Starting phenix.real_space_refine on Fri Sep 11 15:22:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x68_22073/09_2026/6x68_22073.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x68_22073/09_2026/6x68_22073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x68_22073/09_2026/6x68_22073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x68_22073/09_2026/6x68_22073.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x68_22073/09_2026/6x68_22073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x68_22073/09_2026/6x68_22073.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6x68_22073/09_2026/6x68_22073.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x68_22073/09_2026/6x68_22073.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 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 Ca 4 9.91 5 Zn 4 6.06 5 P 124 5.49 5 S 88 5.16 5 C 6063 2.51 5 N 1811 2.21 5 O 2152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10246 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 3848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3848 Classifications: {'peptide': 478} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 452} Chain: "D" Number of atoms: 3848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3848 Classifications: {'peptide': 478} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 452} Chain: "A" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1517 Classifications: {'DNA': 74} Link IDs: {'rna3p': 73} Chain: "B" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1025 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3568 SG CYS C 559 43.876 58.830 53.085 1.00101.37 S ATOM 3593 SG CYS C 562 44.008 62.320 53.323 1.00101.18 S ATOM 3747 SG CYS C 582 44.083 60.658 50.274 1.00102.93 S ATOM 3684 SG CYS C 574 50.264 50.434 49.266 1.00157.97 S ATOM 3708 SG CYS C 577 50.090 49.390 52.178 1.00145.09 S ATOM 3815 SG CYS C 590 51.546 52.352 51.479 1.00159.91 S ATOM 3836 SG CYS C 593 52.626 49.806 51.000 1.00172.88 S ATOM 7416 SG CYS D 559 50.389 56.078 28.512 1.00 0.00 S ATOM 7441 SG CYS D 562 47.844 55.761 27.137 1.00319.64 S ATOM 7595 SG CYS D 582 47.770 55.742 30.601 1.00289.96 S ATOM 7532 SG CYS D 574 58.188 55.339 37.702 1.00325.15 S ATOM 7556 SG CYS D 577 60.281 55.493 35.331 1.00356.83 S ATOM 7663 SG CYS D 590 58.020 52.711 36.125 1.00303.36 S ATOM 7684 SG CYS D 593 59.976 53.297 37.650 1.00322.51 S Time building chain proxies: 2.62, per 1000 atoms: 0.26 Number of scatterers: 10246 At special positions: 0 Unit cell: (95.04, 90.72, 149.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 88 16.00 P 124 15.00 O 2152 8.00 N 1811 7.00 C 6063 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.71 Conformation dependent library (CDL) restraints added in 258.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 603 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 582 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 562 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 559 " pdb="ZN ZN C 603 " - pdb=" ND1 HIS C 585 " pdb=" ZN C 604 " pdb="ZN ZN C 604 " - pdb=" SG CYS C 577 " pdb="ZN ZN C 604 " - pdb=" SG CYS C 593 " pdb="ZN ZN C 604 " - pdb=" SG CYS C 590 " pdb="ZN ZN C 604 " - pdb=" SG CYS C 574 " pdb=" ZN D 602 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 562 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 582 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 559 " pdb="ZN ZN D 602 " - pdb=" ND1 HIS D 585 " pdb=" ZN D 603 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 574 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 593 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 590 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 577 " Number of angles added : 18 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1820 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 7 sheets defined 46.1% alpha, 11.5% beta 52 base pairs and 103 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'C' and resid 123 through 126 Processing helix chain 'C' and resid 130 through 159 removed outlier: 3.935A pdb=" N PHE C 138 " --> pdb=" O CYS C 134 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ASP C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLU C 142 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE C 143 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 144 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA C 153 " --> pdb=" O LYS C 149 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 154 " --> pdb=" O TRP C 150 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 172 through 189 Processing helix chain 'C' and resid 195 through 200 removed outlier: 3.838A pdb=" N PHE C 200 " --> pdb=" O THR C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 224 Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 241 through 243 No H-bonds generated for 'chain 'C' and resid 241 through 243' Processing helix chain 'C' and resid 244 through 258 removed outlier: 4.611A pdb=" N LEU C 250 " --> pdb=" O LYS C 246 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 333 Processing helix chain 'C' and resid 334 through 337 Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 351 through 358 Processing helix chain 'C' and resid 379 through 384 Processing helix chain 'C' and resid 433 through 443 Processing helix chain 'C' and resid 443 through 453 removed outlier: 4.831A pdb=" N ASP C 447 " --> pdb=" O LYS C 443 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 491 removed outlier: 4.055A pdb=" N LEU C 469 " --> pdb=" O TRP C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 519 removed outlier: 3.680A pdb=" N SER C 512 " --> pdb=" O MET C 508 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N SER C 513 " --> pdb=" O SER C 509 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N PHE C 514 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 519 " --> pdb=" O MET C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 535 Processing helix chain 'C' and resid 563 through 567 Processing helix chain 'D' and resid 123 through 126 Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 140 through 159 removed outlier: 4.075A pdb=" N ALA D 153 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU D 154 " --> pdb=" O TRP D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 172 through 190 Processing helix chain 'D' and resid 195 through 200 Processing helix chain 'D' and resid 213 through 224 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 241 through 243 No H-bonds generated for 'chain 'D' and resid 241 through 243' Processing helix chain 'D' and resid 244 through 257 removed outlier: 3.744A pdb=" N GLN D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS D 255 " --> pdb=" O PHE D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 334 through 337 Processing helix chain 'D' and resid 346 through 350 removed outlier: 3.885A pdb=" N THR D 350 " --> pdb=" O ASN D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 358 Processing helix chain 'D' and resid 379 through 384 Processing helix chain 'D' and resid 433 through 443 removed outlier: 3.948A pdb=" N GLN D 441 " --> pdb=" O MET D 437 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR D 442 " --> pdb=" O TYR D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 456 Processing helix chain 'D' and resid 464 through 491 removed outlier: 3.542A pdb=" N ALA D 468 " --> pdb=" O ARG D 464 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU D 470 " --> pdb=" O PRO D 466 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D 479 " --> pdb=" O ASN D 475 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE D 482 " --> pdb=" O CYS D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 519 removed outlier: 5.383A pdb=" N SER D 513 " --> pdb=" O SER D 509 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N PHE D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU D 519 " --> pdb=" O MET D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 536 Processing helix chain 'D' and resid 590 through 594 Processing sheet with id=AA1, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AA2, first strand: chain 'C' and resid 306 through 311 removed outlier: 6.828A pdb=" N MET C 298 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY C 309 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU C 296 " --> pdb=" O GLY C 309 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LYS C 294 " --> pdb=" O PRO C 311 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU C 265 " --> pdb=" O THR C 344 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 572 through 574 removed outlier: 3.539A pdb=" N LYS C 579 " --> pdb=" O CYS C 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 120 through 121 Processing sheet with id=AA5, first strand: chain 'D' and resid 282 through 283 removed outlier: 6.457A pdb=" N ASP D 300 " --> pdb=" O MET D 306 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N MET D 306 " --> pdb=" O ASP D 300 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 282 through 283 removed outlier: 5.029A pdb=" N ILE D 367 " --> pdb=" O SER D 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 572 through 573 332 hydrogen bonds defined for protein. 906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 129 hydrogen bonds 258 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 103 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2084 1.33 - 1.45: 3323 1.45 - 1.58: 4912 1.58 - 1.71: 247 1.71 - 1.83: 136 Bond restraints: 10702 Sorted by residual: bond pdb=" C4' DT A 34 " pdb=" C3' DT A 34 " ideal model delta sigma weight residual 1.529 1.617 -0.088 1.00e-02 1.00e+04 7.83e+01 bond pdb=" O3' DA A 33 " pdb=" P DT A 34 " ideal model delta sigma weight residual 1.607 1.516 0.091 1.20e-02 6.94e+03 5.81e+01 bond pdb=" N SER D 289 " pdb=" CA SER D 289 " ideal model delta sigma weight residual 1.458 1.392 0.066 1.19e-02 7.06e+03 3.10e+01 bond pdb=" C3' DA A 33 " pdb=" O3' DA A 33 " ideal model delta sigma weight residual 1.435 1.366 0.069 1.30e-02 5.92e+03 2.80e+01 bond pdb=" C4' DA A 33 " pdb=" C3' DA A 33 " ideal model delta sigma weight residual 1.529 1.476 0.053 1.00e-02 1.00e+04 2.79e+01 ... (remaining 10697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.39: 14510 4.39 - 8.79: 431 8.79 - 13.18: 25 13.18 - 17.58: 3 17.58 - 21.97: 1 Bond angle restraints: 14970 Sorted by residual: angle pdb=" CA ASN C 384 " pdb=" C ASN C 384 " pdb=" N SER C 385 " ideal model delta sigma weight residual 115.36 93.39 21.97 1.56e+00 4.11e-01 1.98e+02 angle pdb=" O4' DA A 33 " pdb=" C4' DA A 33 " pdb=" C3' DA A 33 " ideal model delta sigma weight residual 106.00 99.02 6.98 6.00e-01 2.78e+00 1.35e+02 angle pdb=" N VAL C 552 " pdb=" CA VAL C 552 " pdb=" C VAL C 552 " ideal model delta sigma weight residual 113.47 101.80 11.67 1.01e+00 9.80e-01 1.33e+02 angle pdb=" C3' DT B -3 " pdb=" O3' DT B -3 " pdb=" P DT B -2 " ideal model delta sigma weight residual 119.70 131.85 -12.15 1.20e+00 6.94e-01 1.03e+02 angle pdb=" N ASN C 384 " pdb=" CA ASN C 384 " pdb=" C ASN C 384 " ideal model delta sigma weight residual 109.85 125.80 -15.95 1.58e+00 4.01e-01 1.02e+02 ... (remaining 14965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.95: 5681 33.95 - 67.90: 571 67.90 - 101.85: 6 101.85 - 135.80: 0 135.80 - 169.75: 2 Dihedral angle restraints: 6260 sinusoidal: 3444 harmonic: 2816 Sorted by residual: dihedral pdb=" C PRO D 408 " pdb=" N PRO D 408 " pdb=" CA PRO D 408 " pdb=" CB