163 loop : -0.75 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 333 HIS 0.002 0.000 HIS B1253 PHE 0.018 0.001 PHE B1117 TYR 0.012 0.001 TYR A 306 ARG 0.002 0.000 ARG A 334 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 3) link_NAG-ASN : angle 3.38066 ( 9) link_BETA1-4 : bond 0.00718 ( 1) link_BETA1-4 : angle 1.27662 ( 3) hydrogen bonds : bond 0.04071 ( 377) hydrogen bonds : angle 4.05553 ( 1086) link_BETA1-6 : bond 0.00746 ( 1) link_BETA1-6 : angle 1.38682 ( 3) covalent geometry : bond 0.00268 ( 8371) covalent geometry : angle 0.45434 (11319) *********************** 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 130 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 1.039 Fit side-chains REVERT: A 227 ASP cc_start: 0.8600 (m-30) cc_final: 0.8273 (m-30) REVERT: A 245 PHE cc_start: 0.8260 (m-80) cc_final: 0.8006 (m-80) REVERT: A 444 ARG cc_start: 0.6038 (ttt180) cc_final: 0.5432 (ttp-110) REVERT: A 513 ASN cc_start: 0.8733 (t0) cc_final: 0.8498 (t0) REVERT: A 533 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: A 568 ASN cc_start: 0.8592 (t0) cc_final: 0.8286 (t0) REVERT: A 680 ASP cc_start: 0.8199 (p0) cc_final: 0.7763 (t0) REVERT: B 905 TYR cc_start: 0.7962 (m-80) cc_final: 0.7739 (m-80) REVERT: B 1118 ASP cc_start: 0.7248 (t0) cc_final: 0.6828 (t70) outliers start: 13 outliers final: 7 residues processed: 125 average time/residue: 0.2844 time to fit residues: 48.1228 Evaluate side-chains 120 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 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 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 66 optimal weight: 0.0020 chunk 19 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.0870 chunk 48 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 overall best weight: 0.5366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.169767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.128325 restraints weight = 8981.528| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.41 r_work: 0.3197 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8376 Z= 0.105 Angle : 0.431 5.240 11334 Z= 0.235 Chirality : 0.041 0.166 1243 Planarity : 0.003 0.031 1426 Dihedral : 4.648 34.994 1205 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.82 % Allowed : 11.60 % Favored : 86.58 % 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: 2.14 (0.26), residues: 412 sheet: 0.50 (0.41), residues: 163 loop : -0.77 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 333 HIS 0.001 0.000 HIS B1253 PHE 0.015 0.001 PHE A 497 TYR 0.011 0.001 TYR A 306 ARG 0.001 0.000 ARG A 334 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 3) link_NAG-ASN : angle 1.74784 ( 9) link_BETA1-4 : bond 0.00696 ( 1) link_BETA1-4 : angle 1.20917 ( 3) hydrogen bonds : bond 0.03828 ( 377) hydrogen bonds : angle 3.93759 ( 1086) link_BETA1-6 : bond 0.00484 ( 1) link_BETA1-6 : angle 1.23703 ( 3) covalent geometry : bond 0.00233 ( 8371) covalent geometry : angle 0.42768 (11319) *********************** 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 126 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.957 Fit side-chains REVERT: A 227 ASP cc_start: 0.8547 (m-30) cc_final: 0.8228 (m-30) REVERT: A 245 PHE cc_start: 0.8186 (m-80) cc_final: 0.7963 (m-80) REVERT: A 444 ARG cc_start: 0.5991 (ttt180) cc_final: 0.5375 (ttp-110) REVERT: A 513 ASN cc_start: 0.8734 (t0) cc_final: 0.8435 (t0) REVERT: A 533 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: A 568 ASN cc_start: 0.8612 (t0) cc_final: 0.8289 (t0) REVERT: A 680 ASP cc_start: 0.8114 (p0) cc_final: 0.7794 (t0) REVERT: B 925 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6649 (mt-10) REVERT: B 1118 ASP cc_start: 0.7185 (t0) cc_final: 0.6782 (t70) outliers start: 16 outliers final: 10 residues processed: 122 average time/residue: 0.2349 time to fit residues: 38.3135 Evaluate side-chains 119 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 690 ASN Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain B residue 909 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 25 