Starting phenix.real_space_refine on Mon Mar 11 03:05:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esm_28577/03_2024/8esm_28577_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esm_28577/03_2024/8esm_28577.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esm_28577/03_2024/8esm_28577_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esm_28577/03_2024/8esm_28577_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esm_28577/03_2024/8esm_28577_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esm_28577/03_2024/8esm_28577.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esm_28577/03_2024/8esm_28577.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esm_28577/03_2024/8esm_28577_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esm_28577/03_2024/8esm_28577_updated.pdb" } resolution = 3.2 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= 0.004 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 42 5.16 5 C 4508 2.51 5 N 1140 2.21 5 O 1088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 116": "OD1" <-> "OD2" Residue "A ASP 127": "OD1" <-> "OD2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "B ASP 127": "OD1" <-> "OD2" Residue "B GLU 161": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "B ASP 251": "OD1" <-> "OD2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "B ASP 315": "OD1" <-> "OD2" Residue "B ARG 318": "NH1" <-> "NH2" Residue "B ARG 362": "NH1" <-> "NH2" Residue "B ARG 424": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6778 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3360 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 18, 'TRANS': 387} Chain breaks: 1 Chain: "B" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3360 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 18, 'TRANS': 387} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'WS0': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'WS0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.06, per 1000 atoms: 0.60 Number of scatterers: 6778 At special positions: 0 Unit cell: (112.23, 94.83, 82.65, 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 42 16.00 O 1088 8.00 N 1140 7.00 C 4508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.1 seconds 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1564 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 0 sheets defined 70.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 88 through 111 removed outlier: 5.768A pdb=" N ARG A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LEU A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 126 Processing helix chain 'A' and resid 132 through 156 removed outlier: 3.653A pdb=" N ILE A 138 " --> pdb=" O PRO A 134 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASN A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 184 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 191 through 227 removed outlier: 3.780A pdb=" N SER A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 275 through 299 Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 316 through 342 removed outlier: 3.772A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.625A pdb=" N GLN A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 Processing helix chain 'A' and resid 391 through 395 Processing helix chain 'A' and resid 400 through 423 removed outlier: 4.019A pdb=" N VAL A 421 " --> pdb=" O TYR A 417 " (cutoff:3.500A) Proline residue: A 422 - end of helix Processing helix chain 'A' and resid 430 through 446 removed outlier: 4.621A pdb=" N ILE A 438 " --> pdb=" O MET A 434 " (cutoff:3.500A) Proline residue: A 439 - end of helix Processing helix chain 'A' and resid 450 through 462 Processing helix chain 'A' and resid 466 through 479 removed outlier: 3.857A