Starting phenix.real_space_refine on Sat May 17 03:02:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xq5_38566/05_2025/8xq5_38566.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xq5_38566/05_2025/8xq5_38566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xq5_38566/05_2025/8xq5_38566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xq5_38566/05_2025/8xq5_38566.map" model { file = "/net/cci-nas-00/data/ceres_data/8xq5_38566/05_2025/8xq5_38566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xq5_38566/05_2025/8xq5_38566.cif" } resolution = 3.15 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= 0.002 sd= 0.031 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: 4 Type Number sf(0) Gaussians S 76 5.16 5 C 9820 2.51 5 N 2540 2.21 5 O 2692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15128 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7564 Classifications: {'peptide': 983} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 29, 'TRANS': 953} Chain breaks: 6 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 107 Chain: "B" Number of atoms: 7564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7564 Classifications: {'peptide': 983} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 29, 'TRANS': 953} Chain breaks: 6 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 107 Time building chain proxies: 9.44, per 1000 atoms: 0.62 Number of scatterers: 15128 At special positions: 0 Unit cell: (104.76, 135, 125.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 76 16.00 O 2692 8.00 N 2540 7.00 C 9820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.55 Conformation dependent library (CDL) restraints added in 1.9 seconds 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3708 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 8 sheets defined 75.8% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 75 through 95 removed outlier: 4.174A pdb=" N VAL A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.957A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.560A pdb=" N HIS A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 223 through 253 removed outlier: 3.821A pdb=" N GLY A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 292 Proline residue: A 276 - end of helix removed outlier: 3.758A pdb=" N HIS A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 317 removed outlier: 4.008A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 338 through 341 Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 376 through 379 removed outlier: 3.979A pdb=" N ALA A 379 " --> pdb=" O ALA A 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 379' Processing helix chain 'A' and resid 381 through 406 Processing helix chain 'A' and resid 406 through 412 Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.727A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 481 removed outlier: 4.373A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 513 Processing helix chain 'A' and resid 522 through 530 Processing helix chain 'A' and resid 572 through 600 removed outlier: 3.547A pdb=" N HIS A 600 " --> pdb=" O LYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 619 Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 639 through 653 removed outlier: 4.334A pdb=" N TRP A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 691 Processing helix chain 'A' and resid 692 through 699 removed outlier: 3.771A pdb=" N ILE A 696 " --> pdb=" O ILE A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 752 Processing helix chain 'A' and resid 763 through 776 Processing helix chain 'A' and resid 803 through 853 Proline residue: A 819 - end of helix removed outlier: 3.617A pdb=" N LEU A 835 " --> pdb=" O ASN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 858 removed outlier: 3.825A pdb=" N MET A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 889 removed outlier: 3.622A pdb=" N HIS A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 Processing helix chain 'A' and resid 923 through 943 removed outlier: 3.731A pdb=" N ASN A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 959 Processing helix chain 'A' and resid 966 through 976 Processing helix chain 'A' and resid 1043 through 1050 Processing helix chain 'A' and resid 1069 through 1080 Processing helix chain 'A' and resid 1085 through 1108 Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1109 through 1111 No H-bonds generated for 'chain 'A' and resid 1109 through 1111' Processing helix chain 'A' and resid 1113 through 1123 removed outlier: 3.671A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 95 removed outlier: 4.126A pdb=" N VAL B 79 " --> pdb=" O PRO B 75 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 120 removed outlier: 3.938A pdb=" N VAL B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 3.521A pdb=" N HIS B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 153 Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 162 through 189 Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 211 through 220 Processing helix chain 'B' and resid 223 through 253 removed outlier: 3.872A pdb=" N GLY B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR B 228 " --> pdb=" O LYS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 292 Proline residue: B 276 - end of helix removed outlier: 3.634A pdb=" N HIS B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 317 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 342 through 375 Processing helix chain 'B' and resid 376 through 379 removed outlier: 4.087A pdb=" N ALA B 379 " --> pdb=" O ALA B 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 376 through 379' Processing helix chain 'B' and resid 381 through 406 Processing helix