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 chunk 71 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN B1270 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.162515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.118218 restraints weight = 8912.011| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.58 r_work: 0.3145 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8376 Z= 0.111 Angle : 0.434 5.265 11334 Z= 0.236 Chirality : 0.041 0.163 1243 Planarity : 0.003 0.030 1426 Dihedral : 4.473 35.673 1205 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.71 % Allowed : 12.06 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.27), residues: 1006 helix: 2.24 (0.26), residues: 409 sheet: 0.48 (0.41), residues: 163 loop : -0.72 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 333 HIS 0.002 0.000 HIS B1253 PHE 0.015 0.001 PHE A 497 TYR 0.012 0.001 TYR A 306 ARG 0.001 0.000 ARG A 262 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 3) link_NAG-ASN : angle 1.75776 ( 9) link_BETA1-4 : bond 0.00623 ( 1) link_BETA1-4 : angle 1.21036 ( 3) hydrogen bonds : bond 0.03883 ( 377) hydrogen bonds : angle 3.91636 ( 1086) link_BETA1-6 : bond 0.00467 ( 1) link_BETA1-6 : angle 1.23579 ( 3) covalent geometry : bond 0.00254 ( 8371) covalent geometry : angle 0.43023 (11319) *********************** 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 127 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 1.429 Fit side-chains REVERT: A 227 ASP cc_start: 0.8606 (m-30) cc_final: 0.8281 (m-30) REVERT: A 245 PHE cc_start: 0.8109 (m-80) cc_final: 0.7901 (m-80) REVERT: A 444 ARG cc_start: 0.5867 (ttt180) cc_final: 0.5230 (ttp-110) REVERT: A 513 ASN cc_start: 0.8653 (t0) cc_final: 0.8314 (t0) REVERT: A 533 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: A 568 ASN cc_start: 0.8604 (t0) cc_final: 0.8261 (t0) REVERT: A 680 ASP cc_start: 0.8086 (p0) cc_final: 0.7779 (t0) REVERT: B 925 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6025 (tp30) REVERT: B 1054 MET cc_start: 0.8315 (tpt) cc_final: 0.7409 (tpt) REVERT: B 1118 ASP cc_start: 0.7123 (t0) cc_final: 0.6714 (t70) outliers start: 15 outliers final: 9 residues processed: 123 average time/residue: 0.2794 time to fit residues: 47.1363 Evaluate side-chains 119 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 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 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 1 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.157917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.113265 restraints weight = 9049.212| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.38 r_work: 0.3049 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 8376 Z= 0.204 Angle : 0.524 5.356 11334 Z= 0.281 Chirality : 0.045 0.153 1243 Planarity : 0.003 0.030 1426 Dihedral : 4.729 37.372 1205 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.28 % Allowed : 11.83 % 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: 0.79 (0.27), residues: 1006 helix: 1.98 (0.26), residues: 406 sheet: 0.29 (0.40), residues: 163 loop : -0.79 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 333 HIS 0.003 0.001 HIS B1253 PHE 0.017 0.002 PHE A 497 TYR 0.019 0.002 TYR A 306 ARG 0.003 0.000 ARG B1061 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 3) link_NAG-ASN : angle 1.98285 ( 9) link_BETA1-4 : bond 0.00553 ( 1) link_BETA1-4 : angle 1.42119 ( 3) hydrogen bonds : bond 0.05033 ( 377) hydrogen bonds : angle 4.14986 ( 1086) link_BETA1-6 : bond 0.00392 ( 1) link_BETA1-6 : angle 1.35560 ( 3) covalent geometry : bond 0.00503 ( 8371) covalent geometry : angle 0.52057 (11319) *********************** 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 131 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.878 Fit side-chains REVERT: A 245 PHE cc_start: 0.8284 (m-80) cc_final: 0.8034 (m-10) REVERT: A 444 ARG cc_start: 0.5962 (ttt180) cc_final: 0.5349 (ttp-110) REVERT: A 513 ASN cc_start: 0.8709 (t0) cc_final: 0.8385 (t0) REVERT: A 533 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: A 568 