pdb=" N LEU A 479 " --> pdb=" O ASP A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 111 removed outlier: 5.769A pdb=" N ARG B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 126 Processing helix chain 'B' and resid 132 through 156 removed outlier: 3.653A pdb=" N ILE B 138 " --> pdb=" O PRO B 134 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASN B 141 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 184 Proline residue: B 179 - end of helix Processing helix chain 'B' and resid 191 through 227 removed outlier: 3.780A pdb=" N SER B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'B' and resid 275 through 299 Processing helix chain 'B' and resid 301 through 306 Processing helix chain 'B' and resid 316 through 342 removed outlier: 3.775A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix Processing helix chain 'B' and resid 345 through 352 Processing helix chain 'B' and resid 370 through 376 removed outlier: 3.625A pdb=" N GLN B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN B 376 " --> pdb=" O TYR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 389 Processing helix chain 'B' and resid 391 through 395 Processing helix chain 'B' and resid 400 through 423 removed outlier: 4.018A pdb=" N VAL B 421 " --> pdb=" O TYR B 417 " (cutoff:3.500A) Proline residue: B 422 - end of helix Processing helix chain 'B' and resid 430 through 446 removed outlier: 4.621A pdb=" N ILE B 438 " --> pdb=" O MET B 434 " (cutoff:3.500A) Proline residue: B 439 - end of helix Processing helix chain 'B' and resid 450 through 462 Processing helix chain 'B' and resid 466 through 479 removed outlier: 3.857A pdb=" N LEU B 479 " --> pdb=" O ASP B 475 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1152 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: 1.66 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1894 1.33 - 1.45: 1352 1.45 - 1.57: 3684 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 6998 Sorted by residual: bond pdb=" N WS0 A 501 " pdb=" C10 WS0 A 501 " ideal model delta sigma weight residual 1.425 1.282 0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" N WS0 B 501 " pdb=" C10 WS0 B 501 " ideal model delta sigma weight residual 1.425 1.283 0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" C14 WS0 B 501 " pdb=" O2 WS0 B 501 " ideal model delta sigma weight residual 1.450 1.325 0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" C14 WS0 A 501 " pdb=" O2 WS0 A 501 " ideal model delta sigma weight residual 1.450 1.326 0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C12 WS0 A 501 " pdb=" N1 WS0 A 501 " ideal model delta sigma weight residual 1.450 1.334 0.116 2.00e-02 2.50e+03 3.38e+01 ... (remaining 6993 not shown) Histogram of bond angle deviations from ideal: 98.54 - 105.66: 152 105.66 - 112.79: 3641 112.79 - 119.92: 2532 119.92 - 127.05: 3077 127.05 - 134.18: 128 Bond angle restraints: 9530 Sorted by residual: angle pdb=" N GLY A 464 " pdb=" CA GLY A 464 " pdb=" C GLY A 464 " ideal model delta sigma weight residual 113.18 121.17 -7.99 2.37e+00 1.78e-01 1.14e+01 angle pdb=" N GLY B 464 " pdb=" CA GLY B 464 " pdb=" C GLY B 464 " ideal model delta sigma weight residual 113.18 121.15 -7.97 2.37e+00 1.78e-01 1.13e+01 angle pdb=" CA GLN A 297 " pdb=" C GLN A 297 " pdb=" N GLN A 298 " ideal model delta sigma weight residual 118.59 123.52 -4.93 1.63e+00 3.76e-01 9.16e+00 angle pdb=" N VAL B 478 " pdb=" CA VAL B 478 " pdb=" C VAL B 478 " ideal model delta sigma weight residual 113.07 109.00 4.07 1.36e+00 5.41e-01 8.95e+00 angle pdb=" N VAL A 478 " pdb=" CA VAL A 478 " pdb=" C VAL A 478 " ideal model delta sigma weight residual 113.07 109.00 4.07 1.36e+00 5.41e-01 8.94e+00 ... (remaining 9525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 