Starting phenix.real_space_refine on Thu Jun 12 01:58:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fyr_50891/06_2025/9fyr_50891_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fyr_50891/06_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_50891/06_2025/9fyr_50891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fyr_50891/06_2025/9fyr_50891.map" model { file = "/net/cci-nas-00/data/ceres_data/9fyr_50891/06_2025/9fyr_50891_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fyr_50891/06_2025/9fyr_50891_trim.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.49, per 1000 atoms: 0.56 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: 3.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.16 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: 4.80 Time building geometry restraints manager: 3.90 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: 4.950 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: 0.240 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 30.810 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.360 ------------------------------------------------------------------------------- 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 : 9.79 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (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 TRP 0.017 0.002 TRP C1289 HIS 0.004 0.001 HIS A 161 PHE 0.025 0.002 PHE A 556 TYR 0.015 0.001 TYR A 677 ARG 0.006 0.001 ARG A 682 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 3) link_NAG-ASN : angle 0.89051 ( 9) link_BETA1-4 : bond 0.00234 ( 2) link_BETA1-4 : angle 1.18498 ( 6) hydrogen bonds : bond 0.18184 ( 403) hydrogen bonds : angle 6.98998 ( 1161) link_BETA1-6 : bond 0.00145 ( 1) link_BETA1-6 : angle 1.26637 ( 3) SS BOND : bond 0.00155 ( 2) SS BOND : angle 1.98344 ( 4) covalent geometry : bond 0.00581 ( 8559) covalent geometry : angle 0.66009 (11586) *********************** 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 : 1.209 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: 0.8292 (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: 0.8860 (p) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.4102 time to fit residues: 119.5728 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 : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 0.0770 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 overall best weight: 1.4144 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.094711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.076339 restraints weight = 61625.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.079453 restraints weight = 23380.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.081441 restraints weight = 13367.526| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8567 Z= 0.162 Angle : 0.563 9.999 11608 Z= 0.291 Chirality : 0.042 0.354 1286 Planarity : 0.004 0.056 1441 Dihedral : 7.957 83.519 1320 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.24 % Allowed : 8.94 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.27), residues: 1009 helix: 1.88 (0.26), residues: 391 sheet: 0.28 (0.42), residues: 152 loop : -0.46 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C1002 HIS 0.003 0.001 HIS A 474 PHE 0.017 0.001 PHE A 499 TYR 0.015 0.001 TYR C1108 ARG 0.002 0.000 ARG A 262 Details of bonding type rmsd link_NAG-ASN : bond 0.00066 ( 3) link_NAG-ASN : angle 1.36044 ( 9) link_BETA1-4 : bond 0.00445 ( 2) link_BETA1-4 : angle 1.21671 ( 6) hydrogen bonds : bond 0.04968 ( 403) hydrogen bonds : angle 5.12487 ( 1161) link_BETA1-6 : bond 0.00162 ( 1) link_BETA1-6 : angle 1.30206 ( 3) SS BOND : bond 0.00184 ( 2) SS BOND : angle 1.55131 ( 4) covalent geometry : bond 0.00344 ( 8559) covalent geometry : angle 0.55994 (11586) *********************** 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 127 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.270 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: A 153 GLU cc_start: 0.8211 (tp30) cc_final: 0.7831 (tp30) REVERT: C 993 VAL cc_start: 0.9541 (OUTLIER) cc_final: 0.9331 (p) REVERT: C 1141 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8159 (mm-40) REVERT: C 1240 MET cc_start: 0.9376 (mtp) cc_final: 0.8363 (mmm) REVERT: C 1247 ASP cc_start: 0.7646 (m-30) cc_final: 0.7441 (m-30) outliers start: 11 outliers final: 9 residues processed: 124 average time/residue: 0.4115 time to fit residues: 71.2985 Evaluate side-chains 109 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain C residue 993 VAL 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 32 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 998 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.094021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.075309 restraints weight = 62405.