Starting phenix.real_space_refine on Thu Sep 18 02:50:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fyr_50891/09_2025/9fyr_50891_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fyr_50891/09_2025/9fyr_50891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fyr_50891/09_2025/9fyr_50891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fyr_50891/09_2025/9fyr_50891.map" model { file = "/net/cci-nas-00/data/ceres_data/9fyr_50891/09_2025/9fyr_50891_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fyr_50891/09_2025/9fyr_50891_trim.cif" } resolution = 3.6 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 45 5.16 5 C 5414 2.51 5 N 1371 2.21 5 O 1521 1.98 5 H 4964 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13315 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 8530 Classifications: {'peptide': 564} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 548} Chain breaks: 3 Chain: "C" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2839 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 11, 'TRANS': 334} Chain breaks: 5 Chain: "D" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1820 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "Z" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {'6UZ': 1, 'NAG': 1, 'UKX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.99, per 1000 atoms: 0.22 Number of scatterers: 13315 At special positions: 0 Unit cell: (84.49, 129.93, 132.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 O 1521 8.00 N 1371 7.00 C 5414 6.00 H 4964 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 583 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 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 Links applied BETA1-4 " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " BETA1-6 " NAG Z 1 " - " FUC Z 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 801 " - " ASN A 498 " " NAG Y 1 " - " ASN A 548 " " NAG Z 1 " - " ASN A 573 " Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 446.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1900 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 41.0% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 145 through 160 removed outlier: 3.505A pdb=" N ALA A 149 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 183 removed outlier: 3.679A pdb=" N TRP A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA A 175 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 197 Proline residue: A 191 - end of helix removed outlier: 4.872A pdb=" N LYS A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 230 removed outlier: 4.276A pdb=" N VAL A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TYR A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 220 " --> pdb=" O MET A 216 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 249 Processing helix chain 'A' and resid 254 through 271 removed outlier: 4.476A pdb=" N GLY A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 282 removed outlier: 3.651A pdb=" N GLU A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 296 removed outlier: 3.667A pdb=" N LEU A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 315 removed outlier: 4.378A pdb=" N MET A 301 " --> pdb=" O CYS A 297 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A 302 " --> pdb=" O MET A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 341 removed outlier: 3.849A pdb=" N VAL A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 352 removed outlier: 3.979A pdb=" N VAL A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 364 removed outlier: 3.734A pdb=" N PHE A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 383 Processing helix chain 'A' and resid 422 through 438 removed outlier: 3.522A pdb=" N CYS A 438 " --> pdb=" O ASN A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 483 Proline residue: A 469 - end of helix Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 596 through 608 Processing helix chain 'A' and resid 608 through 623 removed outlier: 5.294A pdb=" N ASP A 620 " --> pdb=" O ALA A 616 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LYS A 621 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 639 Processing helix chain 'A' and resid 640 through 643 removed outlier: 4.169A pdb=" N SER A 643 " --> pdb=" O PHE A 640 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 640 through 643' Processing helix chain 'A' and resid 647 through 677 removed outlier: 3.616A pdb=" N ILE A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ALA A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N SER A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TRP A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR A 677 " --> pdb=" O THR A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 706 removed outlier: 4.026A pdb=" N SER A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 