3482 16.26 - 32.51: 438 32.51 - 48.77: 100 48.77 - 65.03: 12 65.03 - 81.29: 6 Dihedral angle restraints: 4038 sinusoidal: 1626 harmonic: 2412 Sorted by residual: dihedral pdb=" CA ILE B 463 " pdb=" C ILE B 463 " pdb=" N GLY B 464 " pdb=" CA GLY B 464 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ILE A 463 " pdb=" C ILE A 463 " pdb=" N GLY A 464 " pdb=" CA GLY A 464 " ideal model delta harmonic sigma weight residual 180.00 160.04 19.96 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA TYR B 253 " pdb=" C TYR B 253 " pdb=" N TYR B 254 " pdb=" CA TYR B 254 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 4035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.060: 1028 1.060 - 2.120: 0 2.120 - 3.180: 0 3.180 - 4.240: 0 4.240 - 5.300: 4 Chirality restraints: 1032 Sorted by residual: chirality pdb=" C2 WS0 B 501 " pdb=" C1 WS0 B 501 " pdb=" C21 WS0 B 501 " pdb=" C3 WS0 B 501 " both_signs ideal model delta sigma weight residual False -2.73 2.57 -5.30 2.00e-01 2.50e+01 7.02e+02 chirality pdb=" C2 WS0 A 501 " pdb=" C1 WS0 A 501 " pdb=" C21 WS0 A 501 " pdb=" C3 WS0 A 501 " both_signs ideal model delta sigma weight residual False -2.73 2.57 -5.30 2.00e-01 2.50e+01 7.02e+02 chirality pdb=" C5 WS0 A 501 " pdb=" C20 WS0 A 501 " pdb=" C4 WS0 A 501 " pdb=" C6 WS0 A 501 " both_signs ideal model delta sigma weight residual False -2.73 2.49 -5.22 2.00e-01 2.50e+01 6.81e+02 ... (remaining 1029 not shown) Planarity restraints: 1166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 WS0 B 501 " 0.109 2.00e-02 2.50e+03 6.38e-02 8.14e+01 pdb=" C18 WS0 B 501 " -0.042 2.00e-02 2.50e+03 pdb=" C19 WS0 B 501 " -0.044 2.00e-02 2.50e+03 pdb=" C5 WS0 B 501 " 0.110 2.00e-02 2.50e+03 pdb=" C6 WS0 B 501 " -0.025 2.00e-02 2.50e+03 pdb=" C7 WS0 B 501 " -0.045 2.00e-02 2.50e+03 pdb=" C8 WS0 B 501 " -0.042 2.00e-02 2.50e+03 pdb=" C9 WS0 B 501 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 WS0 A 501 " -0.103 2.00e-02 2.50e+03 6.09e-02 7.43e+01 pdb=" C18 WS0 A 501 " 0.039 2.00e-02 2.50e+03 pdb=" C19 WS0 A 501 " 0.044 2.00e-02 2.50e+03 pdb=" C5 WS0 A 501 " -0.106 2.00e-02 2.50e+03 pdb=" C6 WS0 A 501 " 0.025 2.00e-02 2.50e+03 pdb=" C7 WS0 A 501 " 0.043 2.00e-02 2.50e+03 pdb=" C8 WS0 A 501 " 0.039 2.00e-02 2.50e+03 pdb=" C9 WS0 A 501 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N WS0 B 501 " -0.082 2.00e-02 2.50e+03 4.71e-02 4.99e+01 pdb=" C11 WS0 B 501 " -0.008 2.00e-02 2.50e+03 pdb=" C12 WS0 B 501 " 0.014 2.00e-02 2.50e+03 pdb=" C13 WS0 B 501 " -0.029 2.00e-02 2.50e+03 pdb=" C14 WS0 B 501 " -0.008 2.00e-02 2.50e+03 pdb=" N1 WS0 B 501 " 0.056 2.00e-02 2.50e+03 pdb=" N2 WS0 B 501 " 0.001 2.00e-02 2.50e+03 pdb=" N3 WS0 B 501 " -0.033 2.00e-02 2.50e+03 pdb=" O2 WS0 B 501 " 0.088 2.00e-02 2.50e+03 ... (remaining 1163 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 191 2.69 - 3.24: 6986 3.24 - 3.80: 11180 3.80 - 4.35: 13596 4.35 - 4.90: 23157 Nonbonded interactions: 55110 Sorted by model distance: nonbonded pdb=" OE2 GLU B 284 " pdb=" OH TYR B 339 " model vdw 2.141 2.440 nonbonded pdb=" OE2 GLU A 284 " pdb=" OH TYR A 339 " model vdw 2.141 2.440 nonbonded pdb=" OG SER A 210 " pdb=" NE2 HIS A 388 " model vdw 2.240 2.520 nonbonded pdb=" OG SER B 210 " pdb=" NE2 HIS B 388 " model vdw 2.240 2.520 nonbonded pdb=" O SER A 399 " pdb=" N MET A 402 " model vdw 2.244 2.520 ... (remaining 55105 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 'A' selection = chain 'B' } 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: 0.790 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: 3.900 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.440 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 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 : 0.010 0.143 6998 Z= 0.633 Angle : 