Starting phenix.real_space_refine on Mon Mar 18 20:11:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt2_17866/03_2024/8pt2_17866.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt2_17866/03_2024/8pt2_17866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt2_17866/03_2024/8pt2_17866.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt2_17866/03_2024/8pt2_17866.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt2_17866/03_2024/8pt2_17866.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt2_17866/03_2024/8pt2_17866.pdb" } resolution = 2.59 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= 0.001 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: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 27 5.49 5 S 63 5.16 5 C 6950 2.51 5 N 1972 2.21 5 O 2175 1.98 5 H 10901 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 33": "OE1" <-> "OE2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "B TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 115": "OE1" <-> "OE2" Residue "C GLU 181": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22091 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6652 Classifications: {'peptide': 417} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 394} Chain: "B" Number of atoms: 7900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 7900 Classifications: {'peptide': 512} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 490} Chain breaks: 1 Chain: "C" Number of atoms: 6676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6676 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 22, 'TRANS': 403} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "V" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 406 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 6} Link IDs: {'rna2p': 5, 'rna3p': 7} Chain: "D" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 453 Classifications: {'RNA': 14} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 4, 'rna3p': 9} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2585 SG CYS A 161 46.153 53.513 18.541 1.00 47.15 S ATOM 4473 SG CYS A 282 43.740 52.013 15.789 1.00 59.75 S ATOM 18156 SG CYS C 233 22.092 62.596 107.997 1.00 74.16 S ATOM 18180 SG CYS C 235 22.631 64.040 104.434 1.00 71.02 S ATOM 16822 SG CYS C 146 10.935 72.545 88.479 1.00 81.71 S ATOM 17010 SG CYS C 159 11.925 75.602 90.433 1.00 89.66 S ATOM 17066 SG CYS C 163 14.226 72.636 90.449 1.00 72.58 S ATOM 17076 SG CYS C 164 13.852 74.746 87.284 1.00 73.55 S Time building chain proxies: 10.72, per 1000 atoms: 0.49 Number of scatterers: 22091 At special positions: 0 Unit cell: (92.4, 110.88, 125.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 63 16.00 P 27 15.00 O 2175 8.00 N 1972 7.00 C 6950 6.00 H 10901 1.00 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: 17.88 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 284 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 296 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 161 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 191 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 184 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 233 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 235 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 159 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 163 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 146 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 164 " Number of angles added : 9 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 15 sheets defined 42.1% alpha, 14.2% beta 6 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 10.33 Creating SS restraints... Processing helix chain 'A' and resid 2 through 4 No H-bonds generated for 'chain 'A' and resid 2 through 4' Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 141 through 157 removed outlier: 3.515A pdb=" N ILE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 312 through 323 removed outlier: 4.431A pdb=" N ASP A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.893A pdb=" N ALA A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 392 Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.565A pdb=" N GLN B 5 " --> pdb=" O TRP B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 92 through 103 Processing helix chain 'B' and resid 107 through 118 Processing helix chain 'B' and resid 129 through 138 removed outlier: 3.654A pdb=" N ARG B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 183 removed outlier: 3.590A pdb=" N VAL B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 216 through 221 removed outlier: 3.552A pdb=" N ILE B 221 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 235 through 248 removed outlier: 3.612A pdb=" N GLY B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 removed outlier: 3.733A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 356 through 372 Processing helix chain 'B' and resid 376 through 396 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.563A pdb=" N GLY B 413 " --> pdb=" O