Starting phenix.real_space_refine on Mon May 6 23:25:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpr_18560/05_2024/8qpr_18560.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpr_18560/05_2024/8qpr_18560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpr_18560/05_2024/8qpr_18560.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpr_18560/05_2024/8qpr_18560.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpr_18560/05_2024/8qpr_18560.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpr_18560/05_2024/8qpr_18560.pdb" } resolution = 3.8 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= 0.027 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 22 5.16 5 C 3691 2.51 5 N 945 2.21 5 O 1129 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "D TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 5787 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3844 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 28, 'TRANS': 462} Chain breaks: 4 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "D" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 803 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "E" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 117} 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 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: "F" 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: "c" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" 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: "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 Time building chain proxies: 3.74, per 1000 atoms: 0.65 Number of scatterers: 5787 At special positions: 0 Unit cell: (81.12, 75.66, 149.76, 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 22 16.00 O 1129 8.00 N 945 7.00 C 3691 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG a 1 " - " NAG a 2 " " NAG c 1 " - " NAG c 2 " " NAG e 1 " - " NAG e 2 " BETA1-6 " NAG G 1 " - " FUC G 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG c 1 " - " FUC c 3 " " NAG e 1 " - " FUC e 3 " NAG-ASN " NAG B 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 61 " " NAG G 1 " - " ASN A 331 " " NAG a 1 " - " ASN A 282 " " NAG c 1 " - " ASN A 343 " " NAG e 1 " - " ASN E 59 " Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 998.3 milliseconds 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1332 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 11 sheets defined 4.8% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.611A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 386 through 390 removed outlier: 4.049A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.797A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.959A pdb=" N THR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.166A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.843A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.340A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 328 removed outlier: 3.984A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.622A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AA8, first strand: chain 'D' and resid 19 through 23 removed outlier: 3.884A pdb=" N SER D 67 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 47 through 51 removed outlier: 6.362A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP D 87 " --> pdb=" O HIS D 40 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR D 93 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL D 100 " --> pdb=" O TYR D 93 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.606A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.833A pdb=" N ALA E 92 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) 140 hydrogen bonds defined for protein. 348 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: 1.42 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1802 1.35 - 1.47: 1626 1.47 - 1.59: 2481 1.59 - 1.71: 0 1.71 - 1.83: 25 Bond restraints: 5934 Sorted by residual: bond pdb=" C PHE A 559 " pdb=" N LEU A 560 " ideal model delta sigma weight residual 1.329 1.257 0.072 1.86e-02 2.89e+03 1.48e+01 bond pdb=" C1 FUC G 3 " pdb=" C2 FUC G 3 " ideal model delta sigma weight residual 1.528 1.571 -0.043 2.00e-02 2.50e+03 4.67e+00 bond pdb=" C5 FUC G 3 " pdb=" O5 FUC G 3 " ideal model delta sigma weight residual 1.423 1.465 -0.042 2.00e-02 2.50e+03 4.49e+00 bond pdb=" C1 FUC G 3 " pdb=" O5 FUC G 3 " ideal model delta sigma weight residual 1.400 1.437 -0.037 2.00e-02 2.50e+03 3.49e+00 bond pdb=" C5 FUC e 3 " pdb=" O5 FUC e 3 " ideal model delta sigma