Starting phenix.real_space_refine on Thu Apr 11 03:03:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szc_40908/04_2024/8szc_40908_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szc_40908/04_2024/8szc_40908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szc_40908/04_2024/8szc_40908.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szc_40908/04_2024/8szc_40908.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szc_40908/04_2024/8szc_40908_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szc_40908/04_2024/8szc_40908_trim_updated.pdb" } resolution = 3.06 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= 0.029 sd= 0.057 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 P 17 5.49 5 Mg 1 5.21 5 S 41 5.16 5 C 6863 2.51 5 N 1670 2.21 5 O 1919 1.98 5 H 9951 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 320": "OE1" <-> "OE2" Residue "D TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 546": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 20462 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 10683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 10683 Classifications: {'peptide': 664} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 650} Chain: "C" Number of atoms: 9074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 9074 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 19, 'TRANS': 551} Chain breaks: 1 Chain: "D" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 387 Unusual residues: {' MG': 1, 'ATP': 1, 'POV': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 318 Unusual residues: {'ATP': 1, 'HT1': 1, 'POV': 11} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 7, 'POV:plan-2': 3, 'POV:plan-1': 4} Unresolved non-hydrogen planarities: 44 Time building chain proxies: 11.06, per 1000 atoms: 0.54 Number of scatterers: 20462 At special positions: 0 Unit cell: (73.62, 103.886, 155.42, 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) S 41 16.00 P 17 15.00 Mg 1 11.99 O 1919 8.00 N 1670 7.00 C 6863 6.00 H 9951 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: 18.02 Conformation dependent library (CDL) restraints added in 2.3 seconds 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2292 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 5 sheets defined 59.3% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.47 Creating SS restraints... Processing helix chain 'D' and resid 3 through 12 Processing helix chain 'D' and resid 15 through 33 Processing helix chain 'D' and resid 35 through 41 Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 75 through 78 No H-bonds generated for 'chain 'D' and resid 75 through 78' Processing helix chain 'D' and resid 136 through 194 Proline residue: D 144 - end of helix removed outlier: 4.735A pdb=" N LYS D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLY D 148 " --> pdb=" O PRO D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 Processing helix chain 'D' and resid 206 through 248 removed outlier: 4.500A pdb=" N ASP D 216 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR D 217 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 296 removed outlier: 4.318A pdb=" N ILE D 259 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL D 260 " --> pdb=" O ALA D 256 " (cutoff:3.500A) Proline residue: D 261 - end of helix removed outlier: 4.132A pdb=" N TYR D 276 " --> pdb=" O ARG D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 304 Processing helix chain 'D' and resid 308 through 335 Processing helix chain 'D' and resid 338 through 361 Processing helix chain 'D' and resid 369 through 410 removed outlier: 3.598A pdb=" N GLN D 384 " --> pdb=" O ASN D 380 " (cutoff:3.500A) Proline residue: D 385 - end of helix removed outlier: 5.339A pdb=" N GLY D 388 " --> pdb=" O GLN D 384 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLU D 397 " --> pdb=" O PHE D 393 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU D 398 " --> pdb=" O SER D 394 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 477 Processing helix chain 'D' and resid 494 through 496 No H-bonds generated for 'chain 'D' and resid 494 through 496' Processing helix chain 'D' and resid 499 through 503 Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 535 through 541 Processing helix chain 'D' and resid 543 through 549 Proline residue: D 547 - end of helix Processing helix chain 'D' and resid 569 through 583 Processing helix chain 'D' and resid 601 through 611 Processing helix chain 'D' and resid 648 through 652 Processing helix chain 'D' and resid 656 through 663 Processing helix chain 'C' and resid 3 through 7 Processing helix chain 'C' and resid 9 through 14 Processing helix chain 'C' and resid 17 through 48 removed outlier: 3.784A pdb=" N PHE C 35 " --> pdb=" O VAL C 31 " (cutoff:3.500A) Proline residue: C 36 - end of helix Processing helix