PRO D 408 " ideal model delta harmonic sigma weight residual -120.70 -107.37 -13.33 0 2.50e+00 1.60e-01 2.84e+01 dihedral pdb=" C TYR D 527 " pdb=" N TYR D 527 " pdb=" CA TYR D 527 " pdb=" CB TYR D 527 " ideal model delta harmonic sigma weight residual -122.60 -110.50 -12.10 0 2.50e+00 1.60e-01 2.34e+01 dihedral pdb=" C PRO C 541 " pdb=" N PRO C 541 " pdb=" CA PRO C 541 " pdb=" CB PRO C 541 " ideal model delta harmonic sigma weight residual -120.70 -108.72 -11.98 0 2.50e+00 1.60e-01 2.29e+01 ... (remaining 6257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1302 0.098 - 0.196: 296 0.196 - 0.294: 43 0.294 - 0.393: 14 0.393 - 0.491: 3 Chirality restraints: 1658 Sorted by residual: chirality pdb=" CA ASN C 384 " pdb=" N ASN C 384 " pdb=" C ASN C 384 " pdb=" CB ASN C 384 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" CA PRO D 551 " pdb=" N PRO D 551 " pdb=" C PRO D 551 " pdb=" CB PRO D 551 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CA PRO D 410 " pdb=" N PRO D 410 " pdb=" C PRO D 410 " pdb=" CB PRO D 410 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 3.92e+00 ... (remaining 1655 not shown) Planarity restraints: 1472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 594 " -0.034 2.00e-02 2.50e+03 6.58e-02 4.33e+01 pdb=" C PHE D 594 " 0.114 2.00e-02 2.50e+03 pdb=" O PHE D 594 " -0.041 2.00e-02 2.50e+03 pdb=" OXT PHE D 594 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 594 " -0.030 2.00e-02 2.50e+03 5.78e-02 3.34e+01 pdb=" C PHE C 594 " 0.100 2.00e-02 2.50e+03 pdb=" O PHE C 594 " -0.035 2.00e-02 2.50e+03 pdb=" OXT PHE C 594 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 507 " -0.061 2.00e-02 2.50e+03 3.40e-02 2.31e+01 pdb=" CG TYR D 507 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR D 507 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR D 507 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR D 507 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR D 507 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR D 507 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR D 507 " -0.046 2.00e-02 2.50e+03 ... (remaining 1469 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 9 2.30 - 2.95: 4458 2.95 - 3.60: 13893 3.60 - 4.25: 25472 4.25 - 4.90: 37684 Nonbonded interactions: 81516 Sorted by model distance: nonbonded pdb=" OP1 DT A -3 " pdb="CA CA A 101 " model vdw 1.652 2.510 nonbonded pdb=" OD2 ASP D 346 " pdb="CA CA A 101 " model vdw 1.905 2.510 nonbonded pdb=" OD2 ASP C 218 " pdb="CA CA C 602 " model vdw 2.030 2.510 nonbonded pdb=" OD2 ASP C 346 " pdb="CA CA C 601 " model vdw 2.075 2.510 nonbonded pdb=" OP1 DT B -3 " pdb="CA CA C 601 " model vdw 2.105 2.510 ... (remaining 81511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 117 through 601 or resid 603)) selection = (chain 'D' and (resid 117 through 601 or resid 603)) } 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 group one per residue 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.930 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 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 : 0.019 0.619 10718 Z= 1.040 Angle : 1.823 24.715 14988 Z= 1.349 Chirality : 0.088 0.491 1658 Planarity : 0.005 0.066 1472 Dihedral : 21.014 169.750 4440 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.52 % Favored : 97.16 % Rotamer: Outliers : 0.57 % Allowed : 6.90 % Favored : 92.53 % Cbeta Deviations : 1.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.26), residues: 952 helix: -1.14 (0.24), residues: 366 sheet: 1.50 (0.50), residues: 108 loop : 0.25 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 526 TYR 0.061 0.010 TYR D 507 PHE 0.031 0.006 PHE D 349 TRP 0.040 0.009 TRP C 465 HIS 0.009 0.003 HIS C 585 Details of bonding type rmsd/Z covalent geometry : bond 0.01191 / 0.89 (10702) covalent geometry : angle 1.77017 / 1.35 (14970) hydrogen bonds : bond 0.22798 / 14.88 ( 459) hydrogen bonds : angle 6.46602 / 4.60 ( 1164) metal coordination : bond 0.39325 / 26.19 ( 16) metal coordination : angle 12.67705 / 7.37 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 354 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 191 ASP cc_start: 0.7915 (p0) cc_final: 0.7479 (p0) REVERT: C 228 ASP cc_start: 0.7858 (t0) cc_final: 0.7622 (t70) REVERT: C 413 MET cc_start: 0.6567 (mpp) cc_final: 0.6334 (mpp) REVERT: D 206 MET cc_start: 0.8437 (mmm) cc_final: 0.8204 (mmt) outliers start: 5 outliers final: 1 residues processed: 357 average time/residue: 0.1190 time to fit residues: 57.3921 Evaluate side-chains 221 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 179 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 357 ASN C 384 ASN C 440 ASN C 571 ASN D 264 HIS D 347 ASN D 531 ASN D 538 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.145784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.110404 restraints weight = 18427.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114214 restraints weight = 8352.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.116569 restraints weight = 5265.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.117928 restraints weight = 4046.