weight residual 1.423 1.457 -0.034 2.00e-02 2.50e+03 2.92e+00 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.57: 171 106.57 - 113.43: 3224 113.43 - 120.30: 2075 120.30 - 127.16: 2562 127.16 - 134.03: 58 Bond angle restraints: 8090 Sorted by residual: angle pdb=" C TYR D 51 " pdb=" N GLU D 52 " pdb=" CA GLU D 52 " ideal model delta sigma weight residual 121.54 132.03 -10.49 1.91e+00 2.74e-01 3.01e+01 angle pdb=" C PHE A 559 " pdb=" N LEU A 560 " pdb=" CA LEU A 560 " ideal model delta sigma weight residual 121.48 112.16 9.32 2.04e+00 2.40e-01 2.09e+01 angle pdb=" C GLY A 416 " pdb=" N LYS A 417 " pdb=" CA LYS A 417 " ideal model delta sigma weight residual 121.54 129.43 -7.89 1.91e+00 2.74e-01 1.71e+01 angle pdb=" N GLU D 52 " pdb=" CA GLU D 52 " pdb=" C GLU D 52 " ideal model delta sigma weight residual 110.80 119.44 -8.64 2.13e+00 2.20e-01 1.65e+01 angle pdb=" CA LEU A 212 " pdb=" CB LEU A 212 " pdb=" CG LEU A 212 " ideal model delta sigma weight residual 116.30 128.49 -12.19 3.50e+00 8.16e-02 1.21e+01 ... (remaining 8085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.53: 3424 24.53 - 49.07: 163 49.07 - 73.60: 34 73.60 - 98.13: 23 98.13 - 122.67: 9 Dihedral angle restraints: 3653 sinusoidal: 1564 harmonic: 2089 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 35.85 57.15 1 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" CA GLU D 52 " pdb=" C GLU D 52 " pdb=" N VAL D 53 " pdb=" CA VAL D 53 " ideal model delta harmonic sigma weight residual 180.00 149.51 30.49 0 5.00e+00 4.00e-02 3.72e+01 dihedral pdb=" CA TRP A 436 " pdb=" C TRP A 436 " pdb=" N ASN A 437 " pdb=" CA ASN A 437 " ideal model delta harmonic sigma weight residual 180.00 149.85 30.15 0 5.00e+00 4.00e-02 3.64e+01 ... (remaining 3650 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 862 0.092 - 0.185: 76 0.185 - 0.277: 3 0.277 - 0.369: 0 0.369 - 0.462: 1 Chirality restraints: 942 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.33e+00 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB THR A 95 " pdb=" CA THR A 95 " pdb=" OG1 THR A 95 " pdb=" CG2 THR A 95 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 939 not shown) Planarity restraints: 1027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 417 " 0.020 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C LYS A 417 " -0.068 2.00e-02 2.50e+03 pdb=" O LYS A 417 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE A 418 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 52 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.10e+00 pdb=" N PRO E 53 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 53 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 53 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " -0.032 5.00e-02 4.00e+02 4.97e-02 3.94e+00 pdb=" N PRO A 295 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.028 5.00e-02 4.00e+02 ... (remaining 1024 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1236 2.78 - 3.31: 5083 3.31 - 3.84: 8392 3.84 - 4.37: 9195 4.37 - 4.90: 16937 Nonbonded interactions: 40843 Sorted by model distance: nonbonded pdb=" NH1 ARG E 23 " pdb=" O ILE E 76 " model vdw 2.246 2.520 nonbonded pdb=" O PRO D 7 " pdb=" OG1 THR D 105 " model vdw 2.253 2.440 nonbonded pdb=" NE ARG A 357 " pdb=" OD1 ASN A 394 " model vdw 2.264 2.520 nonbonded pdb=" OG SER E 17 " pdb=" OE2 GLU E 82 " model vdw 2.295 2.440 nonbonded pdb=" NH2 ARG A 454 " pdb=" O ASP A 467 " model vdw 2.302 2.520 ... (remaining 40838 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 'F' selection = chain 'a' } ncs_group { reference = chain 'G' selection = chain 'c' selection = chain 'e' } 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 group one per residue 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: 12.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 39.010 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.360 Find NCS groups from input model: 0.160 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 0.072 5934 Z= 0.399 Angle : 0.889 12.191 8090 Z= 0.462 Chirality : 0.054 0.462 942 Planarity : 0.006 0.062 1021 Dihedral : 17.697 122.667 2300 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.55 % Favored : 87.45 % Rotamer: Outliers : 0.16 % Allowed : 0.99 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -3.38 (0.29), residues: 709 helix: -3.62 (0.69), residues: 31 sheet: -0.44 (0.35), residues: 227 loop : -3.35 (0.24), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP D 99 HIS 0.005 0.002 HIS A 66 PHE 0.027 0.002 PHE A 377 TYR 0.023 0.002 TYR E 60 