chain 'C' and resid 54 through 103 removed outlier: 3.542A pdb=" N THR C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 111 Processing helix chain 'C' and resid 114 through 156 removed outlier: 5.053A pdb=" N LEU C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLN C 126 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET C 146 " --> pdb=" O SER C 142 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET C 147 " --> pdb=" O THR C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 206 removed outlier: 3.549A pdb=" N PHE C 163 " --> pdb=" O TRP C 159 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 164 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE C 167 " --> pdb=" O PHE C 163 " (cutoff:3.500A) Proline residue: C 168 - end of helix removed outlier: 3.866A pdb=" N VAL C 171 " --> pdb=" O ILE C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 219 through 269 removed outlier: 3.739A pdb=" N ILE C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU C 244 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N GLU C 246 " --> pdb=" O ASP C 242 " (cutoff:3.500A) Proline residue: C 247 - end of helix removed outlier: 3.532A pdb=" N SER C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 287 Processing helix chain 'C' and resid 289 through 315 removed outlier: 3.663A pdb=" N GLY C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 384 removed outlier: 4.154A pdb=" N ILE C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C 384 " --> pdb=" O ILE C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 428 through 435 removed outlier: 4.281A pdb=" N GLY C 435 " --> pdb=" O ASN C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 450 removed outlier: 4.033A pdb=" N GLN C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 457 No H-bonds generated for 'chain 'C' and resid 454 through 457' Processing helix chain 'C' and resid 477 through 491 removed outlier: 3.867A pdb=" N ALA C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 520 Processing helix chain 'C' and resid 556 through 562 Processing sheet with id= A, first strand: chain 'D' and resid 54 through 57 removed outlier: 3.946A pdb=" N SER D 71 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 89 through 93 Processing sheet with id= C, first strand: chain 'D' and resid 109 through 112 removed outlier: 3.709A pdb=" N ARG D 126 " --> pdb=" O ILE D 119 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 430 through 432 Processing sheet with id= E, first strand: chain 'C' and resid 541 through 545 removed outlier: 6.399A pdb=" N THR C 526 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE C 369 " --> pdb=" O THR C 526 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE C 528 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N GLY C 371 " --> pdb=" O ILE C 528 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 496 " --> pdb=" O THR C 525 " (cutoff:3.500A) 541 hydrogen bonds defined for protein. 1596 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: 6.96 Time building geometry restraints manager: 18.10 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: 9951 1.03 - 1.23: 32 1.23 - 1.42: 4285 1.42 - 1.62: 6267 1.62 - 1.81: 104 Bond restraints: 20639 Sorted by residual: bond pdb=" C29 POV C 601 " pdb="C210 POV C 601 " ideal model delta sigma weight residual 1.333 1.540 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C29 POV C 603 " pdb="C210 POV C 603 " ideal model delta sigma weight residual 1.333 1.537 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C29 POV D 702 " pdb="C210 POV D 702 " ideal model delta sigma weight residual 1.333 1.534 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C29 POV C 605 " pdb="C210 POV C 605 " ideal model delta sigma weight residual 1.333 1.534 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C29 POV D 706 " pdb="C210 POV D 706 " ideal model delta sigma weight residual 1.333 1.533 -0.200 2.00e-02 2.50e+03 1.01e+02 ... (remaining 20634 not shown) Histogram of bond angle deviations from ideal: 97.58 - 105.99: 187 105.99 - 114.40: 24982 114.40 - 122.80: 9647 122.80 - 131.21: 2024 131.21 - 139.62: 28 Bond angle restraints: 36868 Sorted by residual: angle pdb=" C29 POV D 703 " pdb="C210 POV D 703 " pdb="C211 POV D 703 " ideal model delta sigma weight residual 127.67 107.67 20.00 3.00e+00 1.11e-01 4.44e+01 angle pdb=" C28 POV C 603 " pdb=" C29 POV C 603 " pdb="C210 POV C 603 " ideal model delta sigma weight residual 127.79 107.91 19.88 3.00e+00 1.11e-01 4.39e+01 angle pdb=" O13 POV D 710 " pdb=" P POV D 710 " pdb=" O14 POV D 710 " ideal model delta sigma weight residual 121.11 101.33 19.78 3.00e+00 1.11e-01 4.35e+01 angle pdb=" O13 POV C 602 " pdb=" P POV C 602 " pdb=" O14 POV C 602 " ideal model delta sigma weight residual 121.11 101.61 19.50 3.00e+00 1.11e-01 4.23e+01 angle pdb=" O13 