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.078436 restraints weight = 23786.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.080397 restraints weight = 13722.899| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8567 Z= 0.141 Angle : 0.485 4.997 11608 Z= 0.258 Chirality : 0.038 0.143 1286 Planarity : 0.003 0.043 1441 Dihedral : 4.797 86.252 1320 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.70 % Allowed : 9.62 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.27), residues: 1009 helix: 2.08 (0.25), residues: 385 sheet: 0.46 (0.40), residues: 162 loop : -0.41 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 955 HIS 0.007 0.001 HIS A 474 PHE 0.010 0.001 PHE A 499 TYR 0.010 0.001 TYR C1258 ARG 0.004 0.000 ARG C1076 Details of bonding type rmsd link_NAG-ASN : bond 0.00069 ( 3) link_NAG-ASN : angle 1.10046 ( 9) link_BETA1-4 : bond 0.00223 ( 2) link_BETA1-4 : angle 1.15694 ( 6) hydrogen bonds : bond 0.04411 ( 403) hydrogen bonds : angle 4.74858 ( 1161) link_BETA1-6 : bond 0.00168 ( 1) link_BETA1-6 : angle 1.48218 ( 3) SS BOND : bond 0.00156 ( 2) SS BOND : angle 1.36391 ( 4) covalent geometry : bond 0.00304 ( 8559) covalent geometry : angle 0.48224 (11586) *********************** 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 119 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 1.083 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 153 GLU cc_start: 0.8181 (tp30) cc_final: 0.7647 (tm-30) REVERT: A 236 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8128 (mp) REVERT: A 301 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7758 (ptt) REVERT: C 1169 LEU cc_start: 0.9093 (tp) cc_final: 0.8834 (tt) REVERT: C 1208 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8845 (mp) REVERT: C 1209 VAL cc_start: 0.9583 (t) cc_final: 0.9357 (m) REVERT: C 1240 MET cc_start: 0.9317 (mtp) cc_final: 0.8627 (mmm) REVERT: C 1247 ASP cc_start: 0.7685 (m-30) cc_final: 0.7473 (m-30) REVERT: C 1274 GLN cc_start: 0.9122 (tt0) cc_final: 0.8749 (tm-30) outliers start: 15 outliers final: 10 residues processed: 113 average time/residue: 0.4599 time to fit residues: 76.6632 Evaluate side-chains 107 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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 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 1310 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 38 optimal weight: 0.0270 chunk 49 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 overall best weight: 0.9040 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.094351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.075767 restraints weight = 61682.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.078874 restraints weight = 23685.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.080856 restraints weight = 13719.329| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3616 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= 0.111 Angle : 0.457 5.160 11608 Z= 0.242 Chirality : 0.038 0.138 1286 Planarity : 0.003 0.041 1441 Dihedral : 4.370 85.873 1320 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.36 % Allowed : 10.52 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.27), residues: 1009 helix: 2.24 (0.25), residues: 385 sheet: 0.58 (0.39), residues: 162 loop : -0.38 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 955 HIS 0.007 0.001 HIS A 474 PHE 0.009 0.001 PHE A 245 TYR 0.012 0.001 TYR C1105 ARG 0.003 0.000 ARG A 520 Details of bonding type rmsd link_NAG-ASN : bond 0.00061 ( 3) link_NAG-ASN : angle 1.03629 ( 9) link_BETA1-4 : bond 0.00241 ( 2) link_BETA1-4 : angle 1.09867 ( 6) hydrogen bonds : bond 0.04041 ( 403) hydrogen bonds : angle 4.51804 ( 1161) link_BETA1-6 : bond 0.00000 ( 1) link_BETA1-6 : angle 1.36935 ( 3) SS BOND : bond 0.00183 ( 2) SS BOND : angle 1.27111 ( 4) covalent geometry : bond 0.00237 ( 8559) covalent geometry : angle 0.45462 (11586) *********************** 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: 