732 removed outlier: 3.999A pdb=" N ILE A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 969 Processing helix chain 'C' and resid 1097 through 1109 Processing helix chain 'C' and resid 1288 through 1293 removed outlier: 3.595A pdb=" N PHE C1291 " --> pdb=" O ASN C1288 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 485 through 488 removed outlier: 4.001A pdb=" N LYS A 485 " --> pdb=" O ASN A 503 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLU A 502 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N SER A 525 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN A 504 " --> pdb=" O SER A 525 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N GLU A 527 " --> pdb=" O GLN A 504 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N HIS A 506 " --> pdb=" O GLU A 527 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 535 through 542 current: chain 'A' and resid 566 through 567 Processing sheet with id=AA2, first strand: chain 'A' and resid 496 through 497 removed outlier: 5.862A pdb=" N PHE A 497 " --> pdb=" O ILE A 517 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 520 through 527 current: chain 'A' and resid 575 through 577 Processing sheet with id=AA3, first strand: chain 'C' and resid 1164 through 1167 removed outlier: 6.695A pdb=" N TYR A 511 " --> pdb=" O GLU A 532 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A 571 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ALA D 53 " --> pdb=" O MET D 37 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N MET D 37 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 95 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR D 121 " --> pdb=" O TYR D 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 1052 through 1056 removed outlier: 5.414A pdb=" N LEU C1052 " --> pdb=" O ILE C1048 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE C1048 " --> pdb=" O LEU C1052 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY C1054 " --> pdb=" O LEU C1046 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N THR C 951 " --> pdb=" O ILE C1091 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE C1091 " --> pdb=" O THR C 951 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N SER C 953 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N PHE C1089 " --> pdb=" O SER C 953 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 1014 through 1017 removed outlier: 5.763A pdb=" N LEU C 995 " --> pdb=" O SER C 975 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N SER C 975 " --> pdb=" O LEU C 995 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR C 974 " --> pdb=" O ASP C1075 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASP C1075 " --> pdb=" O TYR C 974 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE C 976 " --> pdb=" O LYS C1073 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 1130 through 1132 Processing sheet with id=AA7, first strand: chain 'C' and resid 1138 through 1142 Processing sheet with id=AA8, first strand: chain 'C' and resid 1174 through 1179 removed outlier: 4.491A pdb=" N LYS C1174 " --> pdb=" O SER C1201 " (cutoff:3.500A) removed outlier: 14.796A pdb=" N ILE C1196 " --> pdb=" O TYR C1211 " (cutoff:3.500A) removed outlier: 10.780A pdb=" N TYR C1211 " --> pdb=" O ILE C1196 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU C1198 " --> pdb=" O VAL C1209 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 1217 through 1218 removed outlier: 3.930A pdb=" N ARG C1223 " --> pdb=" O ALA C1286 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY C1266 " --> pdb=" O LEU C1257 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C1257 " --> pdb=" O GLY C1266 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LEU C1255 " --> pdb=" O VAL C1268 " (cutoff:3.500A) removed outlier: 14.796A pdb=" N ILE C1196 " --> pdb=" O TYR C1211 " (cutoff:3.500A) removed outlier: 10.780A pdb=" N TYR C1211 " --> pdb=" O ILE C1196 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU C1198 " --> pdb=" O VAL C1209 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 8 through 10 409 hydrogen bonds defined for protein. 