chain 'B' and resid 406 through 412 Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.598A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 482 removed outlier: 4.410A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY B 482 " --> pdb=" O LEU B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 513 Processing helix chain 'B' and resid 522 through 530 Processing helix chain 'B' and resid 572 through 600 Processing helix chain 'B' and resid 604 through 619 Processing helix chain 'B' and resid 631 through 635 Processing helix chain 'B' and resid 639 through 653 removed outlier: 4.308A pdb=" N TRP B 643 " --> pdb=" O GLY B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 691 Processing helix chain 'B' and resid 692 through 699 removed outlier: 3.768A pdb=" N ILE B 696 " --> pdb=" O ILE B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 752 Processing helix chain 'B' and resid 763 through 776 Processing helix chain 'B' and resid 803 through 853 Proline residue: B 819 - end of helix removed outlier: 3.666A pdb=" N LEU B 835 " --> pdb=" O ASN B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 858 removed outlier: 3.769A pdb=" N MET B 857 " --> pdb=" O ILE B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 889 removed outlier: 3.657A pdb=" N HIS B 889 " --> pdb=" O LEU B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 Processing helix chain 'B' and resid 923 through 943 removed outlier: 3.716A pdb=" N ASN B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 959 Processing helix chain 'B' and resid 966 through 976 Processing helix chain 'B' and resid 1043 through 1050 Processing helix chain 'B' and resid 1069 through 1080 Processing helix chain 'B' and resid 1085 through 1108 Proline residue: B1101 - end of helix Processing helix chain 'B' and resid 1113 through 1122 Processing sheet with id=AA1, first strand: chain 'A' and resid 979 through 982 removed outlier: 6.178A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.532A pdb=" N VAL A1057 " --> pdb=" O ILE A 988 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 6.384A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS A1165 " --> pdb=" O LEU A1147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1137 Processing sheet with id=AA5, first strand: chain 'B' and resid 979 through 982 removed outlier: 6.198A pdb=" N GLN B1064 " --> pdb=" O VAL B1002 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 987 through 989 removed outlier: 6.461A pdb=" N VAL B1057 " --> pdb=" O ILE B 988 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1125 through 1126 removed outlier: 6.395A pdb=" N ARG B1185 " --> pdb=" O ILE B1148 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL B1145 " --> pdb=" O ILE B1167 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N CYS B1165 " --> pdb=" O LEU B1147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1135 through 1137 1166 hydrogen bonds defined for protein. 3447 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: 5.58 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4798 1.34 - 1.46: 2778 1.46 - 1.58: 7686 1.58 - 1.70: 2 1.70 - 1.81: 140 Bond restraints: 15404 Sorted by residual: bond pdb=" C SER A 407 " pdb=" N PRO A 408 " ideal model delta sigma weight residual 1.335 1.382 -0.046 1.36e-02 5.41e+03 1.16e+01 bond pdb=" CB ASN A1137 " pdb=" CG ASN A1137 " ideal model delta sigma weight residual 1.516 1.579 -0.063 2.50e-02 1.60e+03 6.42e+00 bond pdb=" CB GLN A1106 " pdb=" CG GLN A1106 " ideal model delta sigma weight residual 1.520 1.588 -0.068 3.00e-02 1.11e+03 5.18e+00 bond pdb=" CB PHE B 163 " pdb=" CG PHE B 163 " ideal model delta sigma weight residual 1.502 1.552 -0.050 2.30e-02 1.89e+03 4.71e+00 bond pdb=" CB PHE A 163 " pdb=" CG PHE A 163 " ideal model delta sigma weight residual 1.502 1.552 -0.050 2.30e-02 1.89e+03 4.66e+00 ... (remaining 15399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 20388 2.80 - 5.60: 410 5.60 - 8.40: 77 8.40 - 11.20: 30 11.20 - 14.00: 7 Bond angle restraints: 20912 Sorted by residual: angle pdb=" CA MET A1107 " pdb=" CB MET A1107 " pdb=" CG MET A1107 " ideal model delta sigma weight residual 114.10 127.86 -13.76 2.00e+00 2.50e-01 4.73e+01 angle pdb=" CB ARG A 499 " pdb=" CG ARG A 499 " pdb=" CD ARG A 499 " ideal model delta sigma weight residual 111.30 123.93 -12.63 2.30e+00 1.89e-01 3.02e+01 angle pdb=" CA MET B1107 " pdb=" CB MET B1107 " pdb=" CG MET B1107 " ideal model delta sigma weight residual 114.10 124.45 -10.35 2.00e+00 2.50e-01 2.68e+01 angle pdb=" CB LYS B 820 " pdb=" CG LYS B 820 " pdb=" CD LYS B 820 " ideal model delta sigma weight residual 111.30 122.52 -11.22 2.30e+00 1.89e-01 2.38e+01 angle pdb=" CA LYS A 250 " pdb=" CB LYS A 250 " pdb=" CG LYS A 250 " ideal model delta sigma weight residual 114.10 123.65 -9.55 2.00e+00 2.50e-01 2.28e+01 ... (remaining 20907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8057 17.90 - 35.80: 946 35.80 - 53.70: 174 53.70 - 71.60: 23 71.60 - 89.50: 10 Dihedral angle restraints: 9210 sinusoidal: 3500 harmonic: 5710 Sorted by residual: dihedral pdb=" CA ARG B1190 " pdb=" C ARG B1190 " pdb=" N ASN B1191 " pdb=" CA ASN B1191 " ideal model delta harmonic sigma weight residual 180.00 152.91 27.09 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA ARG A1190 " pdb=" C ARG A1190 " pdb=" N ASN A1191 " pdb=" CA ASN A1191 " ideal model delta harmonic sigma weight residual 180.00 154.02 25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA TYR B1083 " pdb=" C TYR B1083 " pdb=" N PRO B1084 " pdb=" CA PRO B1084 " ideal model delta harmonic sigma weight residual 180.00 154.17 25.83 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 9207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 