Starting phenix.real_space_refine on Mon Jun 24 20:11:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x1n_37997/06_2024/8x1n_37997_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x1n_37997/06_2024/8x1n_37997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x1n_37997/06_2024/8x1n_37997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x1n_37997/06_2024/8x1n_37997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x1n_37997/06_2024/8x1n_37997_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x1n_37997/06_2024/8x1n_37997_updated.pdb" } resolution = 3.31 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= 0.047 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 40 5.16 5 C 3008 2.51 5 N 792 2.21 5 O 922 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 33": "OD1" <-> "OD2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A ASP 112": "OD1" <-> "OD2" Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A ASP 336": "OD1" <-> "OD2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "A PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 395": "OD1" <-> "OD2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A GLU 400": "OE1" <-> "OE2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 589": "OE1" <-> "OE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 594": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 4763 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4651 Classifications: {'peptide': 591} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 569} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 73 Unusual residues: {' ZN': 1, 'PLM': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 3.48, per 1000 atoms: 0.73 Number of scatterers: 4763 At special positions: 0 Unit cell: (70.484, 93.628, 103.096, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 40 16.00 O 922 8.00 N 792 7.00 C 3008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 124 " distance=2.03 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 193 " distance=2.04 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.04 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 393 " distance=2.04 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 462 " distance=2.04 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 472 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 501 " distance=2.03 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 583 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 591 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A 251 " Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 268 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 264 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 22 " 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 0 sheets defined 67.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 60 through 74 Processing helix chain 'A' and resid 91 through 100 removed outlier: 3.729A pdb=" N CYS A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 118 through 127 Processing helix chain 'A' and resid 147 through 153 removed outlier: 4.292A pdb=" N GLU A 152 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 169 removed outlier: 3.894A pdb=" N ARG A 169 " --> pdb=" O GLU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 192 removed outlier: 3.692A pdb=" N LYS A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 198 through 246 removed outlier: 3.788A pdb=" N ALA A 207 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N ARG A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 270 removed outlier: 3.855A pdb=" N LYS A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 290 Processing helix chain 'A' and resid 297 through 304 removed outlier: 3.950A pdb=" N GLU A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 344 through 361 removed outlier: 3.911A pdb=" N ARG A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 384 Processing helix chain 'A' and resid 390 through 422 removed outlier: 4.063A pdb=" N GLU A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 401 " --> pdb=" O GLY A 397 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLN A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LYS A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N TYR A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN A 406 " --> pdb=" O GLN A 402 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 438 Processing helix chain 'A' and resid 444 through 461 removed outlier: 3.813A pdb=" N CYS A 461 " --> pdb=" O THR A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 490 removed outlier: 4.620A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 501 removed outlier: 3.924A pdb=" N CYS A 500 " --> pdb=" O GLY A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 512 Processing helix chain 'A' and resid 528 through 531 Processing helix chain 'A' and resid 535 through 539 removed outlier: 3.526A pdb=" N GLN A 539 " --> pdb=" O ASP A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 559 removed outlier: 3.812A pdb=" N PHE A 552 " --> pdb=" O MET A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 583 Processing helix chain 'A' and resid 588 through 607 removed outlier: 4.452A pdb=" N GLN A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) 261 hydrogen bonds defined for protein. 