ARG 0.008 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.494 Fit side-chains REVERT: D 56 ARG cc_start: 0.8704 (ttp-110) cc_final: 0.8468 (ttt-90) REVERT: D 107 LEU cc_start: 0.8378 (tp) cc_final: 0.7813 (tp) REVERT: E 63 LYS cc_start: 0.9265 (ttpp) cc_final: 0.9032 (ttpp) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.1821 time to fit residues: 20.3666 Evaluate side-chains 58 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 0.0770 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5934 Z= 0.217 Angle : 0.754 9.507 8090 Z= 0.371 Chirality : 0.049 0.305 942 Planarity : 0.005 0.048 1021 Dihedral : 15.182 110.318 1087 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 1.64 % Allowed : 9.21 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.07 (0.29), residues: 709 helix: -3.60 (0.61), residues: 37 sheet: -0.12 (0.35), residues: 221 loop : -3.14 (0.25), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 50 HIS 0.005 0.001 HIS A 69 PHE 0.024 0.001 PHE A 168 TYR 0.014 0.001 TYR A 473 ARG 0.004 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.610 Fit side-chains REVERT: D 56 ARG cc_start: 0.8754 (ttp-110) cc_final: 0.8476 (ttt-90) REVERT: D 67 SER cc_start: 0.7955 (m) cc_final: 0.7692 (p) REVERT: E 63 LYS cc_start: 0.9166 (ttpp) cc_final: 0.8782 (ttpp) outliers start: 10 outliers final: 6 residues processed: 73 average time/residue: 0.1807 time to fit residues: 17.4144 Evaluate side-chains 71 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain D residue 41 HIS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 4 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 0.0370 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5934 Z= 0.232 Angle : 0.722 10.141 8090 Z= 0.355 Chirality : 0.048 0.291 942 Planarity : 0.005 0.046 1021 Dihedral : 12.538 101.112 1087 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer: Outliers : 2.14 % Allowed : 11.84 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.98 (0.30), residues: 709 helix: -3.75 (0.56), residues: 37 sheet: -0.11 (0.35), residues: 227 loop : -3.06 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.005 0.001 HIS A 66 PHE 0.018 0.001 PHE A 86 TYR 0.016 0.001 TYR D 51 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: D 56 ARG cc_start: 0.8785 (ttp-110) cc_final: 0.8475 (ttt-90) REVERT: E 38 ARG cc_start: 0.8243 (ttp-170) cc_final: 0.7975 (ttp-170) REVERT: E 63 LYS cc_start: 0.9169 (ttpp) cc_final: 0.8831 (ttpp) outliers start: 13 outliers final: 8 residues processed: 76 average time/residue: 0.1854 time to fit residues: 18.5215 Evaluate side-chains 71 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain E residue 4 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 chunk 7 optimal weight: 0.1980 chunk 30 optimal weight: 0.6980 chunk 43 optimal weight: 0.0050 chunk 64 optimal weight: 0.0030 chunk 68 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.2404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN D 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5934 Z= 0.158 Angle : 0.685 14.945 8090 Z= 0.331 Chirality : 0.047 0.304 942 Planarity : 0.004 0.046 1021 Dihedral : 10.856 95.384 1087 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 2.63 % Allowed : 13.82 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.87 (0.30), residues: 709 helix: -3.59 (0.61), residues: 37 sheet: -0.42 (0.34), residues: 251 loop : -2.85 (0.26), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 50 HIS 0.003 0.001 HIS A 207 PHE 0.007 0.001 PHE A 92 TYR 0.011 0.001 TYR E 60 ARG 0.001 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.657 Fit side-chains REVERT: A 415 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8378 (p) REVERT: D 41 HIS cc_start: 0.7918 (OUTLIER) cc_final: 0.7272 (t-90) REVERT: D 52 GLU cc_start: 0.6991 (tt0) cc_final: 0.6789 (tt0) REVERT: D 56 ARG cc_start: 0.8683 (ttp-110) cc_final: 0.8356 (ttt-90) REVERT: E 38 ARG cc_start: 0.8212 (ttp-170) cc_final: 0.7982 (ttp-170) REVERT: E 63 LYS cc_start: 0.9149 (ttpp) cc_final: 0.8805 (ttpp) outliers start: 16 outliers final: 7 residues processed: 83 average time/residue: 0.1855 time to fit residues: 20.3488 Evaluate side-chains 86 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain D residue 41 HIS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 47 optimal weight: 0.0010 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 0.0270 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.0070 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 0.