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118560 restraints weight = 3510.323| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 10718 Z= 0.217 Angle : 0.919 11.541 14988 Z= 0.513 Chirality : 0.055 0.243 1658 Planarity : 0.006 0.055 1472 Dihedral : 24.357 168.735 2456 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.31 % Favored : 97.58 % Rotamer: Outliers : 3.73 % Allowed : 17.87 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.27), residues: 952 helix: 0.34 (0.27), residues: 362 sheet: 1.22 (0.49), residues: 111 loop : -0.13 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 337 TYR 0.020 0.002 TYR D 439 PHE 0.038 0.002 PHE C 241 TRP 0.011 0.002 TRP D 150 HIS 0.003 0.001 HIS D 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.22 (10702) covalent geometry : angle 0.90655 / 0.51 (14970) hydrogen bonds : bond 0.08810 / 5.78 ( 459) hydrogen bonds : angle 4.99914 / 3.60 ( 1164) metal coordination : bond 0.01994 / 1.32 ( 16) metal coordination : angle 4.46329 / 2.38 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 254 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 138 PHE cc_start: 0.8809 (m-80) cc_final: 0.8369 (m-80) REVERT: C 154 GLU cc_start: 0.8230 (mp0) cc_final: 0.7977 (mp0) REVERT: C 182 ILE cc_start: 0.9166 (mm) cc_final: 0.8940 (mm) REVERT: C 257 GLN cc_start: 0.8453 (mm110) cc_final: 0.7969 (tm-30) REVERT: C 384 ASN cc_start: 0.7153 (OUTLIER) cc_final: 0.6866 (m110) REVERT: C 413 MET cc_start: 0.5722 (mpp) cc_final: 0.5266 (mpp) REVERT: D 169 ARG cc_start: 0.7319 (mtm110) cc_final: 0.7064 (mtm110) REVERT: D 225 ARG cc_start: 0.7480 (mmt-90) cc_final: 0.7230 (mpt180) REVERT: D 331 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8205 (tm-30) REVERT: D 332 LEU cc_start: 0.8774 (mm) cc_final: 0.8268 (mm) REVERT: D 372 ARG cc_start: 0.7645 (mtt90) cc_final: 0.7422 (mtm-85) REVERT: D 394 MET cc_start: 0.6848 (mtp) cc_final: 0.6405 (ttm) REVERT: D 503 MET cc_start: 0.8346 (mtp) cc_final: 0.8059 (mtt) REVERT: D 536 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8018 (tp) outliers start: 33 outliers final: 21 residues processed: 272 average time/residue: 0.0988 time to fit residues: 37.9218 Evaluate side-chains 241 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 218 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 254 GLN Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 384 ASN Chi-restraints excluded: chain C residue 465 TRP Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 179 PHE Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 451 GLN Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 527 TYR Chi-restraints excluded: chain D residue 536 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 39 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 10 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 384 ASN C 571 ASN D 254 GLN D 347 ASN D 538 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.146121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.110969 restraints weight = 18618.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114775 restraints weight = 8407.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.117118 restraints weight = 5306.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.118319 restraints weight = 4094.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.118861 restraints weight = 3588.486| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10718 Z= 0.170 Angle : 0.773 7.810 14988 Z= 0.437 Chirality : 0.048 0.220 1658 Planarity : 0.005 0.048 1472 Dihedral : 24.435 163.499 2456 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.05 % Favored : 96.85 % Rotamer: Outliers : 3.51 % Allowed : 18.55 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.27), residues: 952 helix: 0.66 (0.28), residues: 364 sheet: 0.99 (0.49), residues: 112 loop : -0.36 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 499 TYR 0.011 0.001 TYR C 312 PHE 0.021 0.002 PHE D 219 TRP 0.007 0.001 TRP D 150 HIS 0.005 0.001 HIS C 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (10702) covalent geometry : angle 0.76424 / 0.44 (14970) hydrogen bonds : bond 0.06878 / 4.43 ( 459) hydrogen bonds : angle 4.54752 / 3.26 ( 1164) metal coordination : bond 0.01016 / 0.59 ( 16) metal coordination : angle 3.38978 / 2.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 234 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 138 PHE cc_start: 0.8783 (m-80) cc_final: 0.8486 (m-80) REVERT: C 182 ILE cc_start: 0.9126 (mm) cc_final: 0.8841 (mm) REVERT: C 257 GLN cc_start: 0.8374 (mm110) cc_final: 0.8140 (tm-30) REVERT: C 310 MET cc_start: 0.7579 (ptp) cc_final: 0.7214 (ptp) REVERT: C 394 MET cc_start: 0.7026 (ttt) cc_final: 0.6536 (ttt) REVERT: C 413 MET cc_start: 0.5850 (mpp) cc_final: 0.5418 (mpp) REVERT: C 467 MET cc_start: 0.8001 (mmm) cc_final: 0.7742 (mmm) REVERT: C 520 GLU cc_start: 0.8011 (tp30) cc_final: 0.7694 (tp30) REVERT: D 146 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7518 (mt-10) REVERT: D 169 ARG cc_start: 0.7323 (mtm110) cc_final: 0.7091 (mtm110) REVERT: D 218 ASP cc_start: 0.8717 (m-30) cc_final: 0.8492 (m-30) REVERT: D 332 LEU cc_start: 0.8649 (mm) cc_final: 0.8340 (mm) REVERT: D 372 ARG cc_start: 0.7704 (mtt90) cc_final: 0.7437 (mtm-85) REVERT: D 394 MET cc_start: 0.6762 (mtp) cc_final: 0.6483 (ttm) REVERT: D 515 MET cc_start: 0.9128 (mtp) cc_final: 0.8891 (mtm) REVERT: D 536 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8023 (tp) REVERT: D 569 LYS cc_start: 0.6549 (mttt) cc_final: 0.5481 (tmtt) outliers start: 31 outliers final: 18 residues processed: 251 average time/residue: 0.0923 time to fit residues: 33.7364 Evaluate side-chains 229 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 210 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 254 GLN Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 465 TRP Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 527 TYR Chi-restraints excluded: chain D residue 536 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 84 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 94 optimal weight: 50.0000 chunk 28 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 441 GLN C 571 ASN D 440 ASN D 538 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.141782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106331 restraints weight = 19045.