Starting phenix.real_space_refine on Wed Feb 14 15:04:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q61_13849/02_2024/7q61_13849.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q61_13849/02_2024/7q61_13849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q61_13849/02_2024/7q61_13849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q61_13849/02_2024/7q61_13849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q61_13849/02_2024/7q61_13849.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q61_13849/02_2024/7q61_13849.pdb" } resolution = 2.88 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= 0.005 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 46 5.16 5 C 6095 2.51 5 N 1559 2.21 5 O 1835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1026": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9535 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1210, 9437 Classifications: {'peptide': 1210} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1147} Chain breaks: 4 Chain: "X" 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 Chain: "B" 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 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 5.53, per 1000 atoms: 0.58 Number of scatterers: 9535 At special positions: 0 Unit cell: (89.286, 124.224, 124.224, 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 46 16.00 O 1835 8.00 N 1559 7.00 C 6095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 40 " - pdb=" SG CYS A 78 " distance=2.07 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 557 " distance=2.03 Simple disulfide: pdb=" SG CYS A 589 " - pdb=" SG CYS A 769 " distance=2.02 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 694 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 847 " distance=2.04 Simple disulfide: pdb=" SG CYS A 845 " - pdb=" SG CYS A 881 " distance=2.03 Simple disulfide: pdb=" SG CYS A 919 " - pdb=" SG CYS A1307 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1123 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1501 " - " ASN A 328 " " NAG A1502 " - " ASN A 609 " " NAG A1503 " - " ASN A 857 " " NAG B 1 " - " ASN A 867 " " NAG X 1 " - " ASN A 120 " Time building additional restraints: 3.47 Conformation dependent library (CDL) restraints added in 2.0 seconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2252 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 19 sheets defined 15.9% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 508 through 512 removed outlier: 4.001A pdb=" N LYS A 511 " --> pdb=" O ASN A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 602 removed outlier: 3.752A pdb=" N LEU A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 670 through 677 Processing helix chain 'A' and resid 837 through 839 No H-bonds generated for 'chain 'A' and resid 837 through 839' Processing helix chain 'A' and resid 970 through 973 Processing helix chain 'A' and resid 974 through 990 removed outlier: 4.031A pdb=" N ALA A 979 " --> pdb=" O MET A 975 " (cutoff:3.500A) Proline residue: A 980 - end of helix removed outlier: 4.145A pdb=" N TYR A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1011 Processing helix chain 'A' and resid 1034 through 1046 Processing helix chain 'A' and resid 1047 through 1051 removed outlier: 4.044A pdb=" N LYS A1050 " --> pdb=" O GLN A1047 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A1051 " --> pdb=" O ALA A1048 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1047 through 1051' Processing helix chain 'A' and resid 1056 through 1070 removed outlier: 3.756A pdb=" N GLN A1060 " --> pdb=" O PRO A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1106 removed outlier: 3.930A pdb=" N LEU A1106 " --> pdb=" O THR A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1125 removed outlier: 4.078A pdb=" N GLN A1119 " --> pdb=" O PRO A1115 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY A1120 " --> pdb=" O MET A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1131 removed outlier: 3.849A pdb=" N THR A1131 " --> pdb=" O SER A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1144 Processing helix chain 'A' and resid 1192 through 1205 Processing helix chain 'A' and resid 1211 through 1226 removed outlier: 3.645A pdb=" N TRP A1224 " --> pdb=" O SER A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1255 removed outlier: 3.640A pdb=" N VAL A1243 " --> pdb=" O GLN A1239 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 82 removed outlier: 8.357A pdb=" N LYS A 38 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.822A pdb=" N