12 poor density : 97 time to evaluate : 1.086 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: A 153 GLU cc_start: 0.8187 (tp30) cc_final: 0.7656 (tm-30) REVERT: A 236 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8110 (mp) REVERT: A 301 MET cc_start: 0.8058 (ptp) cc_final: 0.7746 (ptt) REVERT: C 1141 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8205 (mm-40) REVERT: C 1240 MET cc_start: 0.9356 (mtp) cc_final: 0.9108 (mpp) REVERT: C 1247 ASP cc_start: 0.7665 (m-30) cc_final: 0.7450 (m-30) REVERT: C 1274 GLN cc_start: 0.9116 (tt0) cc_final: 0.8834 (tm-30) outliers start: 12 outliers final: 11 residues processed: 106 average time/residue: 0.3588 time to fit residues: 52.6048 Evaluate side-chains 105 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 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 1227 VAL 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 36 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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** C1045 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.090830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.072038 restraints weight = 63183.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.074994 restraints weight = 24637.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.076939 restraints weight = 14461.319| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8567 Z= 0.249 Angle : 0.572 5.578 11608 Z= 0.304 Chirality : 0.040 0.144 1286 Planarity : 0.003 0.035 1441 Dihedral : 4.591 80.337 1320 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.15 % Allowed : 11.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1009 helix: 1.81 (0.25), residues: 388 sheet: 0.37 (0.39), residues: 166 loop : -0.61 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 955 HIS 0.003 0.001 HIS A 506 PHE 0.017 0.001 PHE A 361 TYR 0.014 0.002 TYR C1129 ARG 0.003 0.000 ARG A 624 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 3) link_NAG-ASN : angle 1.41069 ( 9) link_BETA1-4 : bond 0.00158 ( 2) link_BETA1-4 : angle 1.32204 ( 6) hydrogen bonds : bond 0.04673 ( 403) hydrogen bonds : angle 4.80297 ( 1161) link_BETA1-6 : bond 0.00487 ( 1) link_BETA1-6 : angle 1.76632 ( 3) SS BOND : bond 0.00143 ( 2) SS BOND : angle 1.26998 ( 4) covalent geometry : bond 0.00536 ( 8559) covalent geometry : angle 0.56879 (11586) *********************** 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 107 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 1.111 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 153 GLU cc_start: 0.8318 (tp30) cc_final: 0.8032 (tp30) REVERT: A 301 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7929 (ptt) REVERT: A 381 ASN cc_start: 0.8438 (m-40) cc_final: 0.8127 (m110) REVERT: C 1169 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9010 (tt) REVERT: C 1208 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8989 (mp) REVERT: C 1240 MET cc_start: 0.9353 (mtp) cc_final: 0.9119 (mpp) REVERT: C 1247 ASP cc_start: 0.7973 (m-30) cc_final: 0.7743 (m-30) REVERT: C 1274 GLN cc_start: 0.9106 (tt0) cc_final: 0.8814 (tm-30) outliers start: 19 outliers final: 16 residues processed: 100 average time/residue: 0.3462 time to fit residues: 49.0631 Evaluate side-chains 99 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 185 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 637 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain C residue 995 LEU 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.091764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.073038 restraints weight = 62970.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.076065 restraints weight = 24101.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.078004 restraints weight = 14028.858| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8567 Z= 0.135 Angle : 0.472 5.909 11608 Z= 0.251 Chirality : 0.038 0.137 1286 Planarity : 0.003 0.038 1441 Dihedral : 4.449 77.009 1320 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.15 % Allowed : 10.97 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1009 helix: 1.95 (0.25), residues: 393 sheet: 0.42 (0.39), residues: 166 loop : -0.53 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 955 HIS 0.002 0.001 HIS A 161 PHE 0.010 0.001 PHE A 245 TYR 0.009 0.001 TYR C1129 ARG 0.002 0.000 ARG C1076 Details of bonding type