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.109988 restraints weight = 8700.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112201 restraints weight = 5550.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.113325 restraints weight = 4322.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114129 restraints weight = 3821.468| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10718 Z= 0.206 Angle : 0.777 6.747 14988 Z= 0.431 Chirality : 0.047 0.202 1658 Planarity : 0.005 0.051 1472 Dihedral : 24.716 163.889 2454 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.68 % Favored : 96.22 % Rotamer: Outliers : 3.62 % Allowed : 19.12 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.28), residues: 952 helix: 0.90 (0.28), residues: 353 sheet: 0.66 (0.49), residues: 117 loop : -0.53 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 126 TYR 0.013 0.002 TYR D 177 PHE 0.038 0.002 PHE C 241 TRP 0.005 0.001 TRP C 465 HIS 0.005 0.001 HIS D 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 (10702) covalent geometry : angle 0.76785 / 0.43 (14970) hydrogen bonds : bond 0.06697 / 4.31 ( 459) hydrogen bonds : angle 4.46618 / 3.19 ( 1164) metal coordination : bond 0.01523 / 0.80 ( 16) metal coordination : angle 3.54805 / 2.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 182 ILE cc_start: 0.9242 (mm) cc_final: 0.8984 (mm) REVERT: C 257 GLN cc_start: 0.8330 (mm110) cc_final: 0.8047 (tm-30) REVERT: C 310 MET cc_start: 0.7721 (ptp) cc_final: 0.7515 (ptp) REVERT: C 315 ARG cc_start: 0.8288 (tpp80) cc_final: 0.7839 (mmm160) REVERT: C 394 MET cc_start: 0.7152 (ttt) cc_final: 0.6745 (ttt) REVERT: C 413 MET cc_start: 0.5856 (mpp) cc_final: 0.5461 (mpp) REVERT: C 520 GLU cc_start: 0.8180 (tp30) cc_final: 0.7822 (tp30) REVERT: D 218 ASP cc_start: 0.8694 (m-30) cc_final: 0.8461 (m-30) REVERT: D 264 HIS cc_start: 0.8642 (m-70) cc_final: 0.8223 (m90) REVERT: D 297 MET cc_start: 0.9024 (ttm) cc_final: 0.8149 (mtp) REVERT: D 331 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8126 (tm-30) REVERT: D 372 ARG cc_start: 0.7977 (mtt90) cc_final: 0.7685 (mtm-85) REVERT: D 394 MET cc_start: 0.6831 (mtp) cc_final: 0.6618 (ttm) REVERT: D 515 MET cc_start: 0.9167 (mtp) cc_final: 0.8905 (mtm) REVERT: D 523 THR cc_start: 0.8434 (p) cc_final: 0.8220 (p) REVERT: D 536 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8111 (tp) REVERT: D 569 LYS cc_start: 0.6633 (mttt) cc_final: 0.5310 (tmtt) REVERT: D 589 MET cc_start: 0.8140 (mtp) cc_final: 0.7738 (mtt) outliers start: 32 outliers final: 24 residues processed: 235 average time/residue: 0.0828 time to fit residues: 28.4866 Evaluate side-chains 229 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 254 GLN Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 527 TYR Chi-restraints excluded: chain D residue 536 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 8 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 105 optimal weight: 30.0000 chunk 15 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 ASN D 480 ASN D 531 ASN D 538 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.143197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107847 restraints weight = 18893.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.111538 restraints weight = 8565.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113761 restraints weight = 5453.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114936 restraints weight = 4246.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.115760 restraints weight = 3740.928| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10718 Z= 0.160 Angle : 0.723 10.890 14988 Z= 0.402 Chirality : 0.046 0.216 1658 Planarity : 0.005 0.054 1472 Dihedral : 24.704 162.947 2454 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.78 % Favored : 96.11 % Rotamer: Outliers : 3.51 % Allowed : 20.48 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.28), residues: 952 helix: 1.11 (0.28), residues: 354 sheet: 0.56 (0.49), residues: 117 loop : -0.66 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 169 TYR 0.013 0.001 TYR D 363 PHE 0.035 0.002 PHE C 241 TRP 0.010 0.001 TRP C 465 HIS 0.002 0.001 HIS C 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (10702) covalent geometry : angle 0.71684 / 0.40 (14970) hydrogen bonds : bond 0.05682 / 3.69 ( 459) hydrogen bonds : angle 4.24151 / 3.03 ( 1164) metal coordination : bond 0.00859 / 0.51 ( 16) metal coordination : angle 2.82787 / 1.58 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: C 310 MET cc_start: 0.7728 (ptp) cc_final: 0.7454 (ptp) REVERT: C 394 MET cc_start: 0.7295 (ttt) cc_final: 0.7061 (ttt) REVERT: C 413 MET cc_start: 0.5889 (mpp) cc_final: 0.5507 (mpp) REVERT: C 440 ASN cc_start: 0.8869 (m-40) cc_final: 0.8654 (m110) REVERT: C 520 GLU cc_start: 0.8147 (tp30) cc_final: 0.7788 (tp30) REVERT: C 534 ASN cc_start: 0.8826 (m-40) cc_final: 0.8397 (t0) REVERT: D 218 ASP cc_start: 0.8699 (m-30) cc_final: 0.8439 (m-30) REVERT: D 286 ASN cc_start: 0.8070 (m-40) cc_final: 0.7857 (p0) REVERT: D 297 MET cc_start: 0.8993 (ttm) cc_final: 0.8128 (mtp) REVERT: D 306 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.8018 (tmt) REVERT: D 331 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8189 (tm-30) REVERT: D 372 ARG cc_start: 0.8062 (mtt90) cc_final: 0.7561 (mtm-85) REVERT: D 374 ASN cc_start: 0.8675 (p0) cc_final: 0.8338 (t0) REVERT: D 456 MET cc_start: 0.8546 (mmt) cc_final: 0.8241 (mmt) REVERT: D 467 MET cc_start: 0.7825 (mmm) cc_final: 0.7164 (mmm) REVERT: D 523 THR cc_start: 0.8414 (p) cc_final: 0.8203 (p) REVERT: D 536 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8096 (tp) REVERT: D 569 LYS cc_start: 0.6671 (mttt) cc_final: 0.5353 (tmtt) REVERT: D 589 MET cc_start: 0.8129 (mtp) cc_final: 0.7883 (mtm) outliers start: 31 outliers final: 26 residues processed: 246 average time/residue: 0.0831 time to fit residues: 30.5690 Evaluate side-chains 234 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 254 GLN Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 306 MET Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 453 CYS Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 557 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 35 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 95 optimal weight: 20.0000 chunk 64 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN ** C 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 HIS D 488 ASN D 538 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.139764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104141 restraints weight = 19261.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.107778 restraints weight = 8667.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.110002 restraints weight = 5500.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.111127 restraints weight = 4276.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111952 restraints weight = 3774.658| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10718 Z= 0.229 Angle : 0.771 8.546 14988 Z= 0.423 Chirality : 0.048 0.218 1658 Planarity : 0.006 0.055 1472 Dihedral : 24.842 164.131 2454 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.52 % Favored : 95.38 % Rotamer: Outliers : 4.64 % Allowed : 21.27 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.27), residues: 952 helix: 1.06 (0.28), residues: 354 sheet: 0.53 (0.50), residues: 115 loop : -0.80 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 281 TYR 0.013 0.002 TYR C 527 PHE 0.039 0.002 PHE C 241 TRP 0.031 0.002 TRP C 465 HIS 0.002 0.001 HIS D 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 (10702) covalent geometry : angle 0.76457 / 0.42 (14970) hydrogen bonds : bond 0.06451 / 4.17 ( 459) hydrogen bonds : angle 4.40584 / 3.14 ( 1164) metal coordination : bond 0.01184 / 0.65 ( 16) metal coordination : angle 3.06378 / 1.95 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 212 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: C 257 GLN cc_start: 0.8353 (tm-30) cc_final: 0.8132 (tm-30) REVERT: C 312 TYR cc_start: 0.8830 (t80) cc_final: 0.8617 (t80) REVERT: C 394 MET cc_start: 0.7001 (ttt) cc_final: 0.6756 (ttt) REVERT: C 413 MET cc_start: 0.5858 (mpp) cc_final: 0.5450 (mpp) REVERT: C 440 ASN cc_start: 0.9020 (m-40) cc_final: 0.8739 (m110) REVERT: C 520 GLU cc_start: 0.8311 (tp30) cc_final: 0.7943 (tp30) REVERT: C 534 ASN cc_start: 0.8775 (m-40) cc_final: 0.8389 (t0) REVERT: D 189 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7953 (mmt90) REVERT: D 206 MET cc_start: 0.8545 (mmt) cc_final: 0.8330 (tpp) REVERT: D 218 ASP cc_start: 0.8695 (m-30) cc_final: 0.8442 (m-30) REVERT: D 297 MET cc_start: 0.9012 (ttm) cc_final: 0.8247 (mtp) REVERT: D 372 ARG cc_start: 0.8201 (mtt90) cc_final: 0.7702 (mtm-85) REVERT: D 374 ASN cc_start: 0.8616 (p0) cc_final: 0.8354 (t0) REVERT: D 456 MET cc_start: 0.8654 (mmt) cc_final: 0.8435 (mmt) REVERT: D 536 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8198 (tp) REVERT: D 569 LYS cc_start: 0.6487 (mttt) cc_final: 0.5144 (tmtt) REVERT: D 589 MET cc_start: 0.8012 (mtp) cc_final: 0.7784 (mtm) outliers start: 41 outliers final: 32 residues processed: 237 average time/residue: 0.0871 time to fit residues: 30.6643 Evaluate side-chains 233 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 189 ARG Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 306 MET Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 453 CYS Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 527 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 557 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 22 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 102 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 100 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS D 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.142803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107982 restraints weight = 18882.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.111628 restraints weight = 8493.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113877 restraints weight = 5387.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.115069 restraints weight = 4175.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.115885 restraints weight = 3667.449| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 2.184 10718 Z= 0.406 Angle : 0.710 8.961 14988 Z= 0.395 Chirality : 0.045 0.218 1658 Planarity : 0.005 0.058 1472 Dihedral : 24.736 162.100 2454 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.47 % Favored : 96.43 % Rotamer: Outliers : 3.73 % Allowed : 21.61 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.28), residues: 952 helix: 1.30 (0.28), residues: 353 sheet: 0.50 (0.50), residues: 115 loop : -0.83 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 189 TYR 0.010 0.001 TYR C 259 PHE 0.037 0.002 PHE C 241 TRP 0.019 0.002 TRP C 465 HIS 0.004 0.000 HIS D 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (10702) covalent geometry : angle 0.70466 / 0.39 (14970) hydrogen bonds : bond 0.05470 / 3.55 ( 459) hydrogen bonds : angle 4.17604 / 2.99 ( 1164) metal coordination : bond 0.54600 / 27.30 ( 16) metal coordination : angle 2.59221 / 1.58 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: C 248 TRP cc_start: 0.8901 (t-100) cc_final: 0.8692 (t-100) REVERT: C 257 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8155 (tm-30) REVERT: C 307 ILE cc_start: 0.9061 (mt) cc_final: 