PHE A 52 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU A 67 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 54 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 126 Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 131 removed outlier: 4.672A pdb=" N THR A 205 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N SER A 156 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 219 through 223 Processing sheet with id=AA6, first strand: chain 'A' and resid 229 through 230 removed outlier: 6.624A pdb=" N LEU A 229 " --> pdb=" O SER A 336 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N HIS A 310 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLN A 311 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS A 261 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 278 " --> pdb=" O GLN A 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 398 through 403 removed outlier: 8.903A pdb=" N SER A 358 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N THR A 347 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS A 360 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLN A 436 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SER A 341 " --> pdb=" O GLN A 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 455 Processing sheet with id=AB1, first strand: chain 'A' and resid 498 through 507 removed outlier: 5.220A pdb=" N LEU A 499 " --> pdb=" O GLY A 495 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLY A 495 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N SER A 488 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE A 539 " --> pdb=" O SER A 488 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 563 through 567 Processing sheet with id=AB3, first strand: chain 'A' and resid 570 through 571 removed outlier: 3.507A pdb=" N GLN A 571 " --> pdb=" O THR A 785 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP A 595 " --> pdb=" O THR A 736 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR A 736 " --> pdb=" O ASP A 595 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 570 through 571 removed outlier: 3.507A pdb=" N GLN A 571 " --> pdb=" O THR A 785 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 729 through 730 removed outlier: 3.505A pdb=" N ILE A 898 " --> pdb=" O ARG A 730 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 729 through 730 removed outlier: 3.505A pdb=" N ILE A 898 " --> pdb=" O ARG A 730 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 790 through 795 Processing sheet with id=AB8, first strand: chain 'A' and resid 908 through 918 Processing sheet with id=AB9, first strand: chain 'A' and resid 921 through 930 removed outlier: 5.040A pdb=" N LYS A 923 " --> pdb=" O GLY A1304 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY A1304 " --> pdb=" O LYS A 923 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1165 through 1166 401 hydrogen bonds defined for protein. 1110 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: 4.61 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 3076 1.36 - 1.50: 2688 1.50 - 1.64: 3914 1.64 - 1.78: 3 1.78 - 1.91: 66 Bond restraints: 9747 Sorted by residual: bond pdb=" CD GLU A 596 " pdb=" OE2 GLU A 596 " ideal model delta sigma weight residual 1.249 1.327 -0.078 1.90e-02 2.77e+03 1.69e+01 bond pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " ideal model delta sigma weight residual 1.808 1.697 0.111 3.30e-02 9.18e+02 1.13e+01 bond pdb=" CB CYS A 40 " pdb=" SG CYS A 40 " ideal model delta sigma weight residual 1.808 1.915 -0.107 3.30e-02 9.18e+02 1.05e+01 bond pdb=" N SER A1024 " pdb=" CA SER A1024 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.37e+00 bond pdb=" N ARG A1029 " pdb=" CA ARG A1029 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 7.03e+00 ... (remaining 9742 not shown) Histogram of bond angle deviations from ideal: 96.89 - 105.97: 246 105.97 - 115.05: 5803 115.05 - 124.12: 6918 124.12 - 133.20: 263 133.20 - 142.28: 13 Bond angle restraints: 13243 Sorted by residual: angle pdb=" CA CYS A 78 " pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " ideal model delta sigma weight residual 114.40 142.28 -27.88 2.30e+00 1.89e-01 1.47e+02 angle pdb=" C ILE A 952 " pdb=" N MET A 953 " pdb=" CA MET A 953 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" CA TYR A1076 " pdb=" CB TYR A1076 " pdb=" CG TYR A1076 " ideal model delta sigma weight residual 113.90 123.65 -9.75 1.80e+00 3.09e-01 2.93e+01 angle pdb=" CA MET A 953 " pdb=" CB MET A 953 " pdb=" CG MET A 953 " ideal model delta sigma weight residual 114.10 