1161 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.14 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 4953 1.02 - 1.22: 19 1.22 - 1.43: 3770 1.43 - 1.63: 4710 1.63 - 1.83: 71 Bond restraints: 13523 Sorted by residual: bond pdb=" C5' 6UZ A 802 " pdb=" O5' 6UZ A 802 " ideal model delta sigma weight residual 1.411 1.543 -0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" C5 6UZ A 802 " pdb=" O5 6UZ A 802 " ideal model delta sigma weight residual 1.420 1.541 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" C5 UKX A 803 " pdb=" N2 UKX A 803 " ideal model delta sigma weight residual 1.340 1.451 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C1 UKX A 803 " pdb=" N1 UKX A 803 " ideal model delta sigma weight residual 1.353 1.464 -0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C5' 6UZ A 802 " pdb=" C6' 6UZ A 802 " ideal model delta sigma weight residual 1.515 1.416 0.099 2.00e-02 2.50e+03 2.47e+01 ... (remaining 13518 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 21801 1.43 - 2.85: 884 2.85 - 4.28: 86 4.28 - 5.71: 19 5.71 - 7.14: 3 Bond angle restraints: 22793 Sorted by residual: angle pdb=" N ILE A 302 " pdb=" CA ILE A 302 " pdb=" C ILE A 302 " ideal model delta sigma weight residual 110.62 107.07 3.55 1.02e+00 9.61e-01 1.21e+01 angle pdb=" N LYS A 366 " pdb=" CA LYS A 366 " pdb=" C LYS A 366 " ideal model delta sigma weight residual 110.44 106.74 3.70 1.20e+00 6.94e-01 9.51e+00 angle pdb=" N ILE A 397 " pdb=" CA ILE A 397 " pdb=" C ILE A 397 " ideal model delta sigma weight residual 110.05 106.87 3.18 1.09e+00 8.42e-01 8.49e+00 angle pdb=" N PHE A 342 " pdb=" CA PHE A 342 " pdb=" C PHE A 342 " ideal model delta sigma weight residual 109.81 116.04 -6.23 2.21e+00 2.05e-01 7.96e+00 angle pdb=" C LYS C1213 " pdb=" N ASP C1214 " pdb=" CA ASP C1214 " ideal model delta sigma weight residual 122.46 125.99 -3.53 1.41e+00 5.03e-01 6.25e+00 ... (remaining 22788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.36: 6457 22.36 - 44.71: 312 44.71 - 67.07: 103 67.07 - 89.42: 11 89.42 - 111.77: 20 Dihedral angle restraints: 6903 sinusoidal: 3447 harmonic: 3456 Sorted by residual: dihedral pdb=" C4 6UZ A 802 " pdb=" C2 6UZ A 802 " pdb=" C3 6UZ A 802 " pdb=" O2 6UZ A 802 " ideal model delta sinusoidal sigma weight residual 179.37 67.60 111.77 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" C5 6UZ A 802 " pdb=" C3 6UZ A 802 " pdb=" C4 6UZ A 802 " pdb=" O3 6UZ A 802 " ideal model delta sinusoidal sigma weight residual -177.91 -67.12 -110.79 1 3.00e+01 1.11e-03 1.45e+01 dihedral pdb=" O3 6UZ A 802 " pdb=" C3 6UZ A 802 " pdb=" C4 6UZ A 802 " pdb=" O4 6UZ A 802 " ideal model delta sinusoidal sigma weight residual -62.61 -172.88 110.27 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 6900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 959 0.042 - 0.084: 230 0.084 - 0.126: 83 0.126 - 0.168: 12 0.168 - 0.210: 2 Chirality restraints: 1286 Sorted by residual: chirality pdb=" C4' 6UZ A 802 " pdb=" C3' 6UZ A 802 " pdb=" C5' 6UZ A 802 " pdb=" O1 6UZ A 802 " both_signs ideal model delta sigma weight residual False -2.55 -2.34 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C5' 6UZ A 802 " pdb=" C4' 6UZ A 802 " pdb=" C6' 6UZ A 802 " pdb=" O5' 6UZ A 802 " both_signs ideal model delta sigma weight residual False -2.49 -2.66 0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" CA ILE A 710 " pdb=" N ILE A 710 " pdb=" C ILE A 710 " pdb=" CB ILE A 710 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 1283 not shown) Planarity restraints: 2067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C1097 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO C1098 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO C1098 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C1098 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 387 " -0.010 2.00e-02 2.50e+03 1.90e-02 3.63e+00 pdb=" C HIS A 387 " 0.033 2.00e-02 2.50e+03 pdb=" O HIS A 387 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO A 388 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 686 " -0.008 2.00e-02 2.50e+03 8.93e-03 2.39e+00 pdb=" CG PHE A 686 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 686 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 686 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 686 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 686 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 686 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 686 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE A 686 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 686 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 686 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 686 " 0.001 2.00e-02 2.50e+03 ... (remaining 2064 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.20: 507 2.20 - 2.80: 20900 2.80 - 3.40: 30778 3.40 - 4.00: 41299 4.00 - 4.60: 63743 Nonbonded interactions: 157227 Sorted by model distance: nonbonded pdb=" O VAL A 674 " pdb="HH12 ARG A 682 " model vdw 1.605 2.450 nonbonded pdb=" O PHE A 360 " pdb="HD21 ASN A 364 " model vdw 1.710 2.450 nonbonded pdb="HH21 ARG A 289 " pdb=" OE2 GLU A 675 " model vdw 1.770 2.450 nonbonded pdb=" HE ARG D 41 " pdb=" OE2 GLU D 49 " model vdw 1.772 2.450 nonbonded pdb=" O ALA A 246 " pdb=" HG SER A 249 " model vdw 1.773 2.450 ... (remaining 157222 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.550 Find NCS groups from input model: 0.050 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 : 0.006 0.132 8567 Z= 0.283 Angle : 0.662 7.137 