rmsd link_NAG-ASN : bond 0.00051 ( 3) link_NAG-ASN : angle 1.12101 ( 9) link_BETA1-4 : bond 0.00145 ( 2) link_BETA1-4 : angle 1.09097 ( 6) hydrogen bonds : bond 0.04219 ( 403) hydrogen bonds : angle 4.52122 ( 1161) link_BETA1-6 : bond 0.00207 ( 1) link_BETA1-6 : angle 1.60085 ( 3) SS BOND : bond 0.00146 ( 2) SS BOND : angle 1.17505 ( 4) covalent geometry : bond 0.00289 ( 8559) covalent geometry : angle 0.46970 (11586) *********************** 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 101 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 1.079 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 153 GLU cc_start: 0.8226 (tp30) cc_final: 0.7954 (tp30) REVERT: A 236 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8180 (mp) REVERT: A 301 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7851 (ptt) REVERT: A 692 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8561 (tt) REVERT: C 1208 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.8997 (mp) REVERT: C 1247 ASP cc_start: 0.7905 (m-30) cc_final: 0.7679 (m-30) REVERT: C 1274 GLN cc_start: 0.9070 (tt0) cc_final: 0.8827 (tm-30) outliers start: 19 outliers final: 14 residues processed: 94 average time/residue: 0.3408 time to fit residues: 45.9898 Evaluate side-chains 98 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 637 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 15 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 82 optimal weight: 0.0060 overall best weight: 1.8002 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.091048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.072325 restraints weight = 63386.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.075311 restraints weight = 24380.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.077211 restraints weight = 14195.123| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8567 Z= 0.174 Angle : 0.496 6.964 11608 Z= 0.263 Chirality : 0.038 0.133 1286 Planarity : 0.003 0.036 1441 Dihedral : 4.398 72.443 1320 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.26 % Allowed : 11.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.27), residues: 1009 helix: 2.05 (0.26), residues: 387 sheet: 0.43 (0.39), residues: 166 loop : -0.50 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 955 HIS 0.002 0.001 HIS A 161 PHE 0.011 0.001 PHE A 361 TYR 0.010 0.001 TYR C1129 ARG 0.002 0.000 ARG A 624 Details of bonding type rmsd link_NAG-ASN : bond 0.00068 ( 3) link_NAG-ASN : angle 1.17198 ( 9) link_BETA1-4 : bond 0.00116 ( 2) link_BETA1-4 : angle 1.09835 ( 6) hydrogen bonds : bond 0.04195 ( 403) hydrogen bonds : angle 4.52097 ( 1161) link_BETA1-6 : bond 0.00248 ( 1) link_BETA1-6 : angle 1.62298 ( 3) SS BOND : bond 0.00136 ( 2) SS BOND : angle 1.21280 ( 4) covalent geometry : bond 0.00376 ( 8559) covalent geometry : angle 0.49362 (11586) *********************** 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 100 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 1.181 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 153 GLU cc_start: 0.8268 (tp30) cc_final: 0.8009 (tp30) REVERT: A 301 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7887 (ptt) REVERT: A 692 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8596 (tt) REVERT: C 1141 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8146 (mm-40) REVERT: C 1208 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8975 (mp) REVERT: C 1240 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.7435 (mpp) REVERT: C 1247 ASP cc_start: 0.7932 (m-30) cc_final: 0.7699 (m-30) REVERT: C 1274 GLN cc_start: 0.9075 (tt0) cc_final: 0.8820 (tm-30) REVERT: D 92 GLU cc_start: 0.8573 (pm20) cc_final: 0.8369 (pm20) outliers start: 20 outliers final: 15 residues processed: 93 average time/residue: 0.3441 time to fit residues: 45.4004 Evaluate side-chains 99 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 637 VAL 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 1240 MET 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 79 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 0.1980 chunk 69 optimal weight: 0.0570 chunk 46 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.092308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.073709 restraints weight = 62674.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.076765 restraints weight = 23797.