0.848 7.986 9530 Z= 0.436 Chirality : 0.331 5.300 1032 Planarity : 0.006 0.064 1166 Dihedral : 14.652 81.285 2474 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 0.56 % Allowed : 10.64 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.85 (0.26), residues: 804 helix: -1.19 (0.19), residues: 604 sheet: None (None), residues: 0 loop : -3.75 (0.36), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 299 HIS 0.006 0.001 HIS B 382 PHE 0.014 0.002 PHE B 277 TYR 0.015 0.002 TYR B 417 ARG 0.003 0.000 ARG B 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 0.757 Fit side-chains REVERT: A 131 TRP cc_start: 0.7103 (m100) cc_final: 0.6471 (m100) REVERT: A 151 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7966 (mm-30) REVERT: A 318 ARG cc_start: 0.6589 (mmp80) cc_final: 0.5597 (mmp-170) REVERT: A 389 PHE cc_start: 0.8804 (t80) cc_final: 0.8520 (t80) REVERT: B 131 TRP cc_start: 0.7146 (m100) cc_final: 0.6504 (m100) REVERT: B 151 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7938 (mm-30) REVERT: B 284 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8220 (mt-10) REVERT: B 318 ARG cc_start: 0.6580 (mmp80) cc_final: 0.5593 (mmp-170) REVERT: B 389 PHE cc_start: 0.8821 (t80) cc_final: 0.8562 (t80) REVERT: B 426 PHE cc_start: 0.8102 (m-80) cc_final: 0.7876 (m-80) REVERT: B 427 ARG cc_start: 0.8194 (mpt90) cc_final: 0.7854 (mpt180) outliers start: 4 outliers final: 2 residues processed: 136 average time/residue: 0.3381 time to fit residues: 54.6067 Evaluate side-chains 101 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain B residue 130 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 GLN A 306 ASN ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN B 292 GLN B 306 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6998 Z= 0.168 Angle : 0.612 7.063 9530 Z= 0.293 Chirality : 0.038 0.115 1032 Planarity : 0.004 0.030 1166 Dihedral : 11.859 113.635 932 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.84 % Allowed : 13.59 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.30), residues: 804 helix: 0.42 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -3.37 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 91 HIS 0.003 0.001 HIS B 201 PHE 0.012 0.001 PHE A 277 TYR 0.013 0.001 TYR B 211 ARG 0.003 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 0.769 Fit side-chains REVERT: A 131 TRP cc_start: 0.6976 (m100) cc_final: 0.6597 (m100) REVERT: A 389 PHE cc_start: 0.8746 (t80) cc_final: 0.8441 (t80) REVERT: A 426 PHE cc_start: 0.8059 (m-80) cc_final: 0.7841 (m-80) REVERT: A 431 PHE cc_start: 0.8813 (t80) cc_final: 0.8563 (t80) REVERT: A 477 TYR cc_start: 0.8494 (t80) cc_final: 0.7703 (t80) REVERT: B 131 TRP cc_start: 0.7137 (m100) cc_final: 0.6661 (m100) REVERT: B 151 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7725 (mm-30) REVERT: B 389 PHE cc_start: 0.8744 (t80) cc_final: 0.8454 (t80) REVERT: B 426 PHE cc_start: 0.8017 (m-80) cc_final: 0.7803 (m-80) REVERT: B 431 PHE cc_start: 0.8820 (t80) cc_final: 0.8554 (t80) REVERT: B 477 TYR cc_start: 0.8513 (t80) cc_final: 0.7758 (t80) outliers start: 6 outliers final: 2 residues processed: 112 average time/residue: 0.1895 time to fit residues: 28.4702 Evaluate side-chains 101 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6998 Z= 0.282 Angle : 0.619 7.036 9530 Z= 0.300 Chirality : 0.041 0.225 1032 Planarity : 0.004 0.029 1166 Dihedral : 9.683 110.398 930 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 1.54 % Allowed : 15.55 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.31), residues: 804 helix: 0.84 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -3.22 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 299 HIS 0.003 0.001 HIS A 382 PHE 0.014 0.001 PHE B 148 TYR 0.015 