ASN cc_start: 0.8632 (t0) cc_final: 0.8298 (t0) REVERT: A 680 ASP cc_start: 0.8191 (p0) cc_final: 0.7675 (t0) REVERT: B 925 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6889 (tt0) REVERT: B 1118 ASP cc_start: 0.7163 (t0) cc_final: 0.6730 (t70) REVERT: B 1266 TRP cc_start: 0.6260 (t60) cc_final: 0.5790 (t60) REVERT: B 1270 GLN cc_start: 0.4078 (OUTLIER) cc_final: 0.3495 (mp-120) outliers start: 20 outliers final: 9 residues processed: 128 average time/residue: 0.2318 time to fit residues: 39.4912 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 : 0.868 ------------------------------------------------------------------------------- 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 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 1270 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 86 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 61 optimal weight: 0.0980 chunk 37 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN B 988 GLN B1245 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.161738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.117432 restraints weight = 9000.881| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.52 r_work: 0.3142 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8376 Z= 0.106 Angle : 0.439 5.266 11334 Z= 0.240 Chirality : 0.041 0.163 1243 Planarity : 0.003 0.029 1426 Dihedral : 4.485 37.002 1205 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.71 % Allowed : 13.31 % Favored : 84.98 % 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: 0.93 (0.27), residues: 1006 helix: 2.17 (0.26), residues: 410 sheet: 0.34 (0.40), residues: 163 loop : -0.81 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 467 HIS 0.001 0.000 HIS B1253 PHE 0.035 0.001 PHE A 497 TYR 0.010 0.001 TYR A 306 ARG 0.002 0.000 ARG B1179 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 3) link_NAG-ASN : angle 1.65315 ( 9) link_BETA1-4 : bond 0.00701 ( 1) link_BETA1-4 : angle 1.20041 ( 3) hydrogen bonds : bond 0.03873 ( 377) hydrogen bonds : angle 3.96923 ( 1086) link_BETA1-6 : bond 0.00440 ( 1) link_BETA1-6 : angle 1.23917 ( 3) covalent geometry : bond 0.00235 ( 8371) covalent geometry : angle 0.43572 (11319) *********************** 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 123 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 1.464 Fit side-chains REVERT: A 227 ASP cc_start: 0.8583 (m-30) cc_final: 0.8318 (m-30) REVERT: A 444 ARG cc_start: 0.5925 (ttt180) cc_final: 0.5292 (ttp-110) REVERT: A 479 ASP cc_start: 0.7983 (t0) cc_final: 0.7782 (t0) REVERT: A 513 ASN cc_start: 0.8717 (t0) cc_final: 0.8442 (t0) REVERT: A 533 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: A 568 ASN cc_start: 0.8628 (t0) cc_final: 0.8295 (t0) REVERT: A 680 ASP cc_start: 0.7998 (p0) cc_final: 0.7693 (t0) REVERT: B 925 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6779 (tt0) REVERT: B 942 SER cc_start: 0.9018 (OUTLIER) cc_final: 0.8701 (p) REVERT: B 1118 ASP cc_start: 0.7084 (t0) cc_final: 0.6672 (t70) outliers start: 15 outliers final: 10 residues processed: 120 average time/residue: 0.2780 time to fit residues: 45.3965 Evaluate side-chains 119 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 909 ILE Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 925 GLU Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 942 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1024 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 41 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN B1188 ASN B1270 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.163108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.122450 restraints weight = 9092.115| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.08 r_work: 0.3119 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8376 Z= 0.126 Angle : 0.452 5.395 11334 Z= 0.246 Chirality : 0.042 0.169 1243 Planarity : 0.003 0.029 1426 Dihedral : 4.447 37.013 1205 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.71 % Allowed : 13.65 % 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: 