0.8341 (mt) REVERT: C 394 MET cc_start: 0.7149 (ttt) cc_final: 0.6909 (ttt) REVERT: C 413 MET cc_start: 0.5570 (mpp) cc_final: 0.5203 (mpp) REVERT: C 440 ASN cc_start: 0.8991 (m-40) cc_final: 0.8725 (m110) REVERT: C 520 GLU cc_start: 0.8154 (tp30) cc_final: 0.7778 (tp30) REVERT: C 534 ASN cc_start: 0.8825 (m-40) cc_final: 0.8456 (t0) REVERT: C 565 LYS cc_start: 0.8872 (ttmt) cc_final: 0.8435 (mmtp) REVERT: D 218 ASP cc_start: 0.8656 (m-30) cc_final: 0.8396 (m-30) REVERT: D 286 ASN cc_start: 0.7995 (m-40) cc_final: 0.7792 (p0) REVERT: D 297 MET cc_start: 0.9008 (ttm) cc_final: 0.8237 (mtp) REVERT: D 332 LEU cc_start: 0.8769 (mm) cc_final: 0.8211 (mm) REVERT: D 372 ARG cc_start: 0.8186 (mtt90) cc_final: 0.7617 (mtm-85) REVERT: D 374 ASN cc_start: 0.8578 (p0) cc_final: 0.8283 (t0) REVERT: D 456 MET cc_start: 0.8636 (mmt) cc_final: 0.8358 (mmt) REVERT: D 569 LYS cc_start: 0.6477 (mttt) cc_final: 0.5150 (tmtt) outliers start: 33 outliers final: 29 residues processed: 230 average time/residue: 0.0838 time to fit residues: 28.5484 Evaluate side-chains 236 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 306 MET Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 453 CYS Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 527 TYR Chi-restraints excluded: chain D residue 557 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 79 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.141044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106206 restraints weight = 19040.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.109726 restraints weight = 8665.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111900 restraints weight = 5549.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.113200 restraints weight = 4324.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113933 restraints weight = 3770.017| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.433 10718 Z= 0.201 Angle : 0.776 19.155 14988 Z= 0.412 Chirality : 0.046 0.223 1658 Planarity : 0.006 0.057 1472 Dihedral : 24.807 162.878 2454 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.52 % Favored : 95.38 % Rotamer: Outliers : 3.62 % Allowed : 21.83 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.27), residues: 952 helix: 1.26 (0.28), residues: 356 sheet: 0.53 (0.50), residues: 115 loop : -0.91 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 169 TYR 0.013 0.002 TYR C 305 PHE 0.033 0.002 PHE C 241 TRP 0.013 0.001 TRP C 465 HIS 0.054 0.004 HIS C 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (10702) covalent geometry : angle 0.73347 / 0.41 (14970) hydrogen bonds : bond 0.05755 / 3.73 ( 459) hydrogen bonds : angle 4.22811 / 3.03 ( 1164) metal coordination : bond 0.10911 / 5.49 ( 16) metal coordination : angle 7.37314 / 4.78 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: C 257 GLN cc_start: 0.8399 (tm-30) cc_final: 0.7806 (tm-30) REVERT: C 394 MET cc_start: 0.7160 (ttt) cc_final: 0.6929 (ttt) REVERT: C 413 MET cc_start: 0.5598 (mpp) cc_final: 0.5258 (mpp) REVERT: C 440 ASN cc_start: 0.9122 (m-40) cc_final: 0.8908 (m110) REVERT: C 520 GLU cc_start: 0.8180 (tp30) cc_final: 0.7806 (tp30) REVERT: C 534 ASN cc_start: 0.8799 (m-40) cc_final: 0.8445 (t0) REVERT: D 297 MET cc_start: 0.9014 (ttm) cc_final: 0.8291 (mtp) REVERT: D 332 LEU cc_start: 0.8695 (mm) cc_final: 0.8256 (mm) REVERT: D 372 ARG cc_start: 0.8249 (mtt90) cc_final: 0.7771 (mtm-85) REVERT: D 374 ASN cc_start: 0.8560 (p0) cc_final: 0.8325 (t0) REVERT: D 456 MET cc_start: 0.8649 (mmt) cc_final: 0.8393 (mmt) REVERT: D 515 MET cc_start: 0.8956 (mtm) cc_final: 0.8754 (mtm) REVERT: D 569 LYS cc_start: 0.6474 (mttt) cc_final: 0.5200 (tmtt) outliers start: 32 outliers final: 31 residues processed: 226 average time/residue: 0.0850 time to fit residues: 28.3767 Evaluate side-chains 237 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 206 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 306 MET Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 453 CYS Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 527 TYR Chi-restraints excluded: chain D residue 557 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 82 optimal weight: 0.6980 chunk 94 optimal weight: 50.0000 chunk 2 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 13 optimal weight: 0.3980 chunk 14 optimal weight: 6.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.141715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.106575 restraints weight = 18899.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110240 restraints weight = 8356.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112498 restraints weight = 5265.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.113812 restraints weight = 4062.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.114395 restraints weight = 3538.994| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.392 10718 Z= 0.184 Angle : 0.763 16.843 14988 Z= 0.408 Chirality : 0.045 0.227 1658 Planarity : 0.006 0.058 1472 Dihedral : 24.819 162.563 2454 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 3.96 % Allowed : 22.06 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.27), residues: 952 helix: 1.25 (0.28), residues: 358 sheet: 0.59 (0.50), residues: 115 loop : -0.99 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 169 TYR 0.012 0.001 TYR C 305 PHE 0.029 0.002 PHE C 241 TRP 0.015 0.001 TRP C 465 HIS 0.044 0.003 HIS C 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (10702) covalent geometry : angle 0.72918 / 0.40 (14970) hydrogen bonds : bond 0.05527 / 3.59 ( 459) hydrogen bonds : angle 4.19535 / 3.01 ( 1164) metal coordination : bond 0.09866 / 4.95 ( 16) metal coordination : angle 6.52878 / 4.