0.001 TYR B 417 ARG 0.003 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 0.767 Fit side-chains REVERT: A 131 TRP cc_start: 0.7022 (m100) cc_final: 0.6610 (m-10) REVERT: A 389 PHE cc_start: 0.8789 (t80) cc_final: 0.8490 (t80) REVERT: A 426 PHE cc_start: 0.8104 (m-80) cc_final: 0.7899 (m-80) REVERT: A 477 TYR cc_start: 0.8503 (t80) cc_final: 0.7677 (t80) REVERT: B 131 TRP cc_start: 0.7123 (m100) cc_final: 0.6637 (m-10) REVERT: B 151 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7824 (mm-30) REVERT: B 389 PHE cc_start: 0.8782 (t80) cc_final: 0.8486 (t80) REVERT: B 431 PHE cc_start: 0.8887 (t80) cc_final: 0.8633 (t80) REVERT: B 477 TYR cc_start: 0.8519 (t80) cc_final: 0.7737 (t80) outliers start: 11 outliers final: 9 residues processed: 114 average time/residue: 0.2179 time to fit residues: 32.1190 Evaluate side-chains 109 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6998 Z= 0.241 Angle : 0.586 6.684 9530 Z= 0.284 Chirality : 0.039 0.135 1032 Planarity : 0.004 0.029 1166 Dihedral : 8.489 96.192 930 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 1.26 % Allowed : 17.09 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.31), residues: 804 helix: 1.18 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -3.12 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 91 HIS 0.003 0.001 HIS B 382 PHE 0.013 0.001 PHE A 277 TYR 0.015 0.001 TYR B 417 ARG 0.003 0.000 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 0.800 Fit side-chains REVERT: A 67 ARG cc_start: 0.6988 (mmm-85) cc_final: 0.6644 (mmm-85) REVERT: A 131 TRP cc_start: 0.6975 (m100) cc_final: 0.6541 (m-10) REVERT: A 389 PHE cc_start: 0.8761 (t80) cc_final: 0.8476 (t80) REVERT: A 426 PHE cc_start: 0.8062 (m-80) cc_final: 0.7849 (m-80) REVERT: A 477 TYR cc_start: 0.8512 (t80) cc_final: 0.7654 (t80) REVERT: B 131 TRP cc_start: 0.7037 (m100) cc_final: 0.6534 (m-10) REVERT: B 151 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7720 (mm-30) REVERT: B 389 PHE cc_start: 0.8757 (t80) cc_final: 0.8479 (t80) REVERT: B 431 PHE cc_start: 0.8865 (t80) cc_final: 0.8600 (t80) REVERT: B 477 TYR cc_start: 0.8526 (t80) cc_final: 0.7678 (t80) outliers start: 9 outliers final: 8 residues processed: 117 average time/residue: 0.1931 time to fit residues: 29.6603 Evaluate side-chains 107 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 69 optimal weight: 0.0980 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6998 Z= 0.272 Angle : 0.593 6.669 9530 Z= 0.289 Chirality : 0.040 0.139 1032 Planarity : 0.004 0.029 1166 Dihedral : 8.565 97.650 930 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 2.10 % Allowed : 17.79 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.31), residues: 804 helix: 1.28 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -3.05 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 299 HIS 0.003 0.001 HIS A 382 PHE 0.016 0.001 PHE B 148 TYR 0.016 0.001 TYR B 417 ARG 0.003 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.778 Fit side-chains REVERT: A 67 ARG cc_start: 0.6972 (mmm-85) cc_final: 0.6637 (mmm-85) REVERT: A 131 TRP cc_start: 0.7021 (m100) cc_final: 0.6569 (m-10) REVERT: A 389 PHE cc_start: 0.8771 (t80) cc_final: 0.8485 (t80) REVERT: A 426 PHE cc_start: 0.8075 (m-80) cc_final: 0.7863 (m-80) REVERT: A 477 TYR cc_start: 0.8522 (t80) cc_final: 0.7612 (t80) REVERT: B 131 TRP cc_start: 0.7031 (m100) cc_final: 0.6538 (m-10) REVERT: B 151 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7756 (mm-30) REVERT: B 389 PHE cc_start: 0.8767 (t80) cc_final: 0.8483 (t80) REVERT: B 477 TYR cc_start: 0.8506 (t80) cc_final: 0.7658 (t80) outliers start: 15 outliers final: 11 residues processed: 115 average time/residue: 0.2098 time to fit residues: 31.4516 Evaluate side-chains 103 