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.078743 restraints weight = 13757.690| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8567 Z= 0.097 Angle : 0.453 8.185 11608 Z= 0.235 Chirality : 0.038 0.140 1286 Planarity : 0.003 0.038 1441 Dihedral : 4.210 64.721 1320 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.36 % Allowed : 12.44 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.27), residues: 1009 helix: 2.31 (0.26), residues: 387 sheet: 0.66 (0.39), residues: 158 loop : -0.32 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 955 HIS 0.002 0.000 HIS A 378 PHE 0.011 0.001 PHE A 245 TYR 0.008 0.001 TYR A 279 ARG 0.002 0.000 ARG A 483 Details of bonding type rmsd link_NAG-ASN : bond 0.00128 ( 3) link_NAG-ASN : angle 0.93899 ( 9) link_BETA1-4 : bond 0.00124 ( 2) link_BETA1-4 : angle 0.98463 ( 6) hydrogen bonds : bond 0.03806 ( 403) hydrogen bonds : angle 4.27531 ( 1161) link_BETA1-6 : bond 0.00030 ( 1) link_BETA1-6 : angle 1.45892 ( 3) SS BOND : bond 0.00142 ( 2) SS BOND : angle 1.16664 ( 4) covalent geometry : bond 0.00204 ( 8559) covalent geometry : angle 0.45143 (11586) *********************** 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 96 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 1.226 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 153 GLU cc_start: 0.8203 (tp30) cc_final: 0.7956 (tp30) REVERT: A 236 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8185 (mp) REVERT: A 301 MET cc_start: 0.8021 (ptp) cc_final: 0.7817 (ptt) REVERT: A 692 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8620 (tt) REVERT: C 1141 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8237 (mm-40) REVERT: C 1208 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.9019 (mp) REVERT: C 1247 ASP cc_start: 0.7863 (m-30) cc_final: 0.7652 (m-30) REVERT: C 1274 GLN cc_start: 0.9081 (tt0) cc_final: 0.8864 (tm-30) outliers start: 12 outliers final: 9 residues processed: 93 average time/residue: 0.3384 time to fit residues: 44.7248 Evaluate side-chains 92 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 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 C residue 1109 LEU Chi-restraints excluded: chain C residue 1208 ILE 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 21 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 78 optimal weight: 0.0970 chunk 61 optimal weight: 0.7980 chunk 66 optimal weight: 0.0870 chunk 96 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.092658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.074254 restraints weight = 62359.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.077294 restraints weight = 23912.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.079211 restraints weight = 13823.425| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8567 Z= 0.093 Angle : 0.462 11.641 11608 Z= 0.237 Chirality : 0.038 0.136 1286 Planarity : 0.002 0.040 1441 Dihedral : 4.027 53.620 1320 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.36 % Allowed : 12.67 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.27), residues: 1009 helix: 2.43 (0.26), residues: 387 sheet: 0.74 (0.39), residues: 158 loop : -0.24 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 955 HIS 0.002 0.000 HIS A 161 PHE 0.010 0.001 PHE A 245 TYR 0.015 0.001 TYR D 105 ARG 0.002 0.000 ARG A 483 Details of bonding type rmsd link_NAG-ASN : bond 0.00092 ( 3) link_NAG-ASN : angle 0.93841 ( 9) link_BETA1-4 : bond 0.00176 ( 2) link_BETA1-4 : angle 1.00213 ( 6) hydrogen bonds : bond 0.03648 ( 403) hydrogen bonds : angle 4.20248 ( 1161) link_BETA1-6 : bond 0.00135 ( 1) link_BETA1-6 : angle 1.41732 ( 3) SS BOND : bond 0.00181 ( 2) SS BOND : angle 1.21706 ( 4) covalent geometry : bond 0.00200 ( 8559) covalent geometry : angle 0.46051 (11586) *********************** 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 98 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 1.147 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 153 GLU cc_start: 0.8215 (tp30) cc_final: 0.7979 (tp30) REVERT: C 1141 GLN cc_start: 0.8682 (mm-40) cc_final: 0.7904 (tm-30) REVERT: C 1208 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.9021 (mp) REVERT: C 1247 ASP cc_start: 0.7812 (m-30) cc_final: 0.7607 (m-30) REVERT: C 1274 GLN cc_start: 0.9064 (tt0) cc_final: 0.8855 (tm-30) REVERT: D 14 LEU cc_start: 0.8389 (tp) cc_final: 0.8025 (tp) outliers start: 12 outliers final: 10 residues processed: 93 average time/residue: 0.3387 time to fit residues: 44.7842 Evaluate side-chains 95 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 613 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain C residue 1109 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.092427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.073774 restraints weight = 63032.