2497 0.161 - 0.323: 25 0.323 - 0.484: 2 0.484 - 0.645: 0 0.645 - 0.807: 2 Chirality restraints: 2526 Sorted by residual: chirality pdb=" CG LEU A 608 " pdb=" CB LEU A 608 " pdb=" CD1 LEU A 608 " pdb=" CD2 LEU A 608 " both_signs ideal model delta sigma weight residual False -2.59 -1.78 -0.81 2.00e-01 2.50e+01 1.63e+01 chirality pdb=" CG LEU B 608 " pdb=" CB LEU B 608 " pdb=" CD1 LEU B 608 " pdb=" CD2 LEU B 608 " both_signs ideal model delta sigma weight residual False -2.59 -1.81 -0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" CG LEU A 584 " pdb=" CB LEU A 584 " pdb=" CD1 LEU A 584 " pdb=" CD2 LEU A 584 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 2523 not shown) Planarity restraints: 2600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 599 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.11e+00 pdb=" CD GLU B 599 " -0.052 2.00e-02 2.50e+03 pdb=" OE1 GLU B 599 " 0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU B 599 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 987 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.80e+00 pdb=" C VAL A 987 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL A 987 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE A 988 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B1072 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.36e+00 pdb=" CG ASP B1072 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASP B1072 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP B1072 " 0.017 2.00e-02 2.50e+03 ... (remaining 2597 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3524 2.79 - 3.32: 14404 3.32 - 3.85: 25697 3.85 - 4.37: 28119 4.37 - 4.90: 50517 Nonbonded interactions: 122261 Sorted by model distance: nonbonded pdb=" O ALA B 307 " pdb=" OG1 THR B 311 " model vdw 2.266 3.040 nonbonded pdb=" O ALA A 307 " pdb=" OG1 THR A 311 " model vdw 2.273 3.040 nonbonded pdb=" O ILE B 469 " pdb=" OG1 THR B 473 " model vdw 2.281 3.040 nonbonded pdb=" O ILE A 469 " pdb=" OG1 THR A 473 " model vdw 2.299 3.040 nonbonded pdb=" O ILE A1075 " pdb=" OG1 THR A1079 " model vdw 2.345 3.040 ... (remaining 122256 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 35.700 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 0.005 0.068 15404 Z= 0.242 Angle : 1.032 13.996 20912 Z= 0.538 Chirality : 0.058 0.807 2526 Planarity : 0.007 0.102 2600 Dihedral : 15.592 89.500 5502 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.95 % Allowed : 24.33 % Favored : 74.71 % 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: -1.55 (0.17), residues: 1938 helix: -0.69 (0.12), residues: 1378 sheet: -0.25 (0.59), residues: 94 loop : -1.77 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 419 HIS 0.006 0.001 HIS B 614 PHE 0.045 0.003 PHE B1032 TYR 0.036 0.002 TYR A 984 ARG 0.021 0.001 ARG A 499 Details of bonding type rmsd hydrogen bonds : bond 0.11327 ( 1166) hydrogen bonds : angle 6.06311 ( 3447) covalent geometry : bond 0.00499 (15404) covalent geometry : angle 1.03156 (20912) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 589 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: A 91 SER cc_start: 0.8725 (m) cc_final: 0.8394 (p) REVERT: A 116 VAL cc_start: 0.8575 (t) cc_final: 0.8225 (t) REVERT: A 165 GLN cc_start: 0.8419 (mt0) cc_final: 0.8202 (mt0) REVERT: A 197 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7721 (mt-10) REVERT: A 205 MET cc_start: 0.7963 (mmm) cc_final: 0.7614 (mmp) REVERT: A 217 LEU cc_start: 0.8577 (mt) cc_final: 0.8318 (mm) REVERT: A 233 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7735 (tm-30) REVERT: A 251 MET cc_start: 0.8199 (tpp) cc_final: 0.7961 (tpp) REVERT: A 284 LYS cc_start: 0.8831 (mmtm) cc_final: 0.8555 (mmmm) REVERT: A 346 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7551 (mt-10) REVERT: A 366 MET cc_start: 0.8385 (mmm) cc_final: 0.8153 (mmm) REVERT: A 375 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8334 (ttmm) REVERT: A 395 ILE cc_start: 0.8213 (tt) cc_final: 0.7616 (pt) REVERT: A 423 VAL cc_start: 0.8685 (t) cc_final: 0.8398 (t) REVERT: A 426 THR cc_start: 0.8713 (m) cc_final: 0.8456 (m) REVERT: A 444 ASN cc_start: 0.8659 (t0) cc_final: 0.8349 (t0) REVERT: A 580 GLU cc_start: 0.7623 (tp30) cc_final: 0.7250 (tp30) REVERT: A 581 GLU cc_start: 0.6968 (tp30) cc_final: 0.6255 (tp30) REVERT: A 583 ARG cc_start: 0.7773 (ttt-90) cc_final: 0.7247 (ttp-170) REVERT: A 586 MET cc_start: 0.8631 (ttm) cc_final: 0.8327 (ttp) REVERT: A 587 LEU cc_start: 0.8783 (mt) cc_final: 0.8425 (mt) REVERT: A 588 LYS cc_start: 0.8279 (tttm) cc_final: 0.7980 (tttm) REVERT: A 592 ILE cc_start: 0.8572 (mt) cc_final: 0.8196 (mm) REVERT: A 602 MET cc_start: 0.8111 (tpp) cc_final: 0.7754 (tpp) REVERT: A 609 ARG cc_start: 0.8008 (mtp-110) cc_final: 0.7607 (tpp80) REVERT: A 613 GLN cc_start: 0.7652 (mt0) cc_final: 0.7299 (mt0) REVERT: A 617 VAL cc_start: 0.7913 (t) cc_final: 0.7617 (m) REVERT: A 632 LYS cc_start: 0.8399 (mtpp) cc_final: 0.8088 (mtmm) REVERT: A 641 TYR cc_start: 0.7874 (m-10) cc_final: 0.7538 (m-80) REVERT: A 828 LYS cc_start: 0.8391 (mmmt) cc_final: 0.8087 (mmmt) REVERT: A 832 GLN cc_start: 0.8622 (tp40) cc_final: 0.8364 (tp40) REVERT: A 837 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.7551 (t80) REVERT: A 841 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7650 (mtpp) REVERT: A 845 ILE cc_start: 0.8641 (mm) cc_final: 0.8423 (mt) REVERT: A 847 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7262 (mm-30) REVERT: A 878 VAL cc_start: 0.8887 (t) cc_final: 0.8676 (t) REVERT: A 900 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8520 (tp-100) REVERT: A 931 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7619 (mm-30) REVERT: A 948 ILE cc_start: 0.8312 (mt) cc_final: 0.8012 (tt) REVERT: A 954 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7187 (mm-30) REVERT: A 1003 SER cc_start: 0.8134 (t) cc_final: 0.7825 (m) REVERT: A 1045 MET cc_start: 0.8436 (ttm) cc_final: 0.8102 (tpp) REVERT: A 1058 THR cc_start: 0.8470 (m) cc_final: 0.8217 (p) REVERT: A 1063 VAL cc_start: 0.8280 (t) cc_final: 0.8008 (p) REVERT: A 1072 ASP cc_start: 0.7555 (t0) cc_final: 0.7286 (t0) REVERT: A 1077 ILE cc_start: 0.8588 (mm) cc_final: 0.8387 (mm) REVERT: A 1104 MET cc_start: 0.7761 (tpt) cc_final: 0.7333 (tpp) REVERT: A 1105 GLU cc_start: 0.8367 (tp30) cc_final: 0.8140 (tp30) REVERT: A 1122 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7570 (tp30) REVERT: B 91 SER cc_start: 0.8787 (m) cc_final: 0.8514 (p) REVERT: B 108 ILE cc_start: 0.8643 (mm) cc_final: 0.8211 (mt) REVERT: B 154 MET cc_start: 0.8251 (tpp) cc_final: 0.7715 (mmm) REVERT: B 155 ASP cc_start: 0.8285 (t0) cc_final: 0.7936 (t0) REVERT: B 197 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7763 (mt-10) REVERT: B 214 VAL cc_start: 0.8607 (t) cc_final: 0.8131 (p) REVERT: B 217 LEU cc_start: 0.8547 (mt) cc_final: 0.8285 (mm) REVERT: B 231 GLU cc_start: 0.8180 (tt0) cc_final: 0.7975 (mt-10) REVERT: B 250 LYS cc_start: 0.8393 (mmmm) cc_final: 0.7896 (mmmm) REVERT: B 267 TYR cc_start: 0.8405 (t80) cc_final: 0.7889 (t80) REVERT: B 269 LEU cc_start: 0.8513 (tp) cc_final: 0.8305 (tt) REVERT: B 280 TYR cc_start: 0.8555 (t80) cc_final: 0.8343 (t80) REVERT: B 292 HIS cc_start: 0.8733 (m-70) cc_final: 0.8523 (m90) REVERT: B 300 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7714 (mt-10) REVERT: B 305 LEU cc_start: 0.8547 (tp) cc_final: 0.8256 (tt) REVERT: B 309 TYR cc_start: 0.8681 (m-80) cc_final: 0.8260 (m-80) REVERT: B 392 TYR cc_start: 0.8406 (t80) cc_final: 0.8147 (t80) REVERT: B 443 GLU cc_start: 0.8037 (tp30) cc_final: 0.7627 (tp30) REVERT: B 444 ASN cc_start: 0.8795 (t0) cc_final: 0.8500 (t0) REVERT: B 476 THR cc_start: 0.8773 (t) cc_final: 0.8438 (m) REVERT: B 486 ILE cc_start: 0.8571 (mm) cc_final: 0.8338 (mm) REVERT: B 500 ARG cc_start: 0.8193 (mmm-85) cc_final: 0.7960 (mmm-85) REVERT: B 511 MET cc_start: 0.8961 (tmm) cc_final: 0.8527 (ttp) REVERT: B 517 PHE cc_start: 0.8311 (m-10) cc_final: 0.8090 (m-10) REVERT: B 579 MET cc_start: 0.7369 (tpt) cc_final: 0.7053 (tpt) REVERT: B 580 GLU cc_start: 0.7827 (tp30) cc_final: 0.7399 (tp30) REVERT: B 581 GLU cc_start: 0.7032 (tp30) cc_final: 0.6261 (tp30) REVERT: B 587 LEU cc_start: 0.8774 (mt) cc_final: 0.8483 (mt) REVERT: B 588 LYS cc_start: 0.8129 (tttm) cc_final: 0.7621 (tttm) REVERT: B 592 ILE cc_start: 0.8536 (mt) cc_final: 0.8098 (mm) REVERT: B 595 TRP cc_start: 0.8498 (m100) cc_final: 0.8065 (m100) REVERT: B 621 GLU cc_start: 0.7146 (mp0) cc_final: 0.6603 (mp0) REVERT: B 624 GLN cc_start: 0.7375 (pt0) cc_final: 0.7048 (pt0) REVERT: B 646 ARG cc_start: 0.7028 (ptp-170) cc_final: 0.6789 (ptp-170) REVERT: B 828 LYS cc_start: 0.8540 (mmtt) cc_final: 0.8208 (mmtt) REVERT: B 835 LEU cc_start: 0.8601 (tp) cc_final: 0.8314 (tt) REVERT: B 837 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7598 (t80) REVERT: B 839 VAL cc_start: 0.8899 (t) cc_final: 0.8531 (t) REVERT: B 843 TYR cc_start: 0.8757 (t80) cc_final: 0.8534 (t80) REVERT: B 845 ILE cc_start: 0.8551 (mm) cc_final: 0.8295 (mt) REVERT: B 866 GLU cc_start: 0.8320 (tp30) cc_final: 0.8049 (tp30) REVERT: B 878 VAL cc_start: 0.8791 (t) cc_final: 0.8542 (t) REVERT: B 926 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7585 (mm-30) REVERT: B 931 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7678 (mm-30) REVERT: B 991 GLU cc_start: 0.7650 (tt0) cc_final: 0.7428 (tp30) REVERT: B 999 PHE cc_start: 0.8336 (m-80) cc_final: 0.7999 (m-80) REVERT: B 1003 SER cc_start: 0.8364 (t) cc_final: 0.8104 (m) REVERT: B 1035 TYR cc_start: 0.8708 (m-80) cc_final: 0.8451 (m-80) REVERT: B 1045 MET cc_start: 0.8387 (ttm) cc_final: 0.8118 (tpp) REVERT: B 1077 ILE cc_start: 0.8551 (mm) cc_final: 0.8171 (mm) REVERT: B 1087 GLU cc_start: 0.8054 (tp30) cc_final: 0.7794 (tp30) REVERT: B 1122 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7395 (mm-30) REVERT: B 1183 GLU cc_start: 0.8117 (tp30) cc_final: 0.7757 (tp30) outliers start: 15 outliers final: 5 residues processed: 593 average time/residue: 0.2740 time to fit residues: 231.6819 Evaluate side-chains 545 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 537 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 837 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 153 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 177 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 900 GLN A 908 HIS A 981 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 832 GLN B 908 HIS B 981 HIS B1135 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.134234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.115074 restraints weight = 23872.761| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.20 r_work: 0.3364 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15404 Z= 0.153 Angle : 0.610 7.984 20912 Z= 0.316 Chirality : 0.041 0.202 2526 Planarity : 0.005 0.044 2600 Dihedral : 5.081 54.344 2106 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.93 % Allowed : 23.13 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.19), residues: 1938 helix: 0.92 (0.13), residues: 1404 sheet: -0.38 (0.57), residues: 96 loop : -1.41 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 353 HIS 0.005 0.001 HIS B 981 PHE 0.017 0.002 PHE A1176 TYR 0.020 0.001 TYR B 984 ARG 0.007 0.001 ARG B 903 Details of bonding type rmsd hydrogen bonds : bond 0.04682 ( 1166) hydrogen bonds : angle 4.38393 ( 3447) covalent geometry : bond 0.00321 (15404) covalent geometry : angle 0.60972 (20912) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 541 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.8695 (m) cc_final: 0.8425 (p) REVERT: A 175 VAL cc_start: 0.8503 (p) cc_final: 0.8166 (m) REVERT: A 217 LEU cc_start: 0.8658 (mt) cc_final: 0.8344 (mm) REVERT: A 233 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7770 (tm-30) REVERT: A 263 GLN cc_start: 0.8064 (mt0) cc_final: 0.7769 (mt0) REVERT: A 267 TYR cc_start: 0.8605 (t80) cc_final: 0.8342 (t80) REVERT: A 284 LYS cc_start: 0.8759 (mmtm) cc_final: 0.8526 (mmmm) REVERT: A 346 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7493 (mt-10) REVERT: A 443 GLU cc_start: 0.8049 (tp30) cc_final: 0.7714 (tp30) REVERT: A 444 ASN cc_start: 0.8750 (t0) cc_final: 0.8383 (t0) REVERT: A 500 ARG cc_start: 0.8374 (mmm-85) cc_final: 0.8062 (tpp80) REVERT: A 511 MET cc_start: 0.9053 (tmm) cc_final: 0.8827 (tmm) REVERT: A 580 GLU cc_start: 0.7726 (tp30) cc_final: 0.7249 (tp30) REVERT: A 581 GLU cc_start: 0.7022 (tp30) cc_final: 0.6334 (tp30) REVERT: A 584 LEU cc_start: 0.8456 (mm) cc_final: 0.7661 (mm) REVERT: A 586 MET cc_start: 0.8738 (ttm) cc_final: 0.8430 (ttp) REVERT: A 588 LYS cc_start: 0.8462 (tttm) cc_final: 0.8140 (tttm) REVERT: A 592 ILE cc_start: 0.8672 (mt) cc_final: 0.8251 (mm) REVERT: A 613 GLN cc_start: 0.7688 (mt0) cc_final: 0.7337 (mt0) REVERT: A 614 HIS cc_start: 0.7770 (m-70) cc_final: 0.7224 (m-70) REVERT: A 617 VAL cc_start: 0.8003 (t) cc_final: 0.7771 (m) REVERT: A 641 TYR cc_start: 0.7952 (m-10) cc_final: 0.7556 (m-80) REVERT: A 643 TRP cc_start: 0.7743 (t-100) cc_final: 0.7295 (t-100) REVERT: A 828 LYS cc_start: 0.8432 (mmmt) cc_final: 0.8143 (mmmt) REVERT: A 832 GLN cc_start: 0.8847 (tp40) cc_final: 0.8552 (tp40) REVERT: A 841 LYS cc_start: 0.8342 (mtpt) cc_final: 0.7993 (mtpt) REVERT: A 847 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7555 (mm-30) REVERT: A 858 VAL cc_start: 0.8370 (p) cc_final: 0.7915 (p) REVERT: A 866 GLU cc_start: 0.8148 (tp30) cc_final: 0.7818 (tp30) REVERT: A 870 ILE cc_start: 0.8503 (mt) cc_final: 0.8217 (mm) REVERT: A 878 VAL cc_start: 0.8921 (t) cc_final: 0.8696 (t) REVERT: A 900 GLN cc_start: 0.8716 (tp40) cc_final: 0.8492 (tp-100) REVERT: A 921 LEU cc_start: 0.8309 (mm) cc_final: 0.8018 (mp) REVERT: A 931 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7746 (mm-30) REVERT: A 932 LEU cc_start: 0.8486 (tt) cc_final: 0.8247 (tp) REVERT: A 948 ILE cc_start: 0.8391 (mt) cc_final: 0.8074 (tt) REVERT: A 958 LYS cc_start: 0.8580 (ttpt) cc_final: 0.8209 (ttpt) REVERT: A 999 PHE cc_start: 0.8070 (m-80) cc_final: 0.7669 (m-80) REVERT: A 1003 SER cc_start: 0.8374 (t) cc_final: 0.8085 (m) REVERT: A 1045 MET cc_start: 0.8519 (ttm) cc_final: 0.8223 (tpp) REVERT: A 1063 VAL cc_start: 0.8326 (t) cc_final: 0.8108 (p) REVERT: A 1077 ILE cc_start: 0.8662 (mm) cc_final: 0.8327 (mm) REVERT: A 1100 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8484 (p) REVERT: A 1103 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8106 (mm) REVERT: A 1104 MET cc_start: 0.7875 (tpt) cc_final: 0.7477 (tpp) REVERT: A 1107 MET cc_start: 0.6931 (tmm) cc_final: 0.6203 (tmm) REVERT: A 1122 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7422 (mm-30) REVERT: B 91 SER cc_start: 0.8741 (m) cc_final: 0.8518 (p) REVERT: B 140 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8247 (mp10) REVERT: B 154 MET cc_start: 0.8466 (tpp) cc_final: 0.7993 (mmm) REVERT: B 197 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7786 (mt-10) REVERT: B 214 VAL cc_start: 0.8754 (t) cc_final: 0.8371 (p) REVERT: B 250 LYS cc_start: 0.8289 (mmmm) cc_final: 0.8081 (mttm) REVERT: B 265 VAL cc_start: 0.8470 (p) cc_final: 0.8242 (p) REVERT: B 267 TYR cc_start: 0.8470 (t80) cc_final: 0.8116 (t80) REVERT: B 300 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7789 (mt-10) REVERT: B 392 TYR cc_start: 0.8604 (t80) cc_final: 0.8377 (t80) REVERT: B 443 GLU cc_start: 0.7958 (tp30) cc_final: 0.7589 (tp30) REVERT: B 444 ASN cc_start: 0.8848 (t0) cc_final: 0.8465 (t0) REVERT: B 476 THR cc_start: 0.8817 (t) cc_final: 0.8554 (m) REVERT: B 485 ASP cc_start: 0.8231 (t0) cc_final: 0.8024 (t0) REVERT: B 486 ILE cc_start: 0.8577 (mm) cc_final: 0.8282 (mm) REVERT: B 520 ASP cc_start: 0.8164 (p0) cc_final: 0.7899 (p0) REVERT: B 579 MET cc_start: 0.7412 (tpt) cc_final: 0.7171 (tpt) REVERT: B 580 GLU cc_start: 0.7933 (tp30) cc_final: 0.7217 (tp30) REVERT: B 581 GLU cc_start: 0.7162 (tp30) cc_final: 0.6409 (tp30) REVERT: B 584 LEU cc_start: 0.8409 (mm) cc_final: 0.7920 (mm) REVERT: B 586 MET cc_start: 0.8792 (ttm) cc_final: 0.8460 (ttm) REVERT: B 587 LEU cc_start: 0.8779 (mt) cc_final: 0.8544 (mt) REVERT: B 588 LYS cc_start: 0.8325 (tttm) cc_final: 0.7887 (tttm) REVERT: B 592 ILE cc_start: 0.8598 (mt) cc_final: 0.8228 (mm) REVERT: B 620 ASP cc_start: 0.7569 (t70) cc_final: 0.7170 (t70) REVERT: B 621 GLU cc_start: 0.7125 (mp0) cc_final: 0.6388 (mp0) REVERT: B 624 GLN cc_start: 0.7558 (pt0) cc_final: 0.7273 (pt0) REVERT: B 828 LYS cc_start: 0.8549 (mmtt) cc_final: 0.8241 (mmtt) REVERT: B 835 LEU cc_start: 0.8691 (tp) cc_final: 0.8434 (tt) REVERT: B 837 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.7829 (t80) REVERT: B 839 VAL cc_start: 0.8829 (t) cc_final: 0.8529 (t) REVERT: B 845 ILE cc_start: 0.8717 (mm) cc_final: 0.8451 (mt) REVERT: B 866 GLU cc_start: 0.8349 (tp30) cc_final: 0.7943 (tp30) REVERT: B 870 ILE cc_start: 0.8643 (mm) cc_final: 0.8329 (mm) REVERT: B 878 VAL cc_start: 0.8846 (t) cc_final: 0.8585 (t) REVERT: B 879 VAL cc_start: 0.8977 (p) cc_final: 0.8776 (t) REVERT: B 921 LEU cc_start: 0.8363 (mm) cc_final: 0.8034 (mp) REVERT: B 926 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7658 (mm-30) REVERT: B 931 