POV D 709 " pdb=" P POV D 709 " pdb=" O14 POV D 709 " ideal model delta sigma weight residual 121.11 101.64 19.47 3.00e+00 1.11e-01 4.21e+01 ... (remaining 36863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.39: 9232 32.39 - 64.77: 563 64.77 - 97.16: 34 97.16 - 129.54: 16 129.54 - 161.93: 9 Dihedral angle restraints: 9854 sinusoidal: 5608 harmonic: 4246 Sorted by residual: dihedral pdb=" C29 POV D 710 " pdb="C210 POV D 710 " pdb="C211 POV D 710 " pdb="C212 POV D 710 " ideal model delta sinusoidal sigma weight residual 112.25 -49.68 161.93 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C39 POV D 705 " pdb="C310 POV D 705 " pdb="C311 POV D 705 " pdb="C312 POV D 705 " ideal model delta sinusoidal sigma weight residual -179.51 -17.93 -161.58 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C29 POV C 603 " pdb="C210 POV C 603 " pdb="C211 POV C 603 " pdb="C212 POV C 603 " ideal model delta sinusoidal sigma weight residual 112.25 -86.31 -161.44 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 9851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1338 0.059 - 0.118: 192 0.118 - 0.177: 16 0.177 - 0.235: 0 0.235 - 0.294: 6 Chirality restraints: 1552 Sorted by residual: chirality pdb=" C2' ATP D 711 " pdb=" C1' ATP D 711 " pdb=" C3' ATP D 711 " pdb=" O2' ATP D 711 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C3' ATP D 711 " pdb=" C2' ATP D 711 " pdb=" C4' ATP D 711 " pdb=" O3' ATP D 711 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C2' ATP C 612 " pdb=" C1' ATP C 612 " pdb=" C3' ATP C 612 " pdb=" O2' ATP C 612 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 1549 not shown) Planarity restraints: 2962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV D 708 " -0.284 2.00e-02 2.50e+03 3.22e-01 1.04e+03 pdb=" C29 POV D 708 " 0.215 2.00e-02 2.50e+03 pdb="C210 POV D 708 " 0.412 2.00e-02 2.50e+03 pdb="C211 POV D 708 " -0.343 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 707 " -0.318 2.00e-02 2.50e+03 3.09e-01 9.56e+02 pdb=" C29 POV D 707 " 0.344 2.00e-02 2.50e+03 pdb="C210 POV D 707 " 0.272 2.00e-02 2.50e+03 pdb="C211 POV D 707 " -0.298 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 706 " -0.157 2.00e-02 2.50e+03 2.94e-01 8.65e+02 pdb=" C29 POV D 706 " 0.397 2.00e-02 2.50e+03 pdb="C210 POV D 706 " -0.380 2.00e-02 2.50e+03 pdb="C211 POV D 706 " 0.140 2.00e-02 2.50e+03 ... (remaining 2959 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 540 2.12 - 2.74: 36893 2.74 - 3.36: 60628 3.36 - 3.98: 76747 3.98 - 4.60: 121232 Nonbonded interactions: 296040 Sorted by model distance: nonbonded pdb=" O ARG D 77 " pdb="HH11 ARG D 77 " model vdw 1.498 1.850 nonbonded pdb=" OE2 GLU D 644 " pdb=" H GLN D 657 " model vdw 1.608 1.850 nonbonded pdb=" O GLN D 92 " pdb=" HE ARG D 110 " model vdw 1.653 1.850 nonbonded pdb=" OD1 ASP D 44 " pdb=" H GLY D 370 " model vdw 1.669 1.850 nonbonded pdb="HE22 GLN D 303 " pdb=" O MET C 104 " model vdw 1.669 1.850 ... (remaining 296035 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: 7.400 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: 0.200 Extract box with map and model: 29.100 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 69.960 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 : 0.011 0.207 10688 Z= 0.738 Angle : 1.338 20.000 14302 Z= 0.506 Chirality : 0.042 0.294 1552 Planarity : 0.021 0.322 1762 Dihedral : 21.695 161.931 4233 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 20.31 % Favored : 79.69 % 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: -0.12 (0.24), residues: 1229 helix: 0.99 (0.19), residues: 761 sheet: -1.95 (0.51), residues: 93 loop : -1.75 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 78 HIS 0.003 0.001 HIS D 505 PHE 0.021 0.001 PHE D 37 TYR 0.019 0.002 TYR C 434 ARG 0.007 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 329 MET cc_start: 0.8623 (tpt) cc_final: 0.8003 (tpt) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.5958 time to fit residues: 77.9961 Evaluate side-chains 92 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 111 optimal weight: 8.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN C 479 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.0560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10688 Z= 0.374 Angle : 0.607 8.999 14302 Z= 0.318 Chirality : 0.040 0.163 1552 Planarity : 0.005 0.054 1762 Dihedral : 21.134 158.364 1896 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 1.14 % Allowed : 20.40 % Favored : 78.46 % 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: -0.26 (0.24), residues: 1229 helix: 0.97 (0.19), residues: 761 sheet: -2.17 (0.50), residues: 94 loop : -1.99 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 78 HIS 0.006 0.001 HIS C 80 PHE 0.017 0.002 PHE D 166 TYR 0.015 0.002 TYR C 19 ARG 0.004 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 