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.076824 restraints weight = 24058.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.078782 restraints weight = 13909.995| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4623 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= 0.120 Angle : 0.472 10.130 11608 Z= 0.245 Chirality : 0.038 0.131 1286 Planarity : 0.003 0.039 1441 Dihedral : 3.898 42.158 1320 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.47 % Allowed : 13.12 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.27), residues: 1009 helix: 2.45 (0.26), residues: 387 sheet: 0.66 (0.39), residues: 163 loop : -0.18 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 955 HIS 0.002 0.001 HIS A 161 PHE 0.010 0.001 PHE A 688 TYR 0.009 0.001 TYR D 105 ARG 0.001 0.000 ARG A 483 Details of bonding type rmsd link_NAG-ASN : bond 0.00045 ( 3) link_NAG-ASN : angle 1.00214 ( 9) link_BETA1-4 : bond 0.00189 ( 2) link_BETA1-4 : angle 1.02214 ( 6) hydrogen bonds : bond 0.03697 ( 403) hydrogen bonds : angle 4.24593 ( 1161) link_BETA1-6 : bond 0.00028 ( 1) link_BETA1-6 : angle 1.44884 ( 3) SS BOND : bond 0.00091 ( 2) SS BOND : angle 1.20567 ( 4) covalent geometry : bond 0.00262 ( 8559) covalent geometry : angle 0.47038 (11586) ********************** 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 98 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 1.048 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 153 GLU cc_start: 0.8228 (tp30) cc_final: 0.7995 (tp30) REVERT: A 460 SER cc_start: 0.9237 (m) cc_final: 0.8912 (t) REVERT: A 692 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8630 (tt) REVERT: C 1141 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8165 (tm-30) REVERT: C 1208 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.9044 (mp) REVERT: C 1247 ASP cc_start: 0.7847 (m-30) cc_final: 0.7636 (m-30) REVERT: D 14 LEU cc_start: 0.8412 (tp) cc_final: 0.8038 (tp) REVERT: D 92 GLU cc_start: 0.8405 (pm20) cc_final: 0.7977 (pm20) outliers start: 13 outliers final: 10 residues processed: 94 average time/residue: 0.3318 time to fit residues: 43.9936 Evaluate side-chains 95 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 613 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain C residue 1109 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 56 optimal weight: 0.0070 chunk 70 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 76 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.4200 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.088739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.070045 restraints weight = 61433.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.072901 restraints weight = 24912.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.074767 restraints weight = 14720.676| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8567 Z= 0.143 Angle : 0.488 9.100 11608 Z= 0.255 Chirality : 0.038 0.130 1286 Planarity : 0.003 0.038 1441 Dihedral : 3.894 42.429 1320 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.24 % Allowed : 13.35 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.27), residues: 1009 helix: 2.27 (0.26), residues: 393 sheet: 0.67 (0.39), residues: 163 loop : -0.21 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 955 HIS 0.002 0.001 HIS A 161 PHE 0.025 0.001 PHE A 688 TYR 0.010 0.001 TYR D 105 ARG 0.002 0.000 ARG C1076 Details of bonding type rmsd link_NAG-ASN : bond 0.00033 ( 3) link_NAG-ASN : angle 1.04368 ( 9) link_BETA1-4 : bond 0.00195 ( 2) link_BETA1-4 : angle 1.06452 ( 6) hydrogen bonds : bond 0.03794 ( 403) hydrogen bonds : angle 4.28999 ( 1161) link_BETA1-6 : bond 0.00251 ( 1) link_BETA1-6 : angle 1.37613 ( 3) SS BOND : bond 0.00089 ( 2) SS BOND : angle 1.23099 ( 4) covalent geometry : bond 0.00311 ( 8559) covalent geometry : angle 0.48602 (11586) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4904.78 seconds wall clock time: 86 minutes 9.50 seconds (5169.50 seconds total)