777 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: 1.15 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1570 1.35 - 1.47: 1031 1.47 - 1.59: 2193 1.59 - 1.71: 0 1.71 - 1.83: 48 Bond restraints: 4842 Sorted by residual: bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" CB CYS A 472 " pdb=" SG CYS A 472 " ideal model delta sigma weight residual 1.808 1.757 0.051 3.30e-02 9.18e+02 2.36e+00 bond pdb=" C1 PLM A 704 " pdb=" C2 PLM A 704 " ideal model delta sigma weight residual 1.542 1.569 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C1 PLM A 703 " pdb=" C2 PLM A 703 " ideal model delta sigma weight residual 1.542 1.569 -0.027 2.00e-02 2.50e+03 1.77e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.45e+00 ... (remaining 4837 not shown) Histogram of bond angle deviations from ideal: 99.76 - 106.59: 110 106.59 - 113.41: 2614 113.41 - 120.24: 1867 120.24 - 127.06: 1879 127.06 - 133.89: 43 Bond angle restraints: 6513 Sorted by residual: angle pdb=" CA CYS A 472 " pdb=" CB CYS A 472 " pdb=" SG CYS A 472 " ideal model delta sigma weight residual 114.40 121.49 -7.09 2.30e+00 1.89e-01 9.50e+00 angle pdb=" N CYS A 461 " pdb=" CA CYS A 461 " pdb=" C CYS A 461 " ideal model delta sigma weight residual 111.71 115.70 -3.99 1.34e+00 5.57e-01 8.88e+00 angle pdb=" N CYS A 462 " pdb=" CA CYS A 462 " pdb=" C CYS A 462 " ideal model delta sigma weight residual 113.01 109.47 3.54 1.20e+00 6.94e-01 8.70e+00 angle pdb=" CA GLN A 291 " pdb=" C GLN A 291 " pdb=" N GLN A 292 " ideal model delta sigma weight residual 114.76 117.84 -3.08 1.14e+00 7.69e-01 7.30e+00 angle pdb=" CB MET A 159 " pdb=" CG MET A 159 " pdb=" SD MET A 159 " ideal model delta sigma weight residual 112.70 120.36 -7.66 3.00e+00 1.11e-01 6.52e+00 ... (remaining 6508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.13: 2802 22.13 - 44.27: 221 44.27 - 66.40: 31 66.40 - 88.53: 14 88.53 - 110.66: 7 Dihedral angle restraints: 3075 sinusoidal: 1338 harmonic: 1737 Sorted by residual: dihedral pdb=" CB CYS A 461 " pdb=" SG CYS A 461 " pdb=" SG CYS A 472 " pdb=" CB CYS A 472 " ideal model delta sinusoidal sigma weight residual -86.00 -176.31 90.31 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 583 " pdb=" CB CYS A 583 " ideal model delta sinusoidal sigma weight residual -86.00 -169.00 83.00 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS A 582 " pdb=" SG CYS A 582 " pdb=" SG CYS A 591 " pdb=" CB CYS A 591 " ideal model delta sinusoidal sigma weight residual -86.00 -167.52 81.52 1 1.00e+01 1.00e-02 8.18e+01 ... (remaining 3072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 638 0.056 - 0.111: 87 0.111 - 0.167: 6 0.167 - 0.223: 0 0.223 - 0.278: 2 Chirality restraints: 733 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 251 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA CYS A 461 " pdb=" N CYS A 461 " pdb=" C CYS A 461 " pdb=" CB CYS A 461 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 730 not shown) Planarity restraints: 843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 132 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 133 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 494 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO A 495 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 495 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 495 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 336 " 0.005 2.00e-02 2.50e+03 1.04e-02 1.09e+00 pdb=" C ASP A 336 " -0.018 2.00e-02 2.50e+03 pdb=" O ASP A 336 " 0.007 2.00e-02 2.50e+03 pdb=" N ARG A 337 " 0.006 2.00e-02 2.50e+03 ... (remaining 840 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1015 2.78 - 3.31: 4425 3.31 - 3.84: 7409 3.84 - 4.37: 7958 4.37 - 4.90: 14932 Nonbonded interactions: 35739 Sorted by model distance: nonbonded pdb=" O SER A 34 " pdb=" OG SER A 34 " model vdw 2.251 2.440 nonbonded pdb=" ND2 ASN A 329 " pdb=" OD1 ASN A 331 " model vdw 2.285 2.520 nonbonded pdb=" OE2 GLU A 392 " pdb=" NZ LYS A 396 " model vdw 2.326 2.520 nonbonded pdb=" O LEU A 432 " pdb=" OG1 THR A 436 " model vdw 2.352 2.440 nonbonded pdb=" O GLU A 88 " pdb=" NE2 GLN A 90 " model vdw 2.395 2.520 ... (remaining 35734 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: 0.470 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: 1.680 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.180 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.003 0.051 4842 Z= 0.192 Angle : 0.594 7.660 6513 Z= 0.327 Chirality : 0.040 0.278 733 Planarity : 0.003 0.041 842 Dihedral : 16.855 110.663 1897 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % 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: 2.01 (0.36), residues: 589 helix: 1.99 (0.27), residues: 397 sheet: None (None), residues: 0 loop : -0.01 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.004 0.001 HIS A 268 PHE 0.010 0.001 PHE A 339 TYR 0.010 0.001 TYR A 435 ARG 0.003 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.506 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.2098 time to fit residues: 12.5586 Evaluate side-chains 46 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.8184 moved from start: 0.0503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4842 Z= 0.216 Angle : 0.496 6.053 6513 Z= 0.254 Chirality : 0.039 0.181 733 Planarity : 0.003 0.040 842 Dihedral : 9.719 61.659 747 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.33 % Allowed : 10.87 % Favored : 86.80 % 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: 1.95 (0.36), residues: 589 helix: 2.00 (0.27), residues: 398 sheet: None (None), residues: 0 loop : -0.18 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.005 