11608 Z= 0.376 Chirality : 0.043 0.210 1286 Planarity : 0.004 0.061 1441 Dihedral : 14.600 111.775 3166 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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 aren not related in a simple way. whole: 0.58 (0.27), residues: 1009 helix: 1.67 (0.27), residues: 386 sheet: 0.08 (0.44), residues: 146 loop : -0.55 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 682 TYR 0.015 0.001 TYR A 677 PHE 0.025 0.002 PHE A 556 TRP 0.017 0.002 TRP C1289 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 8559) covalent geometry : angle 0.66009 (11586) SS BOND : bond 0.00155 ( 2) SS BOND : angle 1.98344 ( 4) hydrogen bonds : bond 0.18184 ( 403) hydrogen bonds : angle 6.98998 ( 1161) link_BETA1-4 : bond 0.00234 ( 2) link_BETA1-4 : angle 1.18498 ( 6) link_BETA1-6 : bond 0.00145 ( 1) link_BETA1-6 : angle 1.26637 ( 3) link_NAG-ASN : bond 0.00156 ( 3) link_NAG-ASN : angle 0.89051 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 ASP cc_start: 0.8529 (t0) cc_final: 0.8291 (t70) REVERT: A 688 PHE cc_start: 0.8628 (t80) cc_final: 0.8415 (t80) REVERT: D 60 THR cc_start: 0.9193 (m) cc_final: 0.8861 (p) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2022 time to fit residues: 58.5860 Evaluate side-chains 113 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 998 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.094872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.076367 restraints weight = 61736.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.079524 restraints weight = 23342.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.081525 restraints weight = 13297.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.082816 restraints weight = 9370.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.083578 restraints weight = 7369.687| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8567 Z= 0.158 Angle : 0.556 10.080 11608 Z= 0.289 Chirality : 0.042 0.356 1286 Planarity : 0.004 0.054 1441 Dihedral : 7.996 83.898 1320 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.02 % Allowed : 9.39 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.27), residues: 1009 helix: 1.90 (0.26), residues: 391 sheet: 0.24 (0.41), residues: 159 loop : -0.43 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 262 TYR 0.014 0.001 TYR C1108 PHE 0.009 0.001 PHE A 188 TRP 0.020 0.002 TRP C1002 HIS 0.002 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8559) covalent geometry : angle 0.55397 (11586) SS BOND : bond 0.00162 ( 2) SS BOND : angle 1.51148 ( 4) hydrogen bonds : bond 0.05073 ( 403) hydrogen bonds : angle 5.12841 ( 1161) link_BETA1-4 : bond 0.00563 ( 2) link_BETA1-4 : angle 1.25985 ( 6) link_BETA1-6 : bond 0.00237 ( 1) link_BETA1-6 : angle 1.33398 ( 3) link_NAG-ASN : bond 0.00120 ( 3) link_NAG-ASN : angle 1.30219 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 993 VAL cc_start: 0.9536 (OUTLIER) cc_final: 0.9317 (p) REVERT: C 1141 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8143 (mm-40) REVERT: C 1240 MET cc_start: 0.9358 (mtp) cc_final: 0.8357 (mmm) outliers start: 9 outliers final: 8 residues processed: 123 average time/residue: 0.1725 time to fit residues: 29.4146 Evaluate side-chains 109 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain C residue 993 VAL Chi-restraints excluded: chain C residue 1101 ILE Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1126 THR Chi-restraints excluded: chain C residue 1169 LEU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1310 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 0.0040 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.094880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.076542 restraints weight = 61798.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.079661 restraints weight = 23054.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.081672 restraints weight = 13141.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.082912 restraints weight = 9220.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.083804 restraints weight = 7283.867| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8567 Z= 0.104 Angle : 0.467 5.676 11608 Z= 0.245 Chirality : 0.038 0.148 1286 Planarity : 0.003 0.045 1441 Dihedral : 4.859 87.368 1320 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.36 % Allowed : 9.73 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.27), residues: 1009 helix: 2.18 (0.26), residues: 385 sheet: 0.48 (0.39), residues: 168 loop : -0.33 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1076 TYR 0.008 0.001 TYR A 279 PHE 0.009 0.001 PHE A 499 TRP 0.028 0.001 TRP C 955 HIS 0.002 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 8559) covalent geometry : angle 0.46508 (11586) SS BOND : bond 0.00163 ( 2) SS BOND : angle 1.34632 ( 4) hydrogen bonds : bond 0.04274 ( 403) hydrogen