THR B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 429 through 436 removed outlier: 4.069A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 Processing helix chain 'B' and resid 479 through 497 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 16 through 23 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 42 through 54 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 145 through 151 removed outlier: 3.773A pdb=" N VAL C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 219 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 281 through 289 Processing helix chain 'C' and resid 303 through 317 removed outlier: 4.168A pdb=" N ARG C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 334 Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.762A pdb=" N LEU C 354 " --> pdb=" O ASN C 350 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER C 356 " --> pdb=" O LYS C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 376 Processing helix chain 'C' and resid 421 through 426 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.726A pdb=" N TRP A 52 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N CYS A 71 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA A 54 " --> pdb=" O CYS A 71 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU A 73 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU A 56 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.314A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.314A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 74 through 80 Processing sheet with id=AA8, first strand: chain 'B' and resid 155 through 159 removed outlier: 7.100A pdb=" N PHE B 140 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AB1, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 83 Processing sheet with id=AB4, first strand: chain 'C' and resid 221 through 224 removed outlier: 6.848A pdb=" N GLY C 262 " --> pdb=" O PHE C 258 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 360 through 363 Processing sheet with id=AB6, first strand: chain 'C' and resid 383 through 388 removed outlier: 6.669A pdb=" N MET C 415 " --> pdb=" O LEU C 387 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 8.07 Time building geometry restraints manager: 18.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10869 1.03 - 1.23: 43 1.23 - 1.42: 4830 1.42 - 1.62: 6544 1.62 - 1.81: 86 Bond restraints: 22372 Sorted by residual: bond pdb=" C LEU B 167 " pdb=" O LEU B 167 " ideal model delta sigma weight residual 1.237 1.245 -0.008 1.19e-02 7.06e+03 4.71e-01 bond pdb=" CB LYS C 352 " pdb=" CG LYS C 352 " ideal model delta sigma weight residual 1.520 1.540 -0.020 3.00e-02 1.11e+03 4.34e-01 bond pdb=" CB GLU C 181 " pdb=" CG GLU C 181 " ideal model delta sigma weight residual 1.520 1.539 -0.019 3.00e-02 1.11e+03 4.19e-01 bond pdb=" CG PRO C 252 " pdb=" CD PRO C 252 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.96e-01 bond pdb=" CG PRO B 502 " pdb=" CD PRO B 502 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.68e-01 ... (remaining 22367 not shown) Histogram of bond angle deviations from ideal: 100.59 - 107.27: 718 107.27 - 113.95: 26567 113.95 - 120.63: 7425 120.63 - 127.32: 5530 127.32 - 134.00: 168 Bond angle restraints: 40408 Sorted by residual: angle pdb=" N LYS C 199 " pdb=" CA LYS C 199 " pdb=" C LYS C 199 " ideal model delta sigma weight residual 114.09 111.09 3.00 1.55e+00 4.16e-01 3.75e+00 angle pdb=" CG ARG B 487 " pdb=" CD ARG B 487 " pdb=" NE ARG B 487 " ideal model delta sigma weight residual 112.00 116.13 -4.13 2.20e+00 2.07e-01 3.53e+00 angle pdb=" CG ARG A 154 " pdb=" CD ARG A 154 " pdb=" NE ARG A 154 " ideal model delta sigma weight residual 112.00 115.79 -3.79 2.20e+00 2.07e-01 2.96e+00 angle pdb=" CD ARG B 487 " pdb=" NE ARG B 487 " pdb=" CZ ARG B 487 " ideal model delta sigma weight residual 124.40 126.76 -2.36 1.40e+00 5.10e-01 2.84e+00 angle pdb=" CG LYS A 147 " pdb=" CD LYS A 147 " pdb=" CE LYS A 147 " ideal model delta sigma weight residual 111.30 115.17 -3.87 2.30e+00 1.89e-01 2.83e+00 ... (remaining 40403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9343 17.98 - 35.95: 788 35.95 - 53.93: 308 53.93 - 71.90: 91 71.90 - 89.88: 31 Dihedral angle restraints: 10561 sinusoidal: 5981 harmonic: 4580 Sorted by residual: dihedral pdb=" CG ARG B 487 " pdb=" CD ARG B 487 " pdb=" NE ARG B 487 " pdb=" CZ ARG B 487 " ideal model delta sinusoidal sigma weight residual -90.00 -39.92 -50.08 2 1.50e+01 4.44e-03 1.25e+01 dihedral pdb=" CB GLU C 115 " pdb=" CG GLU C 115 " pdb=" CD GLU C 115 " pdb=" OE1 GLU C 115 " ideal model delta sinusoidal sigma weight residual 0.00 -89.88 89.88 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG B 63 " pdb=" CD ARG B 63 " pdb=" NE ARG B 63 " pdb=" CZ ARG B 63 " ideal model delta sinusoidal sigma weight residual 90.00 134.84 -44.84 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 10558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1082 0.025 - 0.051: 480 0.051 - 0.076: 102 0.076 - 0.102: 49 