0.001 HIS A 268 PHE 0.010 0.001 PHE A 575 TYR 0.012 0.002 TYR A 425 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 48 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 THR cc_start: 0.6106 (OUTLIER) cc_final: 0.5867 (p) outliers start: 12 outliers final: 8 residues processed: 56 average time/residue: 0.1753 time to fit residues: 12.6084 Evaluate side-chains 54 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 472 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 47 optimal weight: 0.0570 chunk 18 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 HIS A 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 : 0.002 0.028 4842 Z= 0.151 Angle : 0.443 5.033 6513 Z= 0.228 Chirality : 0.037 0.179 733 Planarity : 0.003 0.038 842 Dihedral : 7.650 59.024 747 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.52 % Allowed : 12.04 % Favored : 85.44 % 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: 2.13 (0.36), residues: 589 helix: 2.14 (0.27), residues: 398 sheet: None (None), residues: 0 loop : -0.12 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.003 0.001 HIS A 483 PHE 0.008 0.001 PHE A 575 TYR 0.008 0.001 TYR A 425 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 47 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 306 THR cc_start: 0.5931 (OUTLIER) cc_final: 0.5699 (p) outliers start: 13 outliers final: 9 residues processed: 57 average time/residue: 0.1700 time to fit residues: 12.7152 Evaluate side-chains 53 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 522 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 0.0970 chunk 32 optimal weight: 0.1980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS A 331 ASN A 597 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 4842 Z= 0.138 Angle : 0.445 8.145 6513 Z= 0.230 Chirality : 0.037 0.179 733 Planarity : 0.003 0.037 842 Dihedral : 7.163 59.051 747 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.52 % Allowed : 12.04 % Favored : 85.44 % 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: 2.30 (0.36), residues: 589 helix: 2.35 (0.27), residues: 391 sheet: None (None), residues: 0 loop : -0.14 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 181 HIS 0.003 0.001 HIS A 483 PHE 0.007 0.001 PHE A 512 TYR 0.007 0.001 TYR A 164 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 45 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 306 THR cc_start: 0.5955 (OUTLIER) cc_final: 0.5713 (p) REVERT: A 400 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6916 (pt0) outliers start: 13 outliers final: 9 residues processed: 57 average time/residue: 0.1857 time to fit residues: 13.7847 Evaluate side-chains 52 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 522 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 0.0030 chunk 39 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 597 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 4842 Z= 0.254 Angle : 0.485 6.047 6513 Z= 0.250 Chirality : 0.039 0.182 733 Planarity : 0.003 0.038 842 Dihedral : 7.374 59.065 747 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.72 % Allowed : 12.43 % Favored : 84.85 % 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: 2.11 (0.36), residues: 589 helix: 2.22 (0.27), residues: 390 sheet: None (None), residues: 0 loop : -0.25 (0.44), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.008 0.001 HIS A 268 PHE 0.009 0.001 PHE A 575 TYR 0.011 0.002 TYR A 425 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 46 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 306 THR cc_start: 0.6100 (OUTLIER) cc_final: 0.5864 (p) REVERT: A 331 ASN cc_start: 0.8490 (m110) cc_final: 0.8162 (p0) REVERT: A 400 GLU cc_start: 0.7493 (mm-30) cc_final: 0.6966 (pt0) outliers start: 14 outliers final: 10 residues processed: 58 average time/residue: 0.1689 time to fit residues: 12.8802 Evaluate side-chains 53 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 563 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4842 Z= 0.149 Angle : 0.434 6.059 6513 Z= 0.225 Chirality : 0.037 0.182 733 Planarity : 0.003 0.038 842 Dihedral : 7.050 57.913 747 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.11 % Allowed : 12.82 % Favored : 84.08 % 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: 2.23 (0.36), residues: 589 helix: 2.31 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.22 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.006 0.001 HIS A 268 PHE 0.006 0.001 PHE A 575 TYR 0.008 0.001 TYR A 164 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 47 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 306 THR cc_start: 0.5911 (OUTLIER) cc_final: 0.5659 (p) REVERT: A 400 GLU cc_start: 0.7490 (mm-30) cc_final: 0.6956 (pt0) REVERT: A 511 CYS cc_start: 0.5903 (OUTLIER) cc_final: 0.5586 (t) outliers start: 16 outliers final: 11 residues processed: 59 average time/residue: 0.1708 time to fit residues: 13.3747 Evaluate side-chains 57 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 44 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 563 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 597 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4842 Z= 0.160 Angle : 0.441 6.795 6513 Z= 0.228 Chirality : 0.037 0.180 733 Planarity : 0.003 0.038 842 Dihedral : 6.943 57.674 747 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.72 % Allowed : 13.20 % Favored : 84.08 % 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: 2.27 (0.36), residues: 589 