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 0.4980 chunk 74 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6998 Z= 0.146 Angle : 0.541 6.192 9530 Z= 0.262 Chirality : 0.037 0.137 1032 Planarity : 0.004 0.027 1166 Dihedral : 8.211 94.304 930 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.40 % Allowed : 19.05 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.32), residues: 804 helix: 1.64 (0.22), residues: 614 sheet: None (None), residues: 0 loop : -3.04 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 374 HIS 0.002 0.001 HIS A 201 PHE 0.011 0.001 PHE A 277 TYR 0.015 0.001 TYR B 417 ARG 0.004 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 0.802 Fit side-chains REVERT: A 67 ARG cc_start: 0.6911 (mmm-85) cc_final: 0.6582 (mmm-85) REVERT: A 131 TRP cc_start: 0.6986 (m100) cc_final: 0.6469 (m-10) REVERT: A 389 PHE cc_start: 0.8702 (t80) cc_final: 0.8447 (t80) REVERT: A 431 PHE cc_start: 0.8796 (t80) cc_final: 0.8564 (t80) REVERT: A 477 TYR cc_start: 0.8477 (t80) cc_final: 0.7500 (t80) REVERT: B 131 TRP cc_start: 0.6952 (m100) cc_final: 0.6400 (m-10) REVERT: B 389 PHE cc_start: 0.8701 (t80) cc_final: 0.8450 (t80) REVERT: B 431 PHE cc_start: 0.8792 (t80) cc_final: 0.8567 (t80) REVERT: B 477 TYR cc_start: 0.8475 (t80) cc_final: 0.7560 (t80) outliers start: 10 outliers final: 5 residues processed: 125 average time/residue: 0.2010 time to fit residues: 32.8275 Evaluate side-chains 117 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 8.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6998 Z= 0.237 Angle : 0.573 6.667 9530 Z= 0.280 Chirality : 0.039 0.138 1032 Planarity : 0.004 0.028 1166 Dihedral : 8.313 95.792 930 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 2.10 % Allowed : 19.47 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.31), residues: 804 helix: 1.59 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -2.91 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 334 HIS 0.003 0.001 HIS A 382 PHE 0.011 0.001 PHE A 277 TYR 0.016 0.001 TYR B 417 ARG 0.004 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 0.821 Fit side-chains REVERT: A 67 ARG cc_start: 0.6887 (mmm-85) cc_final: 0.6535 (mmm-85) REVERT: A 131 TRP cc_start: 0.6988 (m100) cc_final: 0.6463 (m-10) REVERT: A 389 PHE cc_start: 0.8735 (t80) cc_final: 0.8465 (t80) REVERT: A 477 TYR cc_start: 0.8501 (t80) cc_final: 0.7511 (t80) REVERT: B 131 TRP cc_start: 0.6968 (m100) cc_final: 0.6420 (m-10) REVERT: B 151 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7713 (mm-30) REVERT: B 389 PHE cc_start: 0.8732 (t80) cc_final: 0.8466 (t80) REVERT: B 477 TYR cc_start: 0.8501 (t80) cc_final: 0.7575 (t80) outliers start: 15 outliers final: 11 residues processed: 127 average time/residue: 0.2165 time to fit residues: 35.4823 Evaluate side-chains 124 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 0.0870 chunk 73 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6998 Z= 0.145 Angle : 0.540 6.269 9530 Z= 0.261 Chirality : 0.037 0.134 1032 Planarity : 0.004 0.028 1166 Dihedral : 8.110 93.787 930 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.54 % Allowed : 20.31 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.32), residues: 804 helix: 1.84 (0.22), residues: 614 sheet: None (None), residues: 0 loop : -2.93 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 374 HIS 0.002 0.000 HIS A 201 PHE 0.011 0.001 PHE A 277 TYR 0.016 0.001 TYR B 417 ARG 0.004 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 0.789 Fit side-chains REVERT: A 131 TRP cc_start: 0.6925 (m100) cc_final: 0.6392 (m-10) REVERT: A 389 PHE cc_start: 0.8688 (t80) cc_final: 0.8422 (t80) REVERT: A 431 PHE cc_start: 0.8796 (t80) cc_final: 0.8545 (t80) REVERT: A 477 TYR cc_start: 0.8470 (t80) cc_final: 