0.93 (0.27), residues: 1006 helix: 2.15 (0.26), residues: 410 sheet: 0.41 (0.40), residues: 162 loop : -0.81 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 333 HIS 0.002 0.000 HIS B1253 PHE 0.033 0.001 PHE A 497 TYR 0.013 0.001 TYR A 306 ARG 0.002 0.000 ARG B1179 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 3) link_NAG-ASN : angle 1.68089 ( 9) link_BETA1-4 : bond 0.00603 ( 1) link_BETA1-4 : angle 1.26652 ( 3) hydrogen bonds : bond 0.04132 ( 377) hydrogen bonds : angle 3.98122 ( 1086) link_BETA1-6 : bond 0.00401 ( 1) link_BETA1-6 : angle 1.22529 ( 3) covalent geometry : bond 0.00296 ( 8371) covalent geometry : angle 0.44905 (11319) *********************** 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 125 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.847 Fit side-chains REVERT: A 227 ASP cc_start: 0.8632 (m-30) cc_final: 0.8304 (m-30) REVERT: A 444 ARG cc_start: 0.6021 (ttt180) cc_final: 0.5391 (ttp-110) REVERT: A 513 ASN cc_start: 0.8702 (t0) cc_final: 0.8420 (t0) REVERT: A 533 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: A 568 ASN cc_start: 0.8629 (t0) cc_final: 0.8291 (t0) REVERT: A 680 ASP cc_start: 0.8037 (p0) cc_final: 0.7724 (t0) REVERT: B 925 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6979 (tt0) REVERT: B 942 SER cc_start: 0.9040 (OUTLIER) cc_final: 0.8743 (p) REVERT: B 1054 MET cc_start: 0.8445 (tpt) cc_final: 0.8234 (mmm) REVERT: B 1118 ASP cc_start: 0.7109 (t0) cc_final: 0.6699 (t70) REVERT: B 1266 TRP cc_start: 0.6182 (t60) cc_final: 0.5941 (t60) outliers start: 15 outliers final: 10 residues processed: 123 average time/residue: 0.2263 time to fit residues: 37.1011 Evaluate side-chains 122 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 909 ILE Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 925 GLU Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 942 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1024 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 94 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 56 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.175035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.134599 restraints weight = 9095.613| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.08 r_work: 0.3145 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8376 Z= 0.112 Angle : 0.435 5.179 11334 Z= 0.238 Chirality : 0.042 0.178 1243 Planarity : 0.003 0.029 1426 Dihedral : 4.360 36.486 1205 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.93 % Allowed : 13.42 % 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: 1.02 (0.27), residues: 1006 helix: 2.24 (0.26), residues: 410 sheet: 0.40 (0.40), residues: 164 loop : -0.77 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 333 HIS 0.001 0.000 HIS B1253 PHE 0.029 0.001 PHE A 497 TYR 0.010 0.001 TYR A 306 ARG 0.002 0.000 ARG B1179 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 3) link_NAG-ASN : angle 1.61416 ( 9) link_BETA1-4 : bond 0.00647 ( 1) link_BETA1-4 : angle 1.21671 ( 3) hydrogen bonds : bond 0.03868 ( 377) hydrogen bonds : angle 3.94026 ( 1086) link_BETA1-6 : bond 0.00419 ( 1) link_BETA1-6 : angle 1.22504 ( 3) covalent geometry : bond 0.00256 ( 8371) covalent geometry : angle 0.43188 (11319) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.888 Fit side-chains REVERT: A 227 ASP cc_start: 0.8611 (m-30) cc_final: 0.8311 (m-30) REVERT: A 444 ARG cc_start: 0.5999 (ttt180) cc_final: 0.5369 (ttp-110) REVERT: A 479 ASP cc_start: 0.8042 (t0) cc_final: 0.7835 (t0) REVERT: A 513 ASN cc_start: 0.8723 (t0) cc_final: 0.8456 (t0) REVERT: A 533 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: A 568 ASN cc_start: 0.8628 (t0) cc_final: 0.8281 (t0) REVERT: A 680 ASP cc_start: 0.8004 (p0) cc_final: 0.7735 (t0) REVERT: B 925 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6973 (tt0) REVERT: B 942 SER cc_start: 0.9003 (OUTLIER) cc_final: 0.8748 (p) REVERT: B 1118 ASP cc_start: 0.7081 (t0) cc_final: 0.6649 (t70) REVERT: B 1266 TRP cc_start: 0.6216 (t60) cc_final: 0.5961 (t60) outliers start: 17 outliers final: 12 