helix: 2.33 (0.27), residues: 391 sheet: None (None), residues: 0 loop : -0.18 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.008 0.001 HIS A 268 PHE 0.009 0.001 PHE A 162 TYR 0.009 0.001 TYR A 164 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 45 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 306 THR cc_start: 0.5925 (OUTLIER) cc_final: 0.5658 (p) REVERT: A 400 GLU cc_start: 0.7456 (mm-30) cc_final: 0.6952 (pt0) REVERT: A 511 CYS cc_start: 0.5965 (OUTLIER) cc_final: 0.5603 (t) outliers start: 14 outliers final: 11 residues processed: 54 average time/residue: 0.1930 time to fit residues: 13.5764 Evaluate side-chains 57 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 44 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 563 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 0.0570 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 597 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4842 Z= 0.181 Angle : 0.452 7.293 6513 Z= 0.234 Chirality : 0.038 0.181 733 Planarity : 0.003 0.038 842 Dihedral : 6.944 57.173 747 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.11 % Allowed : 13.98 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.36), residues: 589 helix: 2.31 (0.27), residues: 391 sheet: None (None), residues: 0 loop : -0.17 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.012 0.002 HIS A 268 PHE 0.008 0.001 PHE A 385 TYR 0.009 0.001 TYR A 164 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 THR cc_start: 0.6003 (OUTLIER) cc_final: 0.5762 (p) REVERT: A 400 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7026 (pt0) REVERT: A 511 CYS cc_start: 0.6044 (OUTLIER) cc_final: 0.5643 (t) outliers start: 16 outliers final: 13 residues processed: 54 average time/residue: 0.1867 time to fit residues: 13.2561 Evaluate side-chains 59 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 44 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 563 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 0.0570 chunk 50 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 597 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4842 Z= 0.181 Angle : 0.453 8.009 6513 Z= 0.234 Chirality : 0.037 0.181 733 Planarity : 0.003 0.037 842 Dihedral : 6.922 57.071 747 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.11 % Allowed : 13.98 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.36), residues: 589 helix: 2.31 (0.27), residues: 391 sheet: None (None), residues: 0 loop : -0.17 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.008 0.001 HIS A 268 PHE 0.008 0.001 PHE A 385 TYR 0.009 0.001 TYR A 164 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 THR cc_start: 0.5998 (OUTLIER) cc_final: 0.5761 (p) REVERT: A 400 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7033 (pt0) REVERT: A 511 CYS cc_start: 0.6039 (OUTLIER) cc_final: 0.5642 (t) outliers start: 16 outliers final: 13 residues processed: 54 average time/residue: 0.1997 time to fit residues: 14.0974 Evaluate side-chains 58 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 43 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 563 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 chunk 37 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 0.0370 chunk 13 optimal weight: 1.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 483 HIS A 597 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4842 Z= 0.124 Angle : 0.428 8.113 6513 Z= 0.220 Chirality : 0.036 0.183 733 Planarity : 0.003 0.038 842 Dihedral : 6.507 57.175 747 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.52 % Allowed : 14.37 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.36), residues: 589 helix: 2.43 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.11 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 181 HIS 0.007 0.001 HIS A 268 PHE 0.009 0.001 PHE A 162 TYR 0.006 0.001 TYR A 426 ARG 0.002 0.000 ARG A 332 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 THR cc_start: 0.5906 (OUTLIER) cc_final: 0.5603 (p) REVERT: A 336 ASP cc_start: 0.7146 (t0) cc_final: 0.6869 (t0) REVERT: A 400 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7021 (pt0) REVERT: A 511 CYS cc_start: 0.6064 (OUTLIER) cc_final: 0.5749 (t) outliers start: 13 outliers final: 10 residues processed: 52 average time/residue: 0.1768 time to fit residues: 12.0119 Evaluate side-chains 55 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 43 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 563 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 0.0050 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.166449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.123278 restraints weight = 5299.441| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.18 r_work: 0.2890 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4842 Z= 0.137 Angle : 0.421 8.102 6513 Z= 0.216 Chirality : 0.036 0.183 733 Planarity : 0.003 0.038 842 Dihedral : 6.422 57.118 747 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.52 % Allowed : 14.17 % Favored : 83.30 % 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: 2.43 (0.36), residues: 589 helix: 2.46 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.13 (0.45), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.006 0.001 HIS A 268 PHE 0.008 0.001 PHE A 162 TYR 0.007 0.001 TYR A 164 ARG 0.001 0.000 ARG A 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1333.39 seconds wall clock time: 24 minutes 19.73 seconds (1459.73 seconds total)