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7741 (mm-30) REVERT: B 932 LEU cc_start: 0.8423 (tt) cc_final: 0.8198 (tp) REVERT: B 972 PHE cc_start: 0.8426 (t80) cc_final: 0.8192 (t80) REVERT: B 999 PHE cc_start: 0.8246 (m-80) cc_final: 0.7798 (m-80) REVERT: B 1003 SER cc_start: 0.8554 (t) cc_final: 0.8222 (m) REVERT: B 1045 MET cc_start: 0.8485 (ttm) cc_final: 0.8195 (tpp) REVERT: B 1058 THR cc_start: 0.8517 (p) cc_final: 0.8298 (p) REVERT: B 1064 GLN cc_start: 0.8438 (mt0) cc_final: 0.8178 (mt0) REVERT: B 1077 ILE cc_start: 0.8623 (mm) cc_final: 0.8313 (mm) REVERT: B 1088 TYR cc_start: 0.7643 (t80) cc_final: 0.7248 (t80) REVERT: B 1104 MET cc_start: 0.8342 (tpp) cc_final: 0.8096 (tpp) REVERT: B 1122 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7438 (mm-30) REVERT: B 1145 VAL cc_start: 0.8462 (t) cc_final: 0.8216 (p) outliers start: 62 outliers final: 33 residues processed: 576 average time/residue: 0.2759 time to fit residues: 230.4737 Evaluate side-chains 559 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 522 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 880 LYS Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1146 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 32 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 184 optimal weight: 0.7980 chunk 189 optimal weight: 0.4980 chunk 87 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 186 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN B 981 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.133415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.114407 restraints weight = 23566.429| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.17 r_work: 0.3364 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15404 Z= 0.149 Angle : 0.589 10.970 20912 Z= 0.303 Chirality : 0.040 0.180 2526 Planarity : 0.004 0.038 2600 Dihedral : 4.634 53.822 2096 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.69 % Allowed : 23.89 % Favored : 71.42 % 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: 1.11 (0.19), residues: 1938 helix: 1.41 (0.14), residues: 1420 sheet: -0.34 (0.56), residues: 96 loop : -1.23 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.005 0.001 HIS B 981 PHE 0.013 0.001 PHE A1067 TYR 0.014 0.001 TYR B 984 ARG 0.006 0.001 ARG B 585 Details of bonding type rmsd hydrogen bonds : bond 0.04561 ( 1166) hydrogen bonds : angle 4.21112 ( 3447) covalent geometry : bond 0.00315 (15404) covalent geometry : angle 0.58920 (20912) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 540 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.8656 (m) cc_final: 0.8370 (p) REVERT: A 137 VAL cc_start: 0.8790 (p) cc_final: 0.8583 (t) REVERT: A 140 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8193 (mp10) REVERT: A 175 VAL cc_start: 0.8508 (p) cc_final: 0.8187 (m) REVERT: A 217 LEU cc_start: 0.8693 (mt) cc_final: 0.8399 (mm) REVERT: A 233 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7694 (tm-30) REVERT: A 263 GLN cc_start: 0.8063 (mt0) cc_final: 0.7743 (mt0) REVERT: A 267 TYR cc_start: 0.8604 (t80) cc_final: 0.8279 (t80) REVERT: A 284 LYS cc_start: 0.8733 (mmtm) cc_final: 0.8506 (mmmm) REVERT: A 291 SER cc_start: 0.8622 (t) cc_final: 0.8363 (p) REVERT: A 335 ASN cc_start: 0.8581 (t0) cc_final: 0.8294 (t0) REVERT: A 346 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7466 (mt-10) REVERT: A 395 ILE cc_start: 0.8213 (tt) cc_final: 0.7667 (pt) REVERT: A 425 MET cc_start: 0.8532 (ttm) cc_final: 0.8260 (mtm) REVERT: A 443 GLU cc_start: 0.8045 (tp30) cc_final: 0.7719 (tp30) REVERT: A 444 ASN cc_start: 0.8736 (t0) cc_final: 0.8368 (t0) REVERT: A 500 ARG cc_start: 0.8364 (mmm-85) cc_final: 0.8139 (tpp80) REVERT: A 580 GLU cc_start: 0.7802 (tp30) cc_final: 0.7117 (tp30) REVERT: A 583 ARG cc_start: 0.8174 (ttp-170) cc_final: 0.7442 (mtp180) REVERT: A 584 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.7394 (mm) REVERT: A 586 MET cc_start: 0.8608 (ttm) cc_final: 0.8368 (ttp) REVERT: A 588 LYS cc_start: 0.8584 (tttm) cc_final: 0.8256 (tttm) REVERT: A 592 ILE cc_start: 0.8745 (mt) cc_final: 0.8326 (mm) REVERT: A 609 ARG cc_start: 0.7872 (mtp-110) cc_final: 0.7627 (mtp-110) REVERT: A 613 GLN cc_start: 0.7707 (mt0) cc_final: 0.7470 (mt0) REVERT: A 614 HIS cc_start: 0.7763 (m-70) cc_final: 0.7368 (m-70) REVERT: A 641 TYR cc_start: 0.8045 (m-80) cc_final: 0.7675 (m-80) REVERT: A 643 TRP cc_start: 0.7838 (t-100) cc_final: 0.7211 (t-100) REVERT: A 644 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8232 (mt) REVERT: A 810 MET cc_start: 0.7326 (ppp) cc_final: 0.6963 (tmm) REVERT: A 828 LYS cc_start: 0.8477 (mmmt) cc_final: 0.8184 (mmmt) REVERT: A 832 GLN cc_start: 0.8756 (tp40) cc_final: 0.8473 (tp40) REVERT: A 837 TYR cc_start: 0.8330 (OUTLIER) cc_final: 0.7855 (t80) REVERT: A 838 ASP cc_start: 0.8320 (t0) cc_final: 0.7949 (t0) REVERT: A 839 VAL cc_start: 0.8860 (t) cc_final: 0.8658 (t) REVERT: A 841 LYS cc_start: 0.8438 (mtpt) cc_final: 0.8089 (mtpp) REVERT: A 847 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7660 (mm-30) REVERT: A 850 VAL cc_start: 0.8896 (p) cc_final: 0.8689 (m) REVERT: A 866 GLU cc_start: 0.8239 (tp30) cc_final: 0.7820 (tp30) REVERT: A 868 LYS cc_start: 0.7832 (mmtp) cc_final: 0.7501 (ttmm) REVERT: A 870 ILE cc_start: 0.8507 (mt) cc_final: 0.8076 (mm) REVERT: A 878 VAL cc_start: 0.8925 (t) cc_final: 0.8668 (t) REVERT: A 900 GLN cc_start: 0.8637 (tp40) cc_final: 0.8419 (tp-100) REVERT: A 911 GLU cc_start: 0.8234 (mt-10) cc_final: 0.8033 (mm-30) REVERT: A 921 LEU cc_start: 0.8302 (mm) cc_final: 0.8034 (mp) REVERT: A 926 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7508 (mp0) REVERT: A 932 LEU cc_start: 0.8495 (tt) cc_final: 0.8242 (tp) REVERT: A 948 ILE cc_start: 0.8412 (mt) cc_final: 0.8093 (tt) REVERT: A 958 LYS cc_start: 0.8609 (ttpt) cc_final: 0.8182 (ttpt) REVERT: A 976 ARG cc_start: 0.7965 (tpp80) cc_final: 0.7713 (ttm170) REVERT: A 999 PHE cc_start: 0.8154 (m-80) cc_final: 0.7686 (m-80) REVERT: A 1003 SER cc_start: 0.8464 (t) cc_final: 0.8189 (m) REVERT: A 1058 THR cc_start: 0.8554 (p) cc_final: 0.8293 (p) REVERT: A 1063 VAL cc_start: 0.8449 (t) cc_final: 0.8162 (p) REVERT: A 1064 GLN cc_start: 0.8390 (mt0) cc_final: 0.8179 (mt0) REVERT: A 1077 ILE cc_start: 0.8760 (mm) cc_final: 0.8447 (mm) REVERT: A 1100 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8526 (m) REVERT: A 1103 ILE cc_start: 0.8531 (mm) cc_final: 0.8156 (mm) REVERT: A 1104 MET cc_start: 0.7848 (tpt) cc_final: 0.7480 (tpp) REVERT: A 1107 MET cc_start: 0.7067 (tmm) cc_final: 0.6082 (tmm) REVERT: A 1122 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7693 (tp30) REVERT: B 91 SER cc_start: 0.8738 (m) cc_final: 0.8490 (p) REVERT: B 140 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8202 (mp10) REVERT: B 154 MET cc_start: 0.8504 (tpp) cc_final: 0.8224 (tpp) REVERT: B 155 ASP cc_start: 0.8438 (t0) cc_final: 0.8038 (t0) REVERT: B 160 MET cc_start: 0.8170 (mmt) cc_final: 0.7932 (mmm) REVERT: B 190 ASN cc_start: 0.7792 (p0) cc_final: 0.7463 (p0) REVERT: B 197 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7721 (mt-10) REVERT: B 214 VAL cc_start: 0.8742 (t) cc_final: 0.8534 (p) REVERT: B 217 LEU cc_start: 0.8693 (mt) cc_final: 0.8460 (mm) REVERT: B 233 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7736 (tm-30) REVERT: B 238 ASP cc_start: 0.7346 (m-30) cc_final: 0.7055 (m-30) REVERT: B 267 TYR cc_start: 0.8481 (t80) cc_final: 0.8177 (t80) REVERT: B 296 ASP cc_start: 0.7568 (p0) cc_final: 0.6952 (p0) REVERT: B 300 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7748 (mt-10) REVERT: B 386 PHE cc_start: 0.8334 (t80) cc_final: 0.8120 (t80) REVERT: B 392 TYR cc_start: 0.8615 (t80) cc_final: 0.8311 (t80) REVERT: B 443 GLU cc_start: 0.7940 (tp30) cc_final: 0.7549 (tp30) REVERT: B 444 ASN cc_start: 0.8764 (t0) cc_final: 0.8418 (t0) REVERT: B 476 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8563 (m) REVERT: B 485 ASP cc_start: 0.8281 (t0) cc_final: 0.8047 (t0) REVERT: B 486 ILE cc_start: 0.8526 (mm) cc_final: 0.8186 (mm) REVERT: B 517 PHE cc_start: 0.8393 (m-10) cc_final: 0.8086 (m-10) REVERT: B 520 ASP cc_start: 0.8013 (p0) cc_final: 0.7681 (p0) REVERT: B 579 MET cc_start: 0.7410 (tpt) cc_final: 0.7166 (tpt) REVERT: B 580 GLU cc_start: 0.7949 (tp30) cc_final: 0.7513 (tp30) REVERT: B 581 GLU cc_start: 0.7221 (tp30) cc_final: 0.6531 (tp30) REVERT: B 585 ARG cc_start: 0.8165 (ttm-80) cc_final: 0.7695 (ttm110) REVERT: B 586 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8601 (ttp) REVERT: B 587 LEU cc_start: 0.8795 (mt) cc_final: 0.8520 (mt) REVERT: B 588 LYS cc_start: 0.8419 (tttm) cc_final: 0.7993 (tttm) REVERT: B 592 ILE cc_start: 0.8698 (mt) cc_final: 0.8343 (mm) REVERT: B 620 ASP cc_start: 0.7677 (t70) cc_final: 0.7249 (t70) REVERT: B 621 GLU cc_start: 0.7272 (mp0) cc_final: 0.6602 (mp0) REVERT: B 828 LYS cc_start: 0.8633 (mmtt) cc_final: 0.8301 (mmtt) REVERT: B 832 GLN cc_start: 0.8684 (tp40) cc_final: 0.8483 (tp40) REVERT: B 835 LEU cc_start: 0.8748 (tp) cc_final: 0.8528 (tt) REVERT: B 837 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.7733 (t80) REVERT: B 839 VAL cc_start: 0.8870 (t) cc_final: 0.8614 (t) REVERT: B 845 ILE cc_start: 0.8839 (mm) cc_final: 0.8516 (mt) REVERT: B 850 VAL cc_start: 0.8980 (OUTLIER) cc_final: 0.8649 (m) REVERT: B 866 GLU cc_start: 0.8363 (tp30) cc_final: 0.7816 (tp30) REVERT: B 870 ILE cc_start: 0.8604 (mm) cc_final: 0.8203 (mm) REVERT: B 878 VAL cc_start: 0.8850 (t) cc_final: 0.8572 (t) REVERT: B 879 VAL cc_start: 0.8980 (p) cc_final: 0.8771 (t) REVERT: B 911 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7763 (mp0) REVERT: B 921 LEU cc_start: 0.8355 (mm) cc_final: 0.8051 (mp) REVERT: B 972 PHE cc_start: 0.8500 (t80) cc_final: 0.8248 (t80) REVERT: B 999 PHE cc_start: 0.8216 (m-80) cc_final: 0.7771 (m-80) REVERT: B 1003 SER cc_start: 0.8707 (t) cc_final: 0.8448 (m) REVERT: B 1045 MET cc_start: 0.8552 (ttm) cc_final: 0.8294 (tpp) REVERT: B 1058 THR cc_start: 0.8557 (p) cc_final: 0.8297 (p) REVERT: B 1077 ILE cc_start: 0.8755 (mm) cc_final: 0.8471 (mm) REVERT: B 1104 MET cc_start: 0.8214 (tpp) cc_final: 0.8013 (tpp) REVERT: B 1105 GLU cc_start: 0.8582 (tp30) cc_final: 0.8201 (tm-30) REVERT: B 1145 VAL cc_start: 0.8516 (t) cc_final: 0.8260 (p) REVERT: B 1183 GLU cc_start: 0.8072 (tp30) cc_final: 0.7860 (tp30) outliers start: 74 outliers final: 40 residues processed: 579 average time/residue: 0.2829 time to fit residues: 239.3904 Evaluate side-chains 574 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 524 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 880 LYS Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1146 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 41 optimal weight: 0.0070 chunk 189 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 188 optimal weight: 0.6980 chunk 111 optimal weight: 0.0470 chunk 12 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 167 optimal weight: 0.3980 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.135181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.116009 restraints weight = 23509.485| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.18 r_work: 0.3389 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15404 Z= 0.120 Angle : 0.559 8.331 20912 Z= 0.285 Chirality : 0.039 0.191 2526 Planarity : 0.004 0.033 2600 Dihedral : 4.529 55.679 2096 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.75 % Allowed : 24.90 % Favored : 70.34 % 