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5934 Z= 0.172 Angle : 0.666 12.098 8090 Z= 0.326 Chirality : 0.047 0.292 942 Planarity : 0.004 0.047 1021 Dihedral : 9.986 88.793 1087 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 2.96 % Allowed : 14.80 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.74 (0.30), residues: 709 helix: -3.32 (0.73), residues: 31 sheet: -0.26 (0.35), residues: 247 loop : -2.84 (0.26), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 50 HIS 0.004 0.001 HIS A 207 PHE 0.010 0.001 PHE A 86 TYR 0.012 0.001 TYR D 51 ARG 0.002 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.700 Fit side-chains REVERT: A 298 GLU cc_start: 0.8117 (tt0) cc_final: 0.7883 (mt-10) REVERT: A 415 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8424 (p) REVERT: D 56 ARG cc_start: 0.8644 (ttp-110) cc_final: 0.8328 (ttt-90) REVERT: E 63 LYS cc_start: 0.9146 (ttpp) cc_final: 0.8824 (ttpp) outliers start: 18 outliers final: 15 residues processed: 88 average time/residue: 0.1790 time to fit residues: 20.8950 Evaluate side-chains 87 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 7 optimal weight: 0.2980 chunk 39 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5934 Z= 0.265 Angle : 0.707 10.949 8090 Z= 0.350 Chirality : 0.047 0.289 942 Planarity : 0.005 0.047 1021 Dihedral : 9.671 78.275 1087 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 4.77 % Allowed : 15.95 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -2.72 (0.30), residues: 709 helix: -2.96 (0.86), residues: 25 sheet: -0.23 (0.35), residues: 240 loop : -2.85 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 37 HIS 0.003 0.001 HIS E 35 PHE 0.024 0.001 PHE A 86 TYR 0.018 0.001 TYR D 51 ARG 0.007 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 69 time to evaluate : 0.650 Fit side-chains REVERT: D 41 HIS cc_start: 0.7965 (OUTLIER) cc_final: 0.7361 (t-90) REVERT: D 56 ARG cc_start: 0.8775 (ttp-110) cc_final: 0.8442 (ttt-90) REVERT: E 63 LYS cc_start: 0.9194 (ttpp) cc_final: 0.8916 (ttpp) outliers start: 29 outliers final: 20 residues processed: 84 average time/residue: 0.2002 time to fit residues: 21.8645 Evaluate side-chains 89 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 68 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 41 HIS Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 0.0370 chunk 57 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5934 Z= 0.227 Angle : 0.704 10.573 8090 Z= 0.346 Chirality : 0.047 0.295 942 Planarity : 0.005 0.047 1021 Dihedral : 9.179 62.891 1087 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 3.95 % Allowed : 15.95 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -2.66 (0.30), residues: 709 helix: -2.94 (0.86), residues: 25 sheet: -0.17 (0.36), residues: 232 loop : -2.77 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 37 HIS 0.003 0.001 HIS A 207 PHE 0.016 0.001 PHE A 86 TYR 0.015 0.001 TYR D 51 ARG 0.007 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 68 time to evaluate : 0.659 Fit side-chains REVERT: A 357 ARG cc_start: 0.6961 (tpt-90) cc_final: 0.6632 (tpt-90) REVERT: A 394 ASN cc_start: 0.7376 (m-40) cc_final: 0.6780 (m-40) REVERT: D 41 HIS cc_start: 0.7981 (OUTLIER) cc_final: 0.7388 (t-90) REVERT: D 56 ARG cc_start: 0.8749 (ttp-110) cc_final: 0.8387 (ttt-90) REVERT: E 63 LYS cc_start: 0.9186 (ttpp) cc_final: 0.8882 (ttpp) outliers start: 24 outliers final: 18 residues processed: 82 average time/residue: 0.1770 time to fit residues: 19.3060 Evaluate side-chains 88 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 69 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 41 HIS Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 65 optimal weight: 0.0020 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 38 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5934 Z= 0.176 Angle : 0.678 10.072 8090 Z= 0.330 Chirality : 0.046 0.299 942 Planarity : 0.004 0.044 1021 Dihedral : 8.497 59.778 1087 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 3.62 % Allowed : 16.78 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -2.58 (0.31), residues: 709 helix: -2.84 (0.88), residues: 25 sheet: -0.17 (0.36), residues: 236 loop : -2.70 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 37 HIS 0.004 0.001 HIS A 207 PHE 0.009 0.001 PHE A 86 TYR 0.010 0.001 TYR D 51 ARG 0.007 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 75 time to evaluate : 0.571 Fit side-chains REVERT: A 357 ARG cc_start: 0.7020 (tpt-90) cc_final: 0.6598 (tpt-90) REVERT: A 394 ASN cc_start: 0.7407 (m-40) cc_final: 