residues processed: 127 average time/residue: 0.2443 time to fit residues: 41.7503 Evaluate side-chains 125 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 909 ILE Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 925 GLU Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 942 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1024 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.164311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.123607 restraints weight = 8952.889| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.09 r_work: 0.3110 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8376 Z= 0.131 Angle : 0.453 5.198 11334 Z= 0.247 Chirality : 0.042 0.181 1243 Planarity : 0.003 0.029 1426 Dihedral : 4.388 37.054 1205 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.59 % Allowed : 13.77 % 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: 0.97 (0.27), residues: 1006 helix: 2.21 (0.26), residues: 408 sheet: 0.37 (0.40), residues: 164 loop : -0.80 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 371 HIS 0.002 0.000 HIS B1253 PHE 0.028 0.001 PHE A 497 TYR 0.013 0.001 TYR A 306 ARG 0.002 0.000 ARG B1179 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 3) link_NAG-ASN : angle 1.67432 ( 9) link_BETA1-4 : bond 0.00552 ( 1) link_BETA1-4 : angle 1.26214 ( 3) hydrogen bonds : bond 0.04137 ( 377) hydrogen bonds : angle 3.98285 ( 1086) link_BETA1-6 : bond 0.00386 ( 1) link_BETA1-6 : angle 1.23117 ( 3) covalent geometry : bond 0.00310 ( 8371) covalent geometry : angle 0.44953 (11319) ********************** 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 126 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.879 Fit side-chains REVERT: A 227 ASP cc_start: 0.8638 (m-30) cc_final: 0.8313 (m-30) REVERT: A 444 ARG cc_start: 0.5945 (ttt180) cc_final: 0.5310 (ttp-110) REVERT: A 513 ASN cc_start: 0.8695 (t0) cc_final: 0.8417 (t0) REVERT: A 533 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: A 568 ASN cc_start: 0.8621 (t0) cc_final: 0.8272 (t0) REVERT: A 680 ASP cc_start: 0.8026 (p0) cc_final: 0.7706 (t0) REVERT: B 925 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6669 (mt-10) REVERT: B 942 SER cc_start: 0.9028 (OUTLIER) cc_final: 0.8744 (p) REVERT: B 1118 ASP cc_start: 0.7061 (t0) cc_final: 0.6640 (t70) REVERT: B 1266 TRP cc_start: 0.6173 (t60) cc_final: 0.5937 (t60) outliers start: 14 outliers final: 11 residues processed: 124 average time/residue: 0.2385 time to fit residues: 39.3768 Evaluate side-chains 122 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 909 ILE 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 1024 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 0.2980 chunk 81 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 94 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.171619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.131720 restraints weight = 8973.131| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.09 r_work: 0.3183 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8376 Z= 0.104 Angle : 0.427 5.182 11334 Z= 0.234 Chirality : 0.041 0.186 1243 Planarity : 0.003 0.029 1426 Dihedral : 4.278 36.327 1205 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.82 % Allowed : 13.65 % Favored : 84.53 % 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: 2.29 (0.26), residues: 409 sheet: 0.47 (0.40), residues: 164 loop : -0.70 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 371 HIS 0.001 0.000 HIS B1253 PHE 0.026 0.001 PHE A 497 TYR 0.009 0.001 TYR A 306 ARG 0.002 0.000 ARG B1023 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 3) link_NAG-ASN : angle 1.61864 ( 9) link_BETA1-4 : bond 0.00667 ( 1) link_BETA1-4 : angle 1.19598 ( 3) hydrogen bonds : bond 0.03732 ( 377) hydrogen bonds : angle 3.91916 ( 1086) link_BETA1-6 : bond 0.00415 ( 1) link_BETA1-6 : angle 1.19966 ( 3) covalent geometry : bond 0.00233 ( 8371) covalent geometry : angle 0.42368 (11319) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5516.82 seconds wall clock time: 96 minutes 40.13 seconds (5800.13 seconds total)