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: C 257 GLN cc_start: 0.8436 (tm-30) cc_final: 0.7861 (tm-30) REVERT: C 394 MET cc_start: 0.7052 (ttt) cc_final: 0.6817 (ttp) REVERT: C 413 MET cc_start: 0.5433 (mpp) cc_final: 0.5074 (mpp) REVERT: C 440 ASN cc_start: 0.9120 (m-40) cc_final: 0.8897 (m110) REVERT: C 520 GLU cc_start: 0.8320 (tp30) cc_final: 0.7934 (tp30) REVERT: C 534 ASN cc_start: 0.8871 (m-40) cc_final: 0.8481 (t0) REVERT: D 169 ARG cc_start: 0.7588 (mtm110) cc_final: 0.7371 (ptp90) REVERT: D 297 MET cc_start: 0.8986 (ttm) cc_final: 0.8294 (mtp) REVERT: D 372 ARG cc_start: 0.8249 (mtt90) cc_final: 0.7720 (mtm-85) REVERT: D 374 ASN cc_start: 0.8554 (p0) cc_final: 0.8332 (t0) REVERT: D 456 MET cc_start: 0.8651 (mmt) cc_final: 0.8385 (mmt) REVERT: D 569 LYS cc_start: 0.6346 (mttt) cc_final: 0.5269 (tmtt) outliers start: 35 outliers final: 32 residues processed: 223 average time/residue: 0.0799 time to fit residues: 26.2780 Evaluate side-chains 232 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 306 MET Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 453 CYS Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 527 TYR Chi-restraints excluded: chain D residue 557 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 4.9990 chunk 104 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 538 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.140567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105820 restraints weight = 18921.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.109241 restraints weight = 8766.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111354 restraints weight = 5680.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.112427 restraints weight = 4461.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.113209 restraints weight = 3948.867| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.348 10718 Z= 0.213 Angle : 0.797 17.901 14988 Z= 0.424 Chirality : 0.046 0.230 1658 Planarity : 0.006 0.063 1472 Dihedral : 24.916 163.832 2454 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.52 % Favored : 95.38 % Rotamer: Outliers : 3.73 % Allowed : 22.51 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.27), residues: 952 helix: 1.19 (0.28), residues: 362 sheet: 0.52 (0.51), residues: 111 loop : -1.02 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 277 TYR 0.014 0.002 TYR C 527 PHE 0.027 0.002 PHE C 241 TRP 0.020 0.002 TRP C 465 HIS 0.041 0.004 HIS C 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (10702) covalent geometry : angle 0.76503 / 0.42 (14970) hydrogen bonds : bond 0.06056 / 3.94 ( 459) hydrogen bonds : angle 4.32505 / 3.09 ( 1164) metal coordination : bond 0.08752 / 4.39 ( 16) metal coordination : angle 6.51135 / 4.03 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: C 257 GLN cc_start: 0.8444 (tm-30) cc_final: 0.7921 (tm-30) REVERT: C 315 ARG cc_start: 0.8487 (tpp80) cc_final: 0.8013 (mmm160) REVERT: C 394 MET cc_start: 0.7087 (ttt) cc_final: 0.6865 (ttt) REVERT: C 440 ASN cc_start: 0.9188 (m-40) cc_final: 0.8818 (m110) REVERT: C 520 GLU cc_start: 0.8242 (tp30) cc_final: 0.7882 (tp30) REVERT: C 534 ASN cc_start: 0.8840 (m-40) cc_final: 0.8451 (t0) REVERT: C 565 LYS cc_start: 0.8974 (ttmt) cc_final: 0.8660 (mttt) REVERT: C 584 GLU cc_start: 0.9291 (tp30) cc_final: 0.9061 (tm-30) REVERT: D 169 ARG cc_start: 0.7690 (mtm110) cc_final: 0.7478 (ptp90) REVERT: D 297 MET cc_start: 0.9027 (ttm) cc_final: 0.8294 (mtp) REVERT: D 372 ARG cc_start: 0.8365 (mtt90) cc_final: 0.7846 (mtm-85) REVERT: D 374 ASN cc_start: 0.8522 (p0) cc_final: 0.8309 (t0) REVERT: D 456 MET cc_start: 0.8658 (mmt) cc_final: 0.8408 (mmt) REVERT: D 467 MET cc_start: 0.7968 (mmm) cc_final: 0.7226 (mmm) REVERT: D 589 MET cc_start: 0.8040 (ptt) cc_final: 0.7759 (ptt) outliers start: 33 outliers final: 30 residues processed: 218 average time/residue: 0.0868 time to fit residues: 28.1025 Evaluate side-chains 231 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 306 MET Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 453 CYS Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 527 TYR Chi-restraints excluded: chain D residue 557 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN D 193 HIS D 320 ASN D 488 ASN D 538 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.141567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107305 restraints weight = 18960.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110869 restraints weight = 8585.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.113071 restraints weight = 5465.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.114392 restraints weight = 4236.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.114992 restraints weight = 3680.521| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.316 10718 Z= 0.179 Angle : 0.772 16.523 14988 Z= 0.410 Chirality : 0.045 0.228 1658 Planarity : 0.006 0.059 1472 Dihedral : 24.904 162.768 2454 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.85 % Allowed : 23.19 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.27), residues: 952 helix: 1.35 (0.29), residues: 356 sheet: 0.48 (0.51), residues: 113 loop : -1.08 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 277 TYR 0.021 0.001 TYR C 312 PHE 0.029 0.002 PHE C 241 TRP 0.020 0.002 TRP C 465 HIS 0.038 0.003 HIS C 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (10702) covalent geometry : angle 0.74366 / 0.41 (14970) hydrogen bonds : bond 0.05557 / 3.61 ( 459) hydrogen bonds : angle 4.22026 / 3.02 ( 1164) metal coordination : bond 0.07959 / 3.99 ( 16) metal coordination : angle 6.03896 / 3.73 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1805.91 seconds wall clock time: 31 minutes 50.65 seconds (1910.65 seconds total)