0.102 - 0.127: 52 Chirality restraints: 1765 Sorted by residual: chirality pdb=" CA ILE A 199 " pdb=" N ILE A 199 " pdb=" C ILE A 199 " pdb=" CB ILE A 199 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA ILE B 253 " pdb=" N ILE B 253 " pdb=" C ILE B 253 " pdb=" CB ILE B 253 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA ILE A 53 " pdb=" N ILE A 53 " pdb=" C ILE A 53 " pdb=" CB ILE A 53 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 1762 not shown) Planarity restraints: 3219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 487 " 0.150 9.50e-02 1.11e+02 5.03e-02 3.04e+00 pdb=" NE ARG B 487 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 487 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 487 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 487 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG B 487 " -0.006 2.00e-02 2.50e+03 pdb="HH12 ARG B 487 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B 487 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 487 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 501 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO B 502 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 217 " -0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO A 218 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 218 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 218 " -0.020 5.00e-02 4.00e+02 ... (remaining 3216 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1319 2.19 - 2.80: 44023 2.80 - 3.40: 60985 3.40 - 4.00: 82553 4.00 - 4.60: 125729 Nonbonded interactions: 314609 Sorted by model distance: nonbonded pdb=" OD1 ASN B 397 " pdb=" HG1 THR B 399 " model vdw 1.593 1.850 nonbonded pdb=" O SER A 128 " pdb="HD22 ASN B 44 " model vdw 1.598 1.850 nonbonded pdb=" H GLY A 239 " pdb=" O ALA A 251 " model vdw 1.628 1.850 nonbonded pdb=" O ALA C 330 " pdb=" HG1 THR C 334 " model vdw 1.662 1.850 nonbonded pdb="HH21 ARG B 145 " pdb="HH11 ARG B 155 " model vdw 1.663 2.100 ... (remaining 314604 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.330 Extract box with map and model: 6.620 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 85.280 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 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:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 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 : 0.002 0.028 11471 Z= 0.146 Angle : 0.446 4.134 15629 Z= 0.232 Chirality : 0.036 0.127 1765 Planarity : 0.004 0.065 1918 Dihedral : 17.636 89.878 4454 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.37 % Allowed : 18.13 % Favored : 80.50 % 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: 1.25 (0.23), residues: 1345 helix: 2.08 (0.24), residues: 528 sheet: -0.54 (0.42), residues: 130 loop : 0.20 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 263 HIS 0.004 0.001 HIS B 174 PHE 0.010 0.001 PHE C 175 TYR 0.010 0.001 TYR A 403 ARG 0.009 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 1.868 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 15 residues processed: 124 average time/residue: 3.4166 time to fit residues: 451.1142 Evaluate side-chains 124 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 388 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 330 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.0695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11471 Z= 0.339 Angle : 0.536 4.701 15629 Z= 0.285 Chirality : 0.040 0.138 1765 Planarity : 0.004 0.042 1918 Dihedral : 11.716 83.534 1907 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.41 % Allowed : 16.32 % Favored : 81.27 % 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: 0.91 (0.23), residues: 1345 helix: 1.80 (0.23), residues: 532 sheet: -0.58 (0.40), residues: 130 loop : -0.04 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 2 HIS 0.007 0.001 HIS B 174 PHE 0.019 0.002 PHE C 175 TYR 0.016 0.002 TYR A 403 ARG 0.005 0.001 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 112 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 356 SER cc_start: 0.8035 (OUTLIER) cc_final: 0.7751 (t) outliers start: 28 outliers final: 18 residues processed: 132 average time/residue: 3.2452 time to fit residues: 457.9937 Evaluate side-chains 125 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 330 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11471 Z= 0.277 Angle : 0.507 4.392 15629 Z= 0.268 Chirality : 0.039 0.134 1765 Planarity : 0.004 0.040 1918 Dihedral : 11.524 85.919 1900 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.49 % Allowed : 16.67 % Favored : 80.84 % 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: 0.86 (0.22), residues: 1345 helix: 1.74 (0.23), residues: 533 sheet: -0.45 (0.40), residues: 128 loop : -0.10 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 263 HIS 0.006 0.001 HIS B 174 PHE 0.016 0.001 PHE C 175 TYR 0.014 0.001 TYR A 403 ARG 0.005 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 1.895 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 