124.83 -10.73 2.00e+00 2.50e-01 2.88e+01 angle pdb=" C ASN A 459 " pdb=" CA ASN A 459 " pdb=" CB ASN A 459 " ideal model delta sigma weight residual 117.23 110.43 6.80 1.36e+00 5.41e-01 2.50e+01 ... (remaining 13238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.49: 5567 20.49 - 40.97: 288 40.97 - 61.46: 48 61.46 - 81.95: 20 81.95 - 102.43: 18 Dihedral angle restraints: 5941 sinusoidal: 2432 harmonic: 3509 Sorted by residual: dihedral pdb=" CA PHE A 616 " pdb=" C PHE A 616 " pdb=" N PRO A 617 " pdb=" CA PRO A 617 " ideal model delta harmonic sigma weight residual -180.00 -138.24 -41.76 0 5.00e+00 4.00e-02 6.98e+01 dihedral pdb=" CA PRO A1056 " pdb=" C PRO A1056 " pdb=" N LYS A1057 " pdb=" CA LYS A1057 " ideal model delta harmonic sigma weight residual -180.00 -155.10 -24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA TYR A1256 " pdb=" C TYR A1256 " pdb=" N MET A1257 " pdb=" CA MET A1257 " ideal model delta harmonic sigma weight residual 180.00 156.00 24.00 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 5938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1181 0.066 - 0.131: 265 0.131 - 0.197: 54 0.197 - 0.263: 16 0.263 - 0.328: 5 Chirality restraints: 1521 Sorted by residual: chirality pdb=" CA CYS A 78 " pdb=" N CYS A 78 " pdb=" C CYS A 78 " pdb=" CB CYS A 78 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" C1 NAG A1502 " pdb=" ND2 ASN A 609 " pdb=" C2 NAG A1502 " pdb=" O5 NAG A1502 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CB ILE A 952 " pdb=" CA ILE A 952 " pdb=" CG1 ILE A 952 " pdb=" CG2 ILE A 952 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 1518 not shown) Planarity restraints: 1699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 399 " 0.066 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO A 400 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO A 400 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 400 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 733 " 0.016 2.00e-02 2.50e+03 2.20e-02 8.43e+00 pdb=" CG PHE A 733 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 733 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 733 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE A 733 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 733 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 733 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A1055 " 0.044 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO A1056 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A1056 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1056 " 0.038 5.00e-02 4.00e+02 ... (remaining 1696 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2327 2.80 - 3.33: 7797 3.33 - 3.85: 15779 3.85 - 4.38: 17633 4.38 - 4.90: 31021 Nonbonded interactions: 74557 Sorted by model distance: nonbonded pdb=" OE2 GLU A 320 " pdb=" OG1 THR A 323 " model vdw 2.275 2.440 nonbonded pdb=" OD1 ASP A 127 " pdb=" OH TYR A 131 " model vdw 2.319 2.440 nonbonded pdb=" O CYS A 557 " pdb=" OH TYR A 613 " model vdw 2.329 2.440 nonbonded pdb=" O ALA A 827 " pdb=" OH TYR A 832 " model vdw 2.333 2.440 nonbonded pdb=" OE1 GLN A 161 " pdb=" OG1 THR A 955 " model vdw 2.339 2.440 ... (remaining 74552 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'X' } 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: 10.010 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: 28.170 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 30.040 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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:11.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.006 0.111 9747 Z= 0.391 Angle : 1.092 27.881 13243 Z= 0.550 Chirality : 0.063 0.328 1521 Planarity : 0.009 0.100 1694 Dihedral : 14.479 102.431 3659 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.50 % Favored : 95.25 % Rotamer: Outliers : 0.10 % Allowed : 0.19 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -1.84 (0.22), residues: 1200 helix: -3.00 (0.24), residues: 169 sheet: -0.23 (0.23), residues: 486 loop : -1.47 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A1065 HIS 0.007 0.001 HIS A 75 PHE 0.050 0.004 PHE A 733 TYR 0.040 0.003 TYR A1076 ARG 0.006 0.001 ARG A 730 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 1.572 Fit side-chains revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7284 (m90) cc_final: 0.6932 (m90) REVERT: A 395 ASN cc_start: 0.9107 (p0) cc_final: 0.8902 (p0) REVERT: A 548 ASP cc_start: 0.7744 (t70) cc_final: 0.7307 (t70) REVERT: A 1015 MET cc_start: 0.7641 (pmm) cc_final: 0.7375 (pmm) REVERT: A 1045 PHE cc_start: 0.9227 (m-80) cc_final: 0.8761 (m-80) REVERT: A 1311 GLN cc_start: 0.7773 (tt0) cc_final: 0.7512 (tt0) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.9354 time to fit residues: 115.7256 Evaluate side-chains 74 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 57 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN A 561 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9747 Z= 0.292 Angle : 0.703 14.074 13243 Z= 0.348 Chirality : 0.047 0.297 1521 Planarity : 0.005 0.062 1694 Dihedral : 7.978 75.413 1438 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.83 % Favored : 96.00 % Rotamer: Outliers : 1.72 % Allowed : 10.39 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.23), residues: 1200 helix: -1.15 (0.34), residues: 183 sheet: -0.17 (0.23), residues: 499 loop : -1.07 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1065 HIS 0.003 0.001 HIS A 352 PHE 0.018 0.002 PHE A 733 TYR 0.021 0.002 TYR A1076 ARG 0.004 0.000 ARG A 602 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8479 (p0) cc_final: 0.8183 (p0) REVERT: A 310 HIS cc_start: 0.7458 (m90) cc_final: 0.6979 (m90) REVERT: A 395 ASN cc_start: 0.9119 (p0) cc_final: 0.8846 (p0) REVERT: A 548 ASP cc_start: 0.7829 (t70) cc_final: 0.7433 (t70) REVERT: A 945 TYR cc_start: 0.7831 (OUTLIER) cc_final: 0.6833 (p90) REVERT: A 953 MET cc_start: 0.5152 (OUTLIER) cc_final: 0.4663 (ppp) REVERT: A 1005 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7122 (m-80) REVERT: A 1015 MET cc_start: 0.7762 (pmm) cc_final: 0.7511 (pmm) REVERT: A 1045 PHE cc_start: 0.9273 (m-80) cc_final: 0.8760 (m-80) REVERT: A 1213 LYS cc_start: 0.8817 (mmpt) cc_final: 0.8468 (mmmt) REVERT: A 1311 GLN cc_start: 0.7820 (tt0) cc_final: 0.7494 (tt0) outliers start: 18 outliers final: 10 residues processed: 89 average time/residue: 0.8969 time to fit residues: 88.9266 Evaluate side-chains 83 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 953 MET Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain A residue 1171 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS ** A 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 HIS A 958 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9747 Z= 0.289 Angle : 0.685 12.612 13243 Z= 0.336 Chirality : 0.046 0.276 1521 Planarity : 0.005 0.057 1694 Dihedral : 6.662 55.444 1438 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.17 % Favored : 95.67 % Rotamer: Outliers : 2.29 % Allowed : 12.58 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.24), residues: 1200 helix: -0.19 (0.38), residues: 182 sheet: -0.18 (0.23), residues: 513 loop : -0.75 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1036 HIS 0.003 0.001 HIS A 75 PHE 0.016 0.002 PHE A 107 TYR 0.023 0.002 TYR A1076 ARG 0.008 0.001 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 69 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7519 (m90) cc_final: 0.7009 (m90) REVERT: A 395 ASN cc_start: 0.9148 (p0) cc_final: 0.8859 (p0) REVERT: A 945 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.6836 (p90) REVERT: A 966 MET cc_start: -0.2673 (ttt) cc_final: -0.3077 (ttm) REVERT: A 1015 MET cc_start: 0.7793 (pmm) cc_final: 0.7526 (pmm) REVERT: A 1045 PHE cc_start: 0.9305 (m-80) cc_final: 0.8810 (m-80) REVERT: A 1213 LYS cc_start: 0.8838 (mmpt) cc_final: 0.8575 (mmpt) REVERT: A 1311 GLN cc_start: 0.7818 (tt0) cc_final: 0.7430 (tt0) outliers start: 24 outliers final: 16 residues processed: 86 average time/residue: 0.7734 time to fit residues: 74.8919 Evaluate side-chains 81 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 64 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1307 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN ** A 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9747 Z= 0.329 Angle : 0.676 13.142 13243 Z= 0.336 Chirality : 0.046 0.288 1521 Planarity : 0.005 0.055 1694 Dihedral : 5.765 36.300 1438 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.92 % Favored : 95.83 % Rotamer: Outliers : 3.15 % Allowed : 14.59 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.24), residues: 1200 helix: 0.27 (0.39), residues: 184 sheet: -0.19 (0.23), residues: 515 loop : -0.77 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 619 HIS 0.004 0.001 HIS A 75 PHE 0.017 0.002 PHE A 107 TYR 0.019 0.002 TYR A 620 ARG 0.005 0.000 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 66 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7603 (m90) cc_final: 0.7048 (m90) REVERT: A 395 ASN cc_start: 0.9170 (p0) cc_final: 0.8866 (p0) REVERT: A 945 