bonds : angle 4.65000 ( 1161) link_BETA1-4 : bond 0.00245 ( 2) link_BETA1-4 : angle 1.08300 ( 6) link_BETA1-6 : bond 0.00098 ( 1) link_BETA1-6 : angle 1.31691 ( 3) link_NAG-ASN : bond 0.00114 ( 3) link_NAG-ASN : angle 1.03580 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8048 (mp) REVERT: A 301 MET cc_start: 0.7998 (ptp) cc_final: 0.7646 (ptt) REVERT: C 993 VAL cc_start: 0.9538 (t) cc_final: 0.9326 (p) REVERT: C 1141 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8171 (mm-40) REVERT: C 1209 VAL cc_start: 0.9565 (t) cc_final: 0.9298 (m) REVERT: C 1274 GLN cc_start: 0.9049 (tt0) cc_final: 0.8772 (tm-30) outliers start: 12 outliers final: 7 residues processed: 118 average time/residue: 0.1745 time to fit residues: 28.4478 Evaluate side-chains 113 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1225 LEU Chi-restraints excluded: chain C residue 1310 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.093721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.075284 restraints weight = 61936.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.078349 restraints weight = 23793.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.080304 restraints weight = 13774.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.081558 restraints weight = 9784.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.082418 restraints weight = 7758.098| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8567 Z= 0.141 Angle : 0.474 4.905 11608 Z= 0.251 Chirality : 0.038 0.132 1286 Planarity : 0.003 0.044 1441 Dihedral : 4.374 87.422 1320 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.47 % Allowed : 10.97 % Favored : 87.56 % 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 aren not related in a simple way. whole: 1.13 (0.27), residues: 1009 helix: 2.12 (0.25), residues: 392 sheet: 0.53 (0.39), residues: 162 loop : -0.37 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 520 TYR 0.010 0.001 TYR C1105 PHE 0.009 0.001 PHE A 361 TRP 0.017 0.001 TRP C 955 HIS 0.004 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8559) covalent geometry : angle 0.47160 (11586) SS BOND : bond 0.00144 ( 2) SS BOND : angle 1.29722 ( 4) hydrogen bonds : bond 0.04081 ( 403) hydrogen bonds : angle 4.57192 ( 1161) link_BETA1-4 : bond 0.00242 ( 2) link_BETA1-4 : angle 1.11540 ( 6) link_BETA1-6 : bond 0.00034 ( 1) link_BETA1-6 : angle 1.44791 ( 3) link_NAG-ASN : bond 0.00034 ( 3) link_NAG-ASN : angle 1.07494 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7786 (ptt) REVERT: C 1141 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8199 (mm-40) REVERT: C 1240 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.7529 (mpp) REVERT: C 1274 GLN cc_start: 0.9065 (tt0) cc_final: 0.8715 (tm-30) outliers start: 13 outliers final: 11 residues processed: 103 average time/residue: 0.1751 time to fit residues: 24.9466 Evaluate side-chains 104 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1126 THR Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1225 LEU Chi-restraints excluded: chain C residue 1240 MET Chi-restraints excluded: chain C residue 1310 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 75 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 0.0570 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 965 HIS C 968 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.092595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.074202 restraints weight = 63012.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.077197 restraints weight = 24059.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.079146 restraints weight = 13940.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.080270 restraints weight = 9921.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.081097 restraints weight = 8003.783| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8567 Z= 0.151 Angle : 0.484 7.671 11608 Z= 0.256 Chirality : 0.038 0.136 1286 Planarity : 0.003 0.041 1441 Dihedral : 4.352 84.947 1320 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.70 % Allowed : 10.75 % Favored : 87.56 % 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 aren not related in a simple way. whole: 1.10 (0.26), residues: 1009 helix: 2.13 (0.25), residues: 394 sheet: 0.52 (0.39), residues: 159 loop : -0.43 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1076 TYR 0.019 0.001 TYR C1105 PHE 0.012 0.001 PHE A 361 TRP 0.024 0.001 TRP C 955 HIS 0.003 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8559) covalent geometry : angle 0.48181 (11586) SS BOND : bond 0.00156 ( 2) SS BOND : angle 1.21647 ( 4) hydrogen bonds : bond 0.04070 ( 403) hydrogen bonds : angle 4.47387 ( 1161) link_BETA1-4 : bond 0.00206 ( 2) link_BETA1-4 : angle 1.04390 ( 6) link_BETA1-6 : bond 0.00400 ( 1) link_BETA1-6 : angle 1.38165 ( 3) link_NAG-ASN : bond 0.00082 ( 3) link_NAG-ASN : angle 1.06532 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8111 (mp) REVERT: A 301 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7846 (ptt) REVERT: C 1141 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8202 (mm-40) REVERT: C 1274 GLN cc_start: 0.9061 (tt0) cc_final: 0.8846 (tm-30) outliers start: 15 outliers final: 13 residues processed: 102 average time/residue: 0.1622 time to fit residues: 23.1931 Evaluate side-chains 102 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1126 THR Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1225 LEU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1310 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 93 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.092538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.073906 restraints weight = 63104.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.076936 restraints weight = 24172.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.078896 restraints weight = 14091.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.080016 restraints weight = 10062.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.080912 restraints weight = 8153.727| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8567 Z= 0.133 Angle : 0.474 8.560 11608 Z= 0.248 Chirality : 0.038 0.143 1286 Planarity : 0.003 0.041 1441 Dihedral : 4.303 82.101 1320 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.92 % Allowed : 11.43 % Favored : 86.65 % 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 aren not related in a simple way. whole: 1.14 (0.26), residues: 1009 helix: 2.17 (0.26), residues: 394 sheet: 0.54 (0.39), residues: 159 loop : -0.41 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 483 TYR 0.009 0.001 TYR D 105 PHE 0.009 0.001 PHE A 361 TRP 0.021 0.001 TRP C 955 HIS 0.003 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8559) covalent geometry : angle 0.47201 (11586) SS BOND : bond 0.00164 ( 2) SS BOND : angle 1.20650 ( 4) hydrogen bonds : bond 0.03965 ( 403) hydrogen bonds : angle 4.38821 ( 1161) link_BETA1-4 : bond 0.00186 ( 2) link_BETA1-4 : angle 1.04656 ( 6) link_BETA1-6 : bond 0.00038 ( 1) link_BETA1-6 : angle 1.52908 ( 3) link_NAG-ASN : bond 0.00073 ( 3) link_NAG-ASN : angle 1.03658 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8120 (mp) REVERT: A 301 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7825 (ptt) REVERT: C 991 TRP cc_start: 0.7762 (p-90) cc_final: 0.7378 (p-90) REVERT: C 1141 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8233 (mm-40) REVERT: C 1274 GLN cc_start: 0.9039 (tt0) cc_final: 0.8832 (tm-30) outliers start: 17 outliers final: 13 residues processed: 95 average time/residue: 0.1626 time to fit residues: 21.8751 Evaluate side-chains 100 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1126 THR Chi-restraints excluded: chain C residue 1225 LEU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1310 GLU Chi-restraints excluded: chain D residue 86 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 6 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 4 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS ** C 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.092560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.074011 restraints weight = 62518.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.077037 restraints weight = 23921.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.078988 restraints weight = 13889.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.080231 restraints weight = 9898.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.081074 restraints weight = 7879.238| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8567 Z= 0.116 Angle : 0.466 8.169 11608 Z= 0.242 Chirality : 0.038 0.140 1286 Planarity : 0.003 0.041 1441 Dihedral : 4.224 77.205 1320 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.04 % Allowed : 11.20 % Favored : 86.76 % 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 aren not related in a simple way. whole: 1.30 (0.27), residues: 1009 helix: 2.39 (0.26), residues: 387 sheet: 0.61 (0.39), residues: 158 loop : -0.34 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 483 TYR 0.008 0.001 TYR A 462 PHE 0.009 0.001 PHE A 245 TRP 0.023 0.001 TRP C 955 HIS 0.003 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8559) covalent geometry : angle 0.46349 (11586) SS BOND : bond 0.00122 ( 2) SS BOND : angle 1.20665 ( 4) hydrogen bonds : bond 0.03802 ( 403) hydrogen bonds : angle 4.25597 ( 1161) link_BETA1-4 : bond 0.00233 ( 2) link_BETA1-4 : angle 1.05650 ( 6) link_BETA1-6 : bond 0.00002 ( 1) link_BETA1-6 : angle 1.45920 ( 3) link_NAG-ASN : bond 0.00078 ( 3) link_NAG-ASN : angle 1.01265 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8111 (mp) REVERT: A 301 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7822 (ptt) REVERT: A 692 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8546 (tt) REVERT: C 1141 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8234 (mm-40) REVERT: C 1208 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8968 (mp) outliers start: 18 outliers final: 13 residues processed: 95 average time/residue: 0.1633 time to fit residues: 22.0708 Evaluate side-chains 100 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1126 THR Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1208 ILE Chi-restraints excluded: chain C residue 1225 LEU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1310 GLU Chi-restraints excluded: chain D residue 86 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 56 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.091947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.073406 restraints weight = 62791.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.076394 restraints weight = 24038.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.078320 restraints weight = 13967.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.079562 restraints weight = 9978.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.080348 restraints weight = 7977.664| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8567 Z= 0.144 Angle : 0.482 6.873 11608 Z= 0.253 Chirality : 0.038 0.134 1286 Planarity : 0.003 0.040 1441 Dihedral : 4.161 70.199 1320 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.92 % Allowed : 11.65 % Favored : 86.43 % 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 aren not related in a simple way. whole: 1.26 (0.27), residues: 1009 helix: 2.25 (0.26), residues: 393 sheet: 0.64 (0.39), residues: 165 loop : -0.35 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1076 TYR 0.009 0.001 TYR A 462 PHE 0.010 0.001 PHE A 361 TRP 0.015 0.001 TRP C 955 HIS 0.003 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8559) covalent geometry : angle 0.48002 (11586) SS BOND : bond 0.00046 ( 2) SS BOND : angle 1.25453 ( 4) hydrogen bonds : bond 0.03870 ( 403) hydrogen bonds : angle 4.28757 ( 1161) link_BETA1-4 : bond 0.00118 ( 2) link_BETA1-4 : angle 1.03899 ( 6) link_BETA1-6 : bond 0.00129 ( 1) link_BETA1-6 : angle 1.49475 ( 3) link_NAG-ASN : bond 0.00022 ( 3) link_NAG-ASN : angle 1.08106 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7854 (ptt) REVERT: C 1141 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8239 (mm-40) REVERT: C 1208 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.9012 (mp) REVERT: D 14 LEU cc_start: 0.8327 (tp) cc_final: 0.7958 (tp) REVERT: D 92 GLU cc_start: 0.8341 (pm20) cc_final: 0.7919 (pm20) outliers start: 17 outliers final: 12 residues processed: 92 average time/residue: 0.1588 time to fit residues: 20.6680 Evaluate side-chains 95 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1126 THR Chi-restraints excluded: chain C residue 1208 ILE Chi-restraints excluded: chain C residue 1225 LEU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1310 GLU Chi-restraints excluded: chain D residue 86 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 0 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 968 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.091757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.073322 restraints weight = 63109.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.076298 restraints weight = 24256.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.078213 restraints weight = 14083.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.079349 restraints weight = 10062.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.080220 restraints weight = 8130.004| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8567 Z= 0.148 Angle : 0.482 8.366 11608 Z= 0.252 Chirality : 0.038 0.133 1286 Planarity : 0.003 0.040 1441 Dihedral : 4.124 62.095 1320 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.81 % Allowed : 11.88 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.27), residues: 1009 helix: 2.37 (0.26), residues: 387 sheet: 0.50 (0.39), residues: 170 loop : -0.34 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 624 TYR 0.009 0.001 TYR A 462 PHE 0.010 0.001 PHE A 361 TRP 0.021 0.001 TRP C 955 HIS 0.003 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8559) covalent geometry : angle 0.47968 (11586) SS BOND : bond 0.00070 ( 2) SS BOND : angle 1.24893 ( 4) hydrogen bonds : bond 0.03881 ( 403) hydrogen bonds : angle 4.30983 ( 1161) link_BETA1-4 : bond 0.00150 ( 2) link_BETA1-4 : angle 1.05912 ( 6) link_BETA1-6 : bond 0.00187 ( 1) link_BETA1-6 : angle 1.49707 ( 3) link_NAG-ASN : bond 0.00014 ( 3) link_NAG-ASN : angle 1.07216 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7871 (ptt) REVERT: A 692 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8578 (tt) REVERT: C 1141 