22 residues processed: 130 average time/residue: 3.1562 time to fit residues: 439.2809 Evaluate side-chains 125 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 388 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 59 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11471 Z= 0.205 Angle : 0.478 4.101 15629 Z= 0.251 Chirality : 0.037 0.136 1765 Planarity : 0.004 0.042 1918 Dihedral : 11.367 86.430 1898 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.32 % Allowed : 16.58 % Favored : 81.10 % 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: 0.96 (0.22), residues: 1345 helix: 1.85 (0.23), residues: 539 sheet: -0.35 (0.41), residues: 128 loop : -0.09 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 PHE 0.014 0.001 PHE C 175 TYR 0.012 0.001 TYR A 403 ARG 0.007 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 1.889 Fit side-chains revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7561 (mmt90) REVERT: B 148 GLU cc_start: 0.7863 (tt0) cc_final: 0.7323 (mt-10) REVERT: C 28 HIS cc_start: 0.6094 (OUTLIER) cc_final: 0.5865 (p-80) REVERT: C 40 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8490 (tptp) REVERT: C 389 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7617 (mpt-90) outliers start: 27 outliers final: 16 residues processed: 127 average time/residue: 3.3670 time to fit residues: 455.7315 Evaluate side-chains 126 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 28 HIS Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 389 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11471 Z= 0.170 Angle : 0.461 3.881 15629 Z= 0.241 Chirality : 0.037 0.135 1765 Planarity : 0.004 0.048 1918 Dihedral : 11.142 86.509 1894 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.23 % Allowed : 16.75 % Favored : 81.01 % 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 (0.23), residues: 1345 helix: 1.96 (0.23), residues: 540 sheet: -0.18 (0.42), residues: 126 loop : -0.01 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 209 HIS 0.004 0.001 HIS B 174 PHE 0.012 0.001 PHE C 175 TYR 0.012 0.001 TYR A 403 ARG 0.008 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 109 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7540 (mmt90) REVERT: B 148 GLU cc_start: 0.7871 (tt0) cc_final: 0.7329 (mt-10) REVERT: C 40 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8498 (tptp) REVERT: C 108 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8705 (tt) REVERT: C 389 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7606 (mpt-90) outliers start: 26 outliers final: 18 residues processed: 129 average time/residue: 3.4331 time to fit residues: 471.5838 Evaluate side-chains 126 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 389 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 131 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11471 Z= 0.168 Angle : 0.459 4.414 15629 Z= 0.239 Chirality : 0.037 0.136 1765 Planarity : 0.004 0.054 1918 Dihedral : 10.962 86.873 1890 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.23 % Allowed : 16.84 % Favored : 80.93 % 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: 1.14 (0.23), residues: 1345 helix: 2.01 (0.23), residues: 540 sheet: -0.27 (0.42), residues: 128 loop : 0.00 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 209 HIS 0.004 0.001 HIS B 174 PHE 0.012 0.001 PHE C 175 TYR 0.012 0.001 TYR A 403 ARG 0.010 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 106 time to evaluate : 1.716 Fit side-chains revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7536 (mmt90) REVERT: B 148 GLU cc_start: 0.7868 (tt0) cc_final: 0.7336 (mt-10) REVERT: C 108 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8704 (tt) REVERT: C 389 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7597 (mpt-90) outliers start: 26 outliers final: 19 residues processed: 124 average time/residue: 3.4570 time to fit residues: 455.8235 Evaluate side-chains 126 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 389 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 0.0370 chunk 82 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11471 Z= 0.138 Angle : 0.450 4.866 15629 Z= 0.234 Chirality : 0.036 0.135 1765 Planarity : 0.004 0.055 1918 Dihedral : 10.922 86.715 1890 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.06 % Allowed : 17.10 % Favored : 80.84 % 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: 1.24 (0.23), residues: 1345 helix: 2.09 (0.23), residues: 541 sheet: -0.27 (0.43), residues: 128 loop : 0.06 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 209 HIS 0.003 0.001 HIS B 174 PHE 0.011 0.001 PHE C 175 TYR 0.010 0.001 TYR A 403 ARG 0.008 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 1.864 Fit side-chains revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7523 (mmt90) REVERT: B 148 GLU cc_start: 0.7577 (tt0) cc_final: 0.7028 (mt-10) REVERT: C 40 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8457 (tptp) REVERT: C 108 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8692 (tt) REVERT: C 389 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7599 (mpt-90) outliers start: 24 outliers final: 17 residues processed: 123 average time/residue: 3.4891 time to fit residues: 458.5780 Evaluate side-chains 124 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 389 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 0.0980 chunk 103 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11471 Z= 0.166 Angle : 0.458 5.411 15629 Z= 0.238 Chirality : 0.036 0.135 1765 Planarity : 0.004 0.059 1918 Dihedral : 10.924 87.235 1889 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.23 % Allowed : 17.01 % Favored : 80.76 % 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: 1.22 (0.23), residues: 1345 helix: 2.06 (0.23), residues: 541 sheet: -0.24 (0.43), residues: 128 loop : 0.05 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 209 HIS 0.004 0.001 HIS B 174 PHE 0.013 0.001 PHE C 175 TYR 0.012 0.001 TYR A 403 ARG 0.008 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 2.003 Fit side-chains revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7516 (mmt90) REVERT: B 148 GLU cc_start: 0.7736 (tt0) cc_final: 0.7226 (mt-10) REVERT: C 40 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8477 (tptp) REVERT: C 389 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7583 (mpt-90) outliers start: 26 outliers final: 20 residues processed: 127 average time/residue: 3.5195 time to fit residues: 475.7119 Evaluate side-chains 129 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 389 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11471 Z= 0.190 Angle : 0.468 5.249 15629 Z= 0.244 Chirality : 0.037 0.135 1765 Planarity : 0.004 0.061 1918 Dihedral : 10.959 88.050 1889 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.32 % Allowed : 17.01 % 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: 1.17 (0.23), residues: 1345 helix: 2.02 (0.23), residues: 541 sheet: -0.24 (0.43), residues: 128 loop : 0.02 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 209 HIS 0.004 0.001 HIS B 174 PHE 0.014 0.001 PHE C 175 TYR 0.012 0.001 TYR A 403 ARG 0.009 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 1.813 Fit side-chains revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7524 (mmt90) REVERT: B 148 GLU cc_start: 0.7757 (tt0) cc_final: 0.7302 (mt-10) REVERT: C 40 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8495 (tptp) REVERT: C 389 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7595 (mpt-90) outliers start: 27 outliers final: 21 residues processed: 128 average time/residue: 3.4468 time to fit residues: 469.6400 Evaluate side-chains 130 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 389 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 0.0870 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11471 Z= 0.203 Angle : 0.479 6.851 15629 Z= 0.249 Chirality : 0.037 0.134 1765 Planarity : 0.004 0.061 1918 Dihedral : 10.990 88.086 1889 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.15 % Allowed : 17.10 % Favored : 80.76 % 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: 1.14 (0.23), residues: 1345 helix: 2.00 (0.23), residues: 539 sheet: -0.25 (0.43), residues: 128 loop : -0.00 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 PHE 0.014 0.001 PHE C 175 TYR 0.012 0.001 TYR A 403 ARG 0.009 0.000 ARG B 487 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 1.835 Fit side-chains revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7541 (mmt90) REVERT: B 148 GLU cc_start: 0.7782 (tt0) cc_final: 0.7310 (mt-10) REVERT: C 40 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8479 (tptp) REVERT: C 108 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8713 (tt) REVERT: C 389 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7595 (mpt-90) outliers start: 25 outliers final: 21 residues processed: 125 average time/residue: 3.4255 time to fit residues: 456.9999 Evaluate side-chains 131 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 389 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 19 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.109867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.085354 restraints weight = 39419.705| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.76 r_work: 0.2834 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11471 Z= 0.145 Angle : 0.452 5.080 15629 Z= 0.234 Chirality : 0.036 0.134 1765 Planarity : 0.004 0.066 1918 Dihedral : 10.880 86.700 1888 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.72 % Allowed : 17.70 % Favored : 80.58 % 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: 1.30 (0.23), residues: 1345 helix: 2.15 (0.23), residues: 541 sheet: -0.22 (0.43), residues: 128 loop : 0.09 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 209 HIS 0.003 0.000 HIS B 174 PHE 0.011 0.001 PHE C 175 TYR 0.010 0.001 TYR A 403 ARG 0.008 0.000 ARG B 487 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8539.12 seconds wall clock time: 149 minutes 22.83 seconds (8962.83 seconds total)