436 SER cc_start: 0.6293 (OUTLIER) cc_final: 0.5319 (t) outliers start: 12 outliers final: 7 residues processed: 103 average time/residue: 0.5472 time to fit residues: 78.7953 Evaluate side-chains 100 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 544 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 0.0570 chunk 111 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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: 0.7776 moved from start: 0.0618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10688 Z= 0.183 Angle : 0.493 7.592 14302 Z= 0.265 Chirality : 0.036 0.144 1552 Planarity : 0.004 0.052 1762 Dihedral : 19.803 164.599 1896 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.24 % Allowed : 20.40 % Favored : 78.36 % 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: 0.19 (0.25), residues: 1229 helix: 1.33 (0.19), residues: 761 sheet: -1.98 (0.51), residues: 92 loop : -1.83 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 78 HIS 0.004 0.001 HIS D 648 PHE 0.015 0.001 PHE D 162 TYR 0.014 0.001 TYR C 19 ARG 0.004 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 105 average time/residue: 0.5468 time to fit residues: 80.4066 Evaluate side-chains 104 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 544 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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: 0.7783 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10688 Z= 0.213 Angle : 0.494 7.847 14302 Z= 0.267 Chirality : 0.037 0.149 1552 Planarity : 0.004 0.052 1762 Dihedral : 18.813 175.580 1896 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.62 % Allowed : 19.83 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.25), residues: 1229 helix: 1.39 (0.19), residues: 762 sheet: -1.99 (0.51), residues: 92 loop : -1.84 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 78 HIS 0.005 0.001 HIS C 452 PHE 0.014 0.001 PHE D 166 TYR 0.013 0.001 TYR C 19 ARG 0.003 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 436 SER cc_start: 0.6215 (OUTLIER) cc_final: 0.5084 (t) outliers start: 17 outliers final: 11 residues processed: 109 average time/residue: 0.5420 time to fit residues: 83.1420 Evaluate side-chains 107 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 544 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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: 0.7816 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10688 Z= 0.318 Angle : 0.545 8.400 14302 Z= 0.294 Chirality : 0.039 0.158 1552 Planarity : 0.005 0.066 1762 Dihedral : 18.644 174.759 1896 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.81 % Allowed : 20.11 % Favored : 78.07 % 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: -0.08 (0.24), residues: 1229 helix: 1.14 (0.19), residues: 761 sheet: -2.14 (0.50), residues: 92 loop : -1.97 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 78 HIS 0.006 0.001 HIS C 80 PHE 0.017 0.002 PHE D 166 TYR 0.015 0.002 TYR C 19 ARG 0.004 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 436 SER cc_start: 0.6347 (OUTLIER) cc_final: 0.5346 (t) outliers start: 19 outliers final: 14 residues processed: 110 average time/residue: 0.5496 time to fit residues: 84.6311 Evaluate side-chains 110 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 544 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.0870 chunk 23 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 114 optimal weight: 0.0170 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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: 0.7774 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10688 Z= 0.170 Angle : 0.481 7.908 14302 Z= 0.260 Chirality : 0.036 0.148 1552 Planarity : 0.004 0.051 1762 Dihedral : 17.485 162.411 1896 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.72 % Allowed : 20.31 % Favored : 77.98 % 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: 0.30 (0.25), residues: 1229 helix: 1.44 (0.19), residues: 761 sheet: -1.95 (0.51), residues: 92 loop : -1.83 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 78 HIS 0.004 0.001 HIS D 648 PHE 0.015 0.001 PHE D 162 TYR 0.014 0.001 TYR C 19 ARG 0.004 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 436 SER cc_start: 0.6229 (OUTLIER) cc_final: 0.5128 (t) outliers start: 18 outliers final: 14 residues processed: 110 average time/residue: 0.5452 time to fit residues: 84.2964 Evaluate side-chains 109 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 544 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 73 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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: 0.7778 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10688 Z= 0.201 Angle : 0.484 7.929 14302 Z= 0.262 Chirality : 0.036 0.149 1552 Planarity : 0.004 0.056 1762 Dihedral : 16.711 147.545 