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.6858 (p90) REVERT: A 966 MET cc_start: -0.2682 (ttt) cc_final: -0.3084 (ttm) REVERT: A 1015 MET cc_start: 0.7811 (pmm) cc_final: 0.7520 (pmm) REVERT: A 1045 PHE cc_start: 0.9284 (m-80) cc_final: 0.8782 (m-80) REVERT: A 1150 MET cc_start: 0.8746 (mmm) cc_final: 0.8445 (mmm) REVERT: A 1213 LYS cc_start: 0.8855 (mmpt) cc_final: 0.8582 (mmpt) REVERT: A 1301 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7902 (pt0) outliers start: 33 outliers final: 21 residues processed: 91 average time/residue: 0.7289 time to fit residues: 75.1075 Evaluate side-chains 86 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 63 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 953 MET Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1307 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.9990 chunk 1 optimal weight: 0.0570 chunk 87 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 HIS A 914 HIS A1047 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 9747 Z= 0.360 Angle : 0.683 12.414 13243 Z= 0.340 Chirality : 0.046 0.287 1521 Planarity : 0.005 0.056 1694 Dihedral : 5.565 35.950 1438 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.42 % Favored : 95.33 % Rotamer: Outliers : 3.81 % Allowed : 15.44 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.52 (0.24), residues: 1200 helix: 0.69 (0.40), residues: 182 sheet: -0.26 (0.22), residues: 515 loop : -0.67 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 619 HIS 0.003 0.001 HIS A 75 PHE 0.017 0.002 PHE A1286 TYR 0.016 0.002 TYR A1076 ARG 0.005 0.000 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 71 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7677 (m90) cc_final: 0.7102 (m90) REVERT: A 395 ASN cc_start: 0.9208 (p0) cc_final: 0.8894 (p0) REVERT: A 945 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.6934 (p90) REVERT: A 952 ILE cc_start: 0.5243 (OUTLIER) cc_final: 0.4774 (pp) REVERT: A 953 MET cc_start: 0.5763 (OUTLIER) cc_final: 0.5199 (ppp) REVERT: A 966 MET cc_start: -0.2432 (ttt) cc_final: -0.2805 (ttm) REVERT: A 978 PHE cc_start: 0.8701 (t80) cc_final: 0.8399 (t80) REVERT: A 1015 MET cc_start: 0.7840 (pmm) cc_final: 0.7545 (pmm) REVERT: A 1045 PHE cc_start: 0.9269 (m-80) cc_final: 0.8786 (m-80) REVERT: A 1213 LYS cc_start: 0.8870 (mmpt) cc_final: 0.8591 (mmpt) REVERT: A 1301 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7903 (pt0) outliers start: 40 outliers final: 23 residues processed: 104 average time/residue: 0.8532 time to fit residues: 100.1888 Evaluate side-chains 94 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 67 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 953 MET Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1230 ASN Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1307 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9747 Z= 0.243 Angle : 0.649 12.320 13243 Z= 0.320 Chirality : 0.045 0.264 1521 Planarity : 0.004 0.055 1694 Dihedral : 5.293 35.538 1438 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.83 % Favored : 95.83 % Rotamer: Outliers : 3.43 % Allowed : 17.16 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.40 (0.25), residues: 1200 helix: 0.82 (0.40), residues: 182 sheet: -0.14 (0.22), residues: 514 loop : -0.67 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 619 HIS 0.002 0.001 HIS A 75 PHE 0.017 0.001 PHE A 107 TYR 0.017 0.001 TYR A 620 ARG 0.004 0.000 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 76 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7606 (m90) cc_final: 0.7036 (m90) REVERT: A 395 ASN cc_start: 0.9205 (p0) cc_final: 0.8883 (p0) REVERT: A 471 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8770 (tm) REVERT: A 945 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.6901 (p90) REVERT: A 966 MET cc_start: -0.2455 (ttt) cc_final: -0.2865 (ttm) REVERT: A 1015 MET cc_start: 0.7836 (pmm) cc_final: 0.7547 (pmm) REVERT: A 1045 PHE cc_start: 0.9240 (m-80) cc_final: 0.8704 (m-80) REVERT: A 1213 LYS cc_start: 0.8877 (mmpt) cc_final: 0.8585 (mmpt) REVERT: A 1260 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7378 (mm-30) REVERT: A 1301 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7906 (pt0) outliers start: 36 outliers final: 24 residues processed: 104 average time/residue: 0.7872 time to fit residues: 92.0847 Evaluate side-chains 97 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 69 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1307 CYS Chi-restraints excluded: chain A residue 1310 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 