0.7490 (t80) REVERT: B 131 TRP cc_start: 0.6926 (m100) cc_final: 0.6336 (m-10) REVERT: B 389 PHE cc_start: 0.8680 (t80) cc_final: 0.8443 (t80) REVERT: B 431 PHE cc_start: 0.8788 (t80) cc_final: 0.8545 (t80) REVERT: B 477 TYR cc_start: 0.8458 (t80) cc_final: 0.7469 (t80) outliers start: 11 outliers final: 10 residues processed: 125 average time/residue: 0.2014 time to fit residues: 32.9753 Evaluate side-chains 122 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 56 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6998 Z= 0.155 Angle : 0.546 6.111 9530 Z= 0.263 Chirality : 0.037 0.133 1032 Planarity : 0.004 0.027 1166 Dihedral : 8.030 93.045 930 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.54 % Allowed : 20.17 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.32), residues: 804 helix: 1.88 (0.22), residues: 616 sheet: None (None), residues: 0 loop : -2.84 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 299 HIS 0.002 0.000 HIS A 201 PHE 0.010 0.001 PHE A 277 TYR 0.017 0.001 TYR B 417 ARG 0.004 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 0.749 Fit side-chains REVERT: A 131 TRP cc_start: 0.6881 (m100) cc_final: 0.6352 (m-10) REVERT: A 264 GLU cc_start: 0.8370 (tt0) cc_final: 0.8168 (tt0) REVERT: A 431 PHE cc_start: 0.8798 (t80) cc_final: 0.8573 (t80) REVERT: A 477 TYR cc_start: 0.8494 (t80) cc_final: 0.7505 (t80) REVERT: B 389 PHE cc_start: 0.8673 (t80) cc_final: 0.8435 (t80) REVERT: B 431 PHE cc_start: 0.8802 (t80) cc_final: 0.8554 (t80) REVERT: B 477 TYR cc_start: 0.8454 (t80) cc_final: 0.7466 (t80) outliers start: 11 outliers final: 10 residues processed: 121 average time/residue: 0.2058 time to fit residues: 32.6810 Evaluate side-chains 120 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6998 Z= 0.273 Angle : 0.601 6.557 9530 Z= 0.291 Chirality : 0.040 0.138 1032 Planarity : 0.004 0.029 1166 Dihedral : 8.317 96.608 930 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 1.82 % Allowed : 20.45 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.31), residues: 804 helix: 1.70 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -2.78 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 299 HIS 0.003 0.001 HIS A 382 PHE 0.011 0.001 PHE A 277 TYR 0.016 0.001 TYR B 417 ARG 0.005 0.000 ARG B 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.740 Fit side-chains REVERT: A 131 TRP cc_start: 0.6923 (m100) cc_final: 0.6388 (m-10) REVERT: A 477 TYR cc_start: 0.8568 (t80) cc_final: 0.7574 (t80) REVERT: B 131 TRP cc_start: 0.6897 (m100) cc_final: 0.6311 (m-10) REVERT: B 389 PHE cc_start: 0.8741 (t80) cc_final: 0.8429 (t80) REVERT: B 477 TYR cc_start: 0.8494 (t80) cc_final: 0.7503 (t80) outliers start: 13 outliers final: 12 residues processed: 117 average time/residue: 0.2066 time to fit residues: 31.4385 Evaluate side-chains 114 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.146970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.111119 restraints weight = 8903.938| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.08 r_work: 0.3067 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6998 Z= 0.159 Angle : 0.562 6.303 9530 Z= 0.271 Chirality : 0.038 0.136 1032 Planarity : 0.004 0.027 1166 Dihedral : 8.173 95.000 930 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.24 % Allowed : 19.89 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.32), residues: 804 helix: 1.85 (0.22), residues: 616 sheet: None (None), residues: 0 loop : -2.76 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 299 HIS 0.002 0.001 HIS A 201 PHE 0.011 0.001 PHE A 277 TYR 0.017 0.001 TYR B 417 ARG 0.005 0.000 ARG B 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1701.04 seconds wall clock time: 32 minutes 11.31 seconds (1931.31 seconds total)