Starting phenix.real_space_refine on Tue Nov 14 01:27:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esm_28577/11_2023/8esm_28577_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esm_28577/11_2023/8esm_28577.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esm_28577/11_2023/8esm_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_28577/11_2023/8esm_28577_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esm_28577/11_2023/8esm_28577_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esm_28577/11_2023/8esm_28577.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esm_28577/11_2023/8esm_28577.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esm_28577/11_2023/8esm_28577_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esm_28577/11_2023/8esm_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 4.04, 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: 2.54 Conformation dependent library (CDL) restraints added in 1.3 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: 1.11 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: 1.83 Time building geometry restraints manager: 2.75 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: 0.820 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: 3.890 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 21.930 Find NCS groups from input model: 0.330 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.930 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.609 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 136 average time/residue: 0.2999 time to fit residues: 48.4795 Evaluate side-chains 99 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 0.892 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0639 time to fit residues: 1.2939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 33 optimal weight: 0.9980 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: 5.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.8340 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6998 Z= 0.176 Angle : 0.617 7.411 9530 Z= 0.296 Chirality : 0.038 0.159 1032 Planarity : 0.004 0.031 1166 Dihedral : 11.490 112.925 930 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.98 % Allowed : 14.43 % Favored : 84.59 % 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 (0.21), residues: 604 sheet: None (None), residues: 0 loop : -3.36 (0.38), residues: 200 *********************** 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 117 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 0.801 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 114 average time/residue: 0.2056 time to fit residues: 31.1384 Evaluate side-chains 100 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 0.794 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0648 time to fit residues: 1.4243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 60 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 58 optimal weight: 0.0980 chunk 71 optimal weight: 2.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- 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: 0.8415 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 6998 Z= 0.423 Angle : 0.681 7.385 9530 Z= 0.334 Chirality : 0.043 0.225 1032 Planarity : 0.005 0.032 1166 Dihedral : 9.775 111.648 930 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 1.12 % Allowed : 17.09 % Favored : 81.79 % 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: -0.48 (0.30), residues: 804 helix: 0.64 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -3.28 (0.39), residues: 200 *********************** 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 113 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 0.790 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 112 average time/residue: 0.2362 time to fit residues: 33.9299 Evaluate side-chains 106 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.822 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0647 time to fit residues: 1.8997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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: 0.8351 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6998 Z= 0.211 Angle : 0.584 6.966 9530 Z= 0.284 Chirality : 0.039 0.133 1032 Planarity : 0.004 0.030 1166 Dihedral : 8.596 97.212 930 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.42 % Allowed : 18.21 % Favored : 81.37 % 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: 0.18 (0.31), residues: 804 helix: 1.14 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -3.10 (0.39), residues: 202 *********************** 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 115 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 0.786 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 114 average time/residue: 0.1970 time to fit residues: 29.8204 Evaluate side-chains 101 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 0.794 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0629 time to fit residues: 1.0800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2064 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= 0.165 Angle : 0.556 6.437 9530 Z= 0.270 Chirality : 0.037 0.136 1032 Planarity : 0.004 0.042 1166 Dihedral : 8.294 94.592 930 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 1.40 % Allowed : 17.93 % Favored : 80.67 % 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: 0.65 (0.31), residues: 804 helix: 1.49 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -2.97 (0.39), residues: 202 *********************** 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: 10 poor density : 108 time to evaluate : 0.824 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 115 average time/residue: 0.2248 time to fit residues: 33.5795 Evaluate side-chains 110 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.782 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0710 time to fit residues: 1.8002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 6 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8331 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6998 Z= 0.189 Angle : 0.560 6.522 9530 Z= 0.272 Chirality : 0.038 0.136 1032 Planarity : 0.004 0.026 1166 Dihedral : 8.251 94.494 930 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.84 % Allowed : 18.77 % Favored : 80.39 % 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: 1.62 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -2.95 (0.39), residues: 202 *********************** 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 115 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 0.803 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 112 average time/residue: 0.2231 time to fit residues: 32.4501 Evaluate side-chains 109 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 0.827 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0632 time to fit residues: 1.4095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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: 0.8384 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6998 Z= 0.347 Angle : 0.622 6.837 9530 Z= 0.304 Chirality : 0.041 0.139 1032 Planarity : 0.004 0.027 1166 Dihedral : 8.561 98.274 930 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.84 % Allowed : 20.45 % Favored : 78.71 % 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: 0.67 (0.31), residues: 804 helix: 1.48 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -2.87 (0.40), residues: 202 *********************** 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 110 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.777 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 108 average time/residue: 0.2464 time to fit residues: 33.7898 Evaluate side-chains 102 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.783 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0629 time to fit residues: 1.3049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 14 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 0.1980 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8313 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6998 Z= 0.169 Angle : 0.554 6.247 9530 Z= 0.268 Chirality : 0.037 0.132 1032 Planarity : 0.004 0.027 1166 Dihedral : 8.247 95.545 930 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 21.01 % Favored : 78.99 % 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: 1.74 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -2.84 (0.40), residues: 202 *********************** 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 113 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.779 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2183 time to fit residues: 32.0771 Evaluate side-chains 106 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.787 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 43 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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: 0.8385 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 6998 Z= 0.349 Angle : 0.629 6.850 9530 Z= 0.309 Chirality : 0.042 0.141 1032 Planarity : 0.004 0.027 1166 Dihedral : 8.569 99.189 930 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 0.42 % Allowed : 21.01 % Favored : 78.57 % 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 (0.31), residues: 804 helix: 1.51 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -2.73 (0.42), residues: 200 *********************** 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 108 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 0.752 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 108 average time/residue: 0.2371 time to fit residues: 32.7613 Evaluate side-chains 107 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0654 time to fit residues: 1.4123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 49 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8336 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6998 Z= 0.198 Angle : 0.572 6.497 9530 Z= 0.277 Chirality : 0.038 0.141 1032 Planarity : 0.004 0.027 1166 Dihedral : 8.366 97.308 930 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.28 % Allowed : 21.01 % Favored : 78.71 % 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: 1.00 (0.31), residues: 804 helix: 1.70 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -2.71 (0.42), residues: 200 ********************** 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 105 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.780 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 105 average time/residue: 0.2243 time to fit residues: 30.9385 Evaluate side-chains 103 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.762 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0652 time to fit residues: 1.1610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.0770 chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.146583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.110386 restraints weight = 8917.629| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.07 r_work: 0.3004 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6998 Z= 0.184 Angle : 0.564 6.361 9530 Z= 0.274 Chirality : 0.038 0.139 1032 Planarity : 0.004 0.028 1166 Dihedral : 8.269 96.243 930 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.00 % Allowed : 21.15 % Favored : 78.85 % 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: 1.12 (0.31), residues: 804 helix: 1.79 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -2.70 (0.42), residues: 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1714.31 seconds wall clock time: 33 minutes 56.66 seconds (2036.66 seconds total)