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 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9747 Z= 0.238 Angle : 0.648 12.156 13243 Z= 0.317 Chirality : 0.045 0.262 1521 Planarity : 0.004 0.055 1694 Dihedral : 5.140 35.278 1438 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.92 % Favored : 95.75 % Rotamer: Outliers : 3.91 % Allowed : 17.25 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.25 (0.25), residues: 1200 helix: 1.02 (0.40), residues: 182 sheet: -0.08 (0.22), residues: 514 loop : -0.56 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 619 HIS 0.002 0.001 HIS A 75 PHE 0.016 0.002 PHE A 107 TYR 0.016 0.001 TYR A 620 ARG 0.004 0.000 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 74 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7607 (m90) cc_final: 0.7147 (m90) REVERT: A 395 ASN cc_start: 0.9205 (p0) cc_final: 0.8878 (p0) REVERT: A 471 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8779 (tm) REVERT: A 945 TYR cc_start: 0.7824 (OUTLIER) cc_final: 0.6925 (p90) REVERT: A 953 MET cc_start: 0.5921 (OUTLIER) cc_final: 0.5580 (ptp) REVERT: A 1015 MET cc_start: 0.7855 (pmm) cc_final: 0.7564 (pmm) REVERT: A 1045 PHE cc_start: 0.9208 (m-80) cc_final: 0.8676 (m-80) REVERT: A 1213 LYS cc_start: 0.8877 (mmpt) cc_final: 0.8579 (mmpt) REVERT: A 1260 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7408 (mm-30) outliers start: 41 outliers final: 27 residues processed: 105 average time/residue: 0.7516 time to fit residues: 89.1909 Evaluate side-chains 101 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 70 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 953 MET Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1307 CYS Chi-restraints excluded: chain A residue 1310 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 79 optimal weight: 0.0040 chunk 57 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9747 Z= 0.253 Angle : 0.668 12.134 13243 Z= 0.327 Chirality : 0.045 0.262 1521 Planarity : 0.004 0.054 1694 Dihedral : 5.111 35.127 1438 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.08 % Favored : 95.58 % Rotamer: Outliers : 3.91 % Allowed : 18.02 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.24 (0.25), residues: 1200 helix: 1.05 (0.41), residues: 184 sheet: -0.05 (0.22), residues: 513 loop : -0.60 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 619 HIS 0.002 0.001 HIS A 75 PHE 0.018 0.002 PHE A 107 TYR 0.016 0.001 TYR A 620 ARG 0.003 0.000 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 70 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7603 (m90) cc_final: 0.7082 (m90) REVERT: A 395 ASN cc_start: 0.9203 (p0) cc_final: 0.8881 (p0) REVERT: A 471 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8783 (tm) REVERT: A 945 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.6928 (p90) REVERT: A 953 MET cc_start: 0.5885 (OUTLIER) cc_final: 0.5569 (ptp) REVERT: A 975 MET cc_start: 0.7199 (pmm) cc_final: 0.6921 (pmm) REVERT: A 1015 MET cc_start: 0.7859 (pmm) cc_final: 0.7564 (pmm) REVERT: A 1045 PHE cc_start: 0.9205 (m-80) cc_final: 0.8674 (m-80) REVERT: A 1213 LYS cc_start: 0.8876 (mmpt) cc_final: 0.8577 (mmpt) REVERT: A 1260 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7406 (mm-30) REVERT: A 1301 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7900 (pt0) outliers start: 41 outliers final: 27 residues processed: 102 average time/residue: 0.7376 time to fit residues: 84.7411 Evaluate side-chains 101 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 69 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 953 MET Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1229 HIS Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1307 CYS Chi-restraints excluded: chain A residue 1310 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 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 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9747 Z= 0.234 Angle : 0.678 11.978 13243 Z= 0.326 Chirality : 0.045 0.260 1521 Planarity : 0.004 0.054 1694 Dihedral : 5.051 35.023 1438 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.92 % Favored : 95.75 % Rotamer: Outliers : 3.34 % Allowed : 18.97 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.18 (0.25), residues: 1200 helix: 1.08 (0.41), residues: 184 sheet: -0.01 (0.23), residues: 509 loop : -0.55 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 619 HIS 0.002 0.000 HIS A 75 PHE 0.017 0.002 PHE A 387 TYR 0.014 0.001 TYR A 620 ARG 0.004 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 76 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7561 (m90) cc_final: 0.7331 (m90) REVERT: A 395 ASN cc_start: 0.9206 (p0) cc_final: 0.8885 (p0) REVERT: A 471 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8785 (tm) REVERT: A 945 TYR cc_start: 0.7807 (OUTLIER) cc_final: 0.6945 (p90) REVERT: A 953 MET cc_start: 0.5839 (OUTLIER) cc_final: 0.5552 (ptp) REVERT: A 975 MET cc_start: 0.7076 (pmm) cc_final: 0.6836 (pmm) REVERT: A 1005 PHE cc_start: 0.8560 (m-80) cc_final: 0.8238 (m-80) REVERT: A 1015 MET cc_start: 0.7860 (pmm) cc_final: 0.7571 (pmm) REVERT: A 1045 PHE cc_start: 0.9169 (m-80) cc_final: 0.8640 (m-80) REVERT: A 1213 LYS cc_start: 0.8875 (mmpt) cc_final: 0.8573 (mmpt) REVERT: A 1260 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7407 (mm-30) REVERT: A 1301 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7953 (pt0) outliers start: 35 outliers final: 29 residues processed: 103 average time/residue: 0.7958 time to fit residues: 91.7878 Evaluate side-chains 107 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 73 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 953 MET Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1229 HIS Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1307 CYS Chi-restraints excluded: chain A residue 1310 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 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 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9747 Z= 0.279 Angle : 0.706 12.410 13243 Z= 0.340 Chirality : 0.046 0.268 1521 Planarity : 0.004 0.054 1694 Dihedral : 5.083 35.242 1438 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.33 % Favored : 95.33 % Rotamer: Outliers : 3.34 % Allowed : 19.16 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.21 (0.25), residues: 1200 helix: 1.12 (0.41), residues: 184 sheet: -0.04 (0.23), residues: 511 loop : -0.59 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 619 HIS 0.003 0.001 HIS A 855 PHE 0.017 0.002 PHE A 107 TYR 0.014 0.001 TYR A 620 ARG 0.003 0.000 ARG A 610 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 77 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7657 (m90) cc_final: 0.7239 (m90) REVERT: A 395 ASN cc_start: 0.9209 (p0) cc_final: 0.8886 (p0) REVERT: A 471 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8725 (tm) REVERT: A 945 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.6961 (p90) REVERT: A 953 MET cc_start: 0.5863 (OUTLIER) cc_final: 0.5597 (ptp) REVERT: A 975 MET cc_start: 0.7053 (pmm) cc_final: 0.6829 (pmm) REVERT: A 1015 MET cc_start: 0.7882 (pmm) cc_final: 0.7582 (pmm) REVERT: A 1045 PHE cc_start: 0.9174 (m-80) cc_final: 0.8647 (m-80) REVERT: A 1213 LYS cc_start: 0.8892 (mmpt) cc_final: 0.8583 (mmpt) REVERT: A 1260 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7435 (mm-30) REVERT: A 1301 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7977 (pt0) outliers start: 35 outliers final: 27 residues processed: 104 average time/residue: 0.7998 time to fit residues: 93.5539 Evaluate side-chains 104 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 72 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 953 MET Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1229 HIS Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1307 CYS Chi-restraints excluded: chain A residue 1310 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 96 optimal weight: 0.0000 chunk 40 optimal weight: 4.9990 chunk 98 optimal weight: 0.0670 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 overall best weight: 0.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.116044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.080172 restraints weight = 21690.987| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.81 r_work: 0.3267 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9747 Z= 0.181 Angle : 0.682 12.193 13243 Z= 0.327 Chirality : 0.045 0.268 1521 Planarity : 0.004 0.054 1694 Dihedral : 4.862 33.953 1438 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.75 % Favored : 96.00 % Rotamer: Outliers : 2.57 % Allowed : 20.02 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.09 % 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: -0.13 (0.25), residues: 1200 helix: 0.86 (0.40), residues: 184 sheet: 0.09 (0.23), residues: 498 loop : -0.48 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1173 HIS 0.002 0.000 HIS A 75 PHE 0.018 0.001 PHE A1040 TYR 0.011 0.001 TYR A 620 ARG 0.003 0.000 ARG A 610 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3167.94 seconds wall clock time: 58 minutes 37.53 seconds (3517.53 seconds total)