1896 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.33 % Allowed : 20.97 % Favored : 77.69 % 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: 0.34 (0.25), residues: 1229 helix: 1.47 (0.19), residues: 761 sheet: -1.95 (0.52), residues: 92 loop : -1.82 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 78 HIS 0.003 0.001 HIS D 648 PHE 0.013 0.001 PHE D 162 TYR 0.013 0.001 TYR C 19 ARG 0.005 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 436 SER cc_start: 0.6287 (OUTLIER) cc_final: 0.5192 (t) outliers start: 14 outliers final: 12 residues processed: 107 average time/residue: 0.5709 time to fit residues: 85.2920 Evaluate side-chains 107 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 544 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.7791 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10688 Z= 0.245 Angle : 0.505 8.420 14302 Z= 0.272 Chirality : 0.037 0.153 1552 Planarity : 0.005 0.057 1762 Dihedral : 16.388 146.517 1896 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.81 % Allowed : 20.69 % Favored : 77.50 % 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: 0.23 (0.24), residues: 1229 helix: 1.40 (0.19), residues: 760 sheet: -2.04 (0.51), residues: 92 loop : -1.85 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 78 HIS 0.004 0.001 HIS C 80 PHE 0.014 0.001 PHE D 166 TYR 0.014 0.001 TYR C 19 ARG 0.005 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 436 SER cc_start: 0.6294 (OUTLIER) cc_final: 0.5284 (t) outliers start: 19 outliers final: 15 residues processed: 107 average time/residue: 0.5928 time to fit residues: 89.6070 Evaluate side-chains 110 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 544 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7784 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10688 Z= 0.214 Angle : 0.492 8.444 14302 Z= 0.265 Chirality : 0.037 0.148 1552 Planarity : 0.004 0.056 1762 Dihedral : 15.877 142.553 1896 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.43 % Allowed : 21.07 % Favored : 77.50 % 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: 0.30 (0.25), residues: 1229 helix: 1.45 (0.19), residues: 760 sheet: -2.01 (0.51), residues: 92 loop : -1.82 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 78 HIS 0.004 0.001 HIS C 80 PHE 0.015 0.001 PHE D 162 TYR 0.014 0.001 TYR C 19 ARG 0.006 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 436 SER cc_start: 0.6304 (OUTLIER) cc_final: 0.5262 (t) outliers start: 15 outliers final: 14 residues processed: 106 average time/residue: 0.5735 time to fit residues: 85.0445 Evaluate side-chains 108 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 544 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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: 0.7787 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10688 Z= 0.229 Angle : 0.499 8.426 14302 Z= 0.269 Chirality : 0.037 0.149 1552 Planarity : 0.005 0.058 1762 Dihedral : 15.519 136.641 1896 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.53 % Allowed : 21.07 % Favored : 77.41 % 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: 0.28 (0.25), residues: 1229 helix: 1.44 (0.19), residues: 760 sheet: -2.04 (0.51), residues: 92 loop : -1.85 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 78 HIS 0.003 0.001 HIS C 80 PHE 0.014 0.001 PHE D 162 TYR 0.014 0.001 TYR C 19 ARG 0.006 0.000 ARG C 113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 107 ASP cc_start: 0.6838 (t0) cc_final: 0.6637 (t70) REVERT: D 436 SER cc_start: 0.6296 (OUTLIER) cc_final: 0.5287 (t) outliers start: 16 outliers final: 14 residues processed: 106 average time/residue: 0.5619 time to fit residues: 83.3420 Evaluate side-chains 109 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 544 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 5 optimal weight: 0.0570 overall best weight: 0.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.098355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.079323 restraints weight = 64781.196| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.19 r_work: 0.3455 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10688 Z= 0.173 Angle : 0.477 8.125 14302 Z= 0.257 Chirality : 0.036 0.146 1552 Planarity : 0.004 0.054 1762 Dihedral : 15.010 125.375 1896 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.53 % Allowed : 21.16 % Favored : 77.31 % 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: 0.45 (0.25), residues: 1229 helix: 1.58 (0.19), residues: 760 sheet: -1.92 (0.52), residues: 91 loop : -1.80 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 78 HIS 0.003 0.001 HIS D 648 PHE 0.013 0.001 PHE D 162 TYR 0.014 0.001 TYR C 19 ARG 0.006 0.000 ARG C 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4856.47 seconds wall clock time: 89 minutes 25.83 seconds (5365.83 seconds total)