0.6770 (m-40) REVERT: D 41 HIS cc_start: 0.7855 (OUTLIER) cc_final: 0.7378 (t-90) REVERT: D 56 ARG cc_start: 0.8675 (ttp-110) cc_final: 0.8361 (ttt-90) REVERT: E 63 LYS cc_start: 0.9187 (ttpp) cc_final: 0.8931 (ttpp) outliers start: 22 outliers final: 16 residues processed: 87 average time/residue: 0.1789 time to fit residues: 20.6349 Evaluate side-chains 89 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 72 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 41 HIS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 60 optimal weight: 0.0570 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 0.0980 chunk 70 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5934 Z= 0.192 Angle : 0.683 10.152 8090 Z= 0.334 Chirality : 0.046 0.295 942 Planarity : 0.004 0.044 1021 Dihedral : 8.245 54.093 1087 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 3.78 % Allowed : 17.11 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -2.55 (0.31), residues: 709 helix: -2.88 (0.86), residues: 25 sheet: -0.12 (0.36), residues: 236 loop : -2.69 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 37 HIS 0.004 0.001 HIS A 207 PHE 0.013 0.001 PHE A 86 TYR 0.013 0.001 TYR D 51 ARG 0.008 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 71 time to evaluate : 0.697 Fit side-chains REVERT: A 357 ARG cc_start: 0.6988 (tpt-90) cc_final: 0.6573 (tpt-90) REVERT: A 394 ASN cc_start: 0.7462 (m-40) cc_final: 0.6802 (m-40) REVERT: D 56 ARG cc_start: 0.8670 (ttp-110) cc_final: 0.8312 (ttt-90) REVERT: E 63 LYS cc_start: 0.9202 (ttpp) cc_final: 0.8781 (ttpp) outliers start: 23 outliers final: 20 residues processed: 81 average time/residue: 0.1794 time to fit residues: 19.2803 Evaluate side-chains 88 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 68 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 8 optimal weight: 0.0870 chunk 15 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 0.1980 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5934 Z= 0.257 Angle : 0.709 10.092 8090 Z= 0.350 Chirality : 0.047 0.293 942 Planarity : 0.005 0.045 1021 Dihedral : 8.250 52.958 1087 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 4.44 % Allowed : 16.28 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -2.61 (0.31), residues: 709 helix: -2.95 (0.85), residues: 25 sheet: -0.14 (0.36), residues: 232 loop : -2.73 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 37 HIS 0.003 0.001 HIS A 207 PHE 0.020 0.001 PHE A 86 TYR 0.015 0.001 TYR D 51 ARG 0.008 0.000 ARG A 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 67 time to evaluate : 0.606 Fit side-chains REVERT: A 357 ARG cc_start: 0.7061 (tpt-90) cc_final: 0.6680 (tpt-90) REVERT: A 394 ASN cc_start: 0.7500 (m-40) cc_final: 0.6713 (m-40) REVERT: D 41 HIS cc_start: 0.7902 (OUTLIER) cc_final: 0.7372 (t-90) REVERT: D 56 ARG cc_start: 0.8718 (ttp-110) cc_final: 0.8345 (ttt-90) REVERT: E 63 LYS cc_start: 0.9223 (ttpp) cc_final: 0.8818 (ttpp) outliers start: 27 outliers final: 24 residues processed: 83 average time/residue: 0.1802 time to fit residues: 19.9724 Evaluate side-chains 91 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 66 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 41 HIS Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 1 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 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 207 HIS ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.150094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 190)---------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120705 restraints weight = 9530.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.120291 restraints weight = 14875.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 100)---------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110334 restraints weight = 14975.000| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5934 Z= 0.216 Angle : 0.690 9.953 8090 Z= 0.340 Chirality : 0.047 0.300 942 Planarity : 0.004 0.045 1021 Dihedral : 7.992 53.613 1087 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 4.11 % Allowed : 16.94 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -2.55 (0.31), residues: 709 helix: -2.96 (0.83), residues: 25 sheet: -0.00 (0.37), residues: 226 loop : -2.71 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 37 HIS 0.005 0.001 HIS A 207 PHE 0.015 0.001 PHE A 86 TYR 0.013 0.001 TYR D 51 ARG 0.007 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2021.00 seconds wall clock time: 37 minutes 17.12 seconds (2237.12 seconds total)