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8009 (tm-30) REVERT: C 1208 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.9026 (mp) REVERT: D 14 LEU cc_start: 0.8322 (tp) cc_final: 0.7949 (tp) REVERT: D 92 GLU cc_start: 0.8319 (pm20) cc_final: 0.7972 (pm20) outliers start: 16 outliers final: 12 residues processed: 92 average time/residue: 0.1566 time to fit residues: 20.5360 Evaluate side-chains 94 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1126 THR Chi-restraints excluded: chain C residue 1208 ILE Chi-restraints excluded: chain C residue 1225 LEU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1310 GLU Chi-restraints excluded: chain D residue 86 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 27 optimal weight: 0.7980 chunk 89 optimal weight: 0.0970 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.092690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.074286 restraints weight = 62551.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.077261 restraints weight = 23922.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.079224 restraints weight = 13876.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.080437 restraints weight = 9866.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.081287 restraints weight = 7855.443| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8567 Z= 0.098 Angle : 0.461 8.800 11608 Z= 0.239 Chirality : 0.038 0.141 1286 Planarity : 0.003 0.041 1441 Dihedral : 3.985 51.591 1320 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.47 % Allowed : 12.44 % Favored : 86.09 % 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 aren not related in a simple way. whole: 1.49 (0.27), residues: 1009 helix: 2.51 (0.26), residues: 387 sheet: 0.70 (0.39), residues: 165 loop : -0.23 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 483 TYR 0.008 0.001 TYR A 279 PHE 0.010 0.001 PHE A 245 TRP 0.017 0.001 TRP C 955 HIS 0.005 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 8559) covalent geometry : angle 0.45870 (11586) SS BOND : bond 0.00099 ( 2) SS BOND : angle 1.19400 ( 4) hydrogen bonds : bond 0.03642 ( 403) hydrogen bonds : angle 4.16954 ( 1161) link_BETA1-4 : bond 0.00227 ( 2) link_BETA1-4 : angle 1.02687 ( 6) link_BETA1-6 : bond 0.00047 ( 1) link_BETA1-6 : angle 1.39071 ( 3) link_NAG-ASN : bond 0.00140 ( 3) link_NAG-ASN : angle 0.94356 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 692 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8582 (tt) REVERT: C 1141 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8068 (tm-30) REVERT: C 1208 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.9018 (mp) REVERT: D 14 LEU cc_start: 0.8332 (tp) cc_final: 0.7963 (tp) REVERT: D 92 GLU cc_start: 0.8340 (pm20) cc_final: 0.8097 (pm20) outliers start: 13 outliers final: 9 residues processed: 97 average time/residue: 0.1570 time to fit residues: 21.7737 Evaluate side-chains 94 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1126 THR Chi-restraints excluded: chain C residue 1208 ILE Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain D residue 86 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 44 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.089374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.070560 restraints weight = 61342.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.073511 restraints weight = 23987.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.075435 restraints weight = 13887.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.076648 restraints weight = 9877.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.077521 restraints weight = 7859.140| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8567 Z= 0.113 Angle : 0.460 8.844 11608 Z= 0.240 Chirality : 0.038 0.133 1286 Planarity : 0.003 0.041 1441 Dihedral : 3.859 42.792 1320 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.24 % Allowed : 13.01 % Favored : 85.75 % 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 aren not related in a simple way. whole: 1.52 (0.27), residues: 1009 helix: 2.52 (0.26), residues: 387 sheet: 0.75 (0.39), residues: 165 loop : -0.19 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 483 TYR 0.008 0.001 TYR A 279 PHE 0.009 0.001 PHE A 245 TRP 0.017 0.001 TRP C 955 HIS 0.004 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8559) covalent geometry : angle 0.45757 (11586) SS BOND : bond 0.00079 ( 2) SS BOND : angle 1.18514 ( 4) hydrogen bonds : bond 0.03613 ( 403) hydrogen bonds : angle 4.17261 ( 1161) link_BETA1-4 : bond 0.00224 ( 2) link_BETA1-4 : angle 1.03235 ( 6) link_BETA1-6 : bond 0.00021 ( 1) link_BETA1-6 : angle 1.40823 ( 3) link_NAG-ASN : bond 0.00052 ( 3) link_NAG-ASN : angle 0.99773 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2641.29 seconds wall clock time: 45 minutes 59.56 seconds (2759.56 seconds total)