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: 1.51 (0.20), residues: 1938 helix: 1.74 (0.14), residues: 1418 sheet: -0.07 (0.57), residues: 96 loop : -1.25 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.000 HIS B 157 PHE 0.013 0.001 PHE B 289 TYR 0.016 0.001 TYR B 280 ARG 0.006 0.000 ARG A 585 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 1166) hydrogen bonds : angle 4.06914 ( 3447) covalent geometry : bond 0.00244 (15404) covalent geometry : angle 0.55947 (20912) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 545 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.8631 (m) cc_final: 0.8341 (p) REVERT: A 137 VAL cc_start: 0.8732 (p) cc_final: 0.8496 (t) REVERT: A 140 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8071 (mp10) REVERT: A 175 VAL cc_start: 0.8477 (p) cc_final: 0.8158 (m) REVERT: A 195 PHE cc_start: 0.7845 (t80) cc_final: 0.7554 (t80) REVERT: A 217 LEU cc_start: 0.8680 (mt) cc_final: 0.8412 (mm) REVERT: A 231 GLU cc_start: 0.8050 (tt0) cc_final: 0.7830 (mt-10) REVERT: A 233 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7715 (tm-30) REVERT: A 267 TYR cc_start: 0.8579 (t80) cc_final: 0.8282 (t80) REVERT: A 284 LYS cc_start: 0.8740 (mmtm) cc_final: 0.8510 (mmmm) REVERT: A 291 SER cc_start: 0.8593 (t) cc_final: 0.8331 (p) REVERT: A 335 ASN cc_start: 0.8543 (t0) cc_final: 0.8259 (t0) REVERT: A 346 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7454 (mt-10) REVERT: A 395 ILE cc_start: 0.8176 (tt) cc_final: 0.7673 (pt) REVERT: A 443 GLU cc_start: 0.8006 (tp30) cc_final: 0.7719 (tp30) REVERT: A 444 ASN cc_start: 0.8761 (t0) cc_final: 0.8414 (t0) REVERT: A 494 MET cc_start: 0.8596 (tpp) cc_final: 0.7946 (tpp) REVERT: A 500 ARG cc_start: 0.8358 (mmm-85) cc_final: 0.8140 (tpp80) REVERT: A 510 ASN cc_start: 0.8488 (t0) cc_final: 0.8200 (t0) REVERT: A 580 GLU cc_start: 0.7931 (tp30) cc_final: 0.7587 (tp30) REVERT: A 581 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7133 (pp20) REVERT: A 583 ARG cc_start: 0.8161 (ttp-170) cc_final: 0.7258 (mtp180) REVERT: A 584 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8154 (mm) REVERT: A 586 MET cc_start: 0.8623 (ttm) cc_final: 0.8325 (ttp) REVERT: A 588 LYS cc_start: 0.8613 (tttm) cc_final: 0.8275 (tttm) REVERT: A 592 ILE cc_start: 0.8736 (mt) cc_final: 0.8303 (mm) REVERT: A 609 ARG cc_start: 0.7811 (mtp-110) cc_final: 0.7515 (mtp-110) REVERT: A 613 GLN cc_start: 0.7673 (mt0) cc_final: 0.7352 (mt0) REVERT: A 614 HIS cc_start: 0.7757 (m-70) cc_final: 0.7227 (m-70) REVERT: A 641 TYR cc_start: 0.7977 (m-80) cc_final: 0.7540 (m-80) REVERT: A 643 TRP cc_start: 0.7784 (t-100) cc_final: 0.7143 (t-100) REVERT: A 810 MET cc_start: 0.7317 (ppp) cc_final: 0.6939 (tmm) REVERT: A 828 LYS cc_start: 0.8450 (mmmt) cc_final: 0.8208 (mmmt) REVERT: A 832 GLN cc_start: 0.8740 (tp40) cc_final: 0.8457 (tp40) REVERT: A 837 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7793 (t80) REVERT: A 838 ASP cc_start: 0.8320 (t0) cc_final: 0.8103 (t0) REVERT: A 839 VAL cc_start: 0.8872 (t) cc_final: 0.8670 (t) REVERT: A 841 LYS cc_start: 0.8438 (mtpt) cc_final: 0.8076 (mtpp) REVERT: A 847 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7683 (mm-30) REVERT: A 850 VAL cc_start: 0.8928 (p) cc_final: 0.8700 (m) REVERT: A 864 LEU cc_start: 0.8019 (tp) cc_final: 0.7805 (tp) REVERT: A 866 GLU cc_start: 0.8224 (tp30) cc_final: 0.7849 (tp30) REVERT: A 878 VAL cc_start: 0.8924 (t) cc_final: 0.8688 (t) REVERT: A 900 GLN cc_start: 0.8632 (tp40) cc_final: 0.8405 (tp-100) REVERT: A 921 LEU cc_start: 0.8302 (mm) cc_final: 0.8051 (mp) REVERT: A 926 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7428 (mp0) REVERT: A 932 LEU cc_start: 0.8460 (tt) cc_final: 0.8192 (tp) REVERT: A 958 LYS cc_start: 0.8579 (ttpt) cc_final: 0.8155 (ttpt) REVERT: A 999 PHE cc_start: 0.8054 (m-80) cc_final: 0.7663 (m-80) REVERT: A 1003 SER cc_start: 0.8444 (t) cc_final: 0.8135 (m) REVERT: A 1058 THR cc_start: 0.8546 (p) cc_final: 0.8292 (p) REVERT: A 1063 VAL cc_start: 0.8460 (t) cc_final: 0.8119 (p) REVERT: A 1077 ILE cc_start: 0.8747 (mm) cc_final: 0.8474 (mm) REVERT: A 1098 ILE cc_start: 0.9100 (tp) cc_final: 0.8790 (tt) REVERT: A 1100 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8535 (m) REVERT: A 1103 ILE cc_start: 0.8545 (mm) cc_final: 0.8277 (mm) REVERT: A 1104 MET cc_start: 0.7862 (tpt) cc_final: 0.7533 (tpp) REVERT: A 1107 MET cc_start: 0.7128 (tmm) cc_final: 0.6417 (tmm) REVERT: A 1122 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7668 (tp30) REVERT: B 91 SER cc_start: 0.8673 (m) cc_final: 0.8435 (p) REVERT: B 109 LEU cc_start: 0.8477 (mp) cc_final: 0.8270 (mp) REVERT: B 140 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8083 (mp10) REVERT: B 154 MET cc_start: 0.8534 (tpp) cc_final: 0.8193 (tpp) REVERT: B 160 MET cc_start: 0.8420 (mmt) cc_final: 0.8179 (mmm) REVERT: B 197 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7683 (mt-10) REVERT: B 214 VAL cc_start: 0.8673 (t) cc_final: 0.8471 (p) REVERT: B 217 LEU cc_start: 0.8715 (mt) cc_final: 0.8333 (mp) REVERT: B 233 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7687 (tm-30) REVERT: B 238 ASP cc_start: 0.7294 (m-30) cc_final: 0.6997 (m-30) REVERT: B 267 TYR cc_start: 0.8454 (t80) cc_final: 0.8198 (t80) REVERT: B 319 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7971 (mp) REVERT: B 335 ASN cc_start: 0.8552 (t0) cc_final: 0.8233 (t0) REVERT: B 392 TYR cc_start: 0.8605 (t80) cc_final: 0.8385 (t80) REVERT: B 443 GLU cc_start: 0.7897 (tp30) cc_final: 0.7513 (tp30) REVERT: B 444 ASN cc_start: 0.8808 (t0) cc_final: 0.8470 (t0) REVERT: B 476 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8546 (m) REVERT: B 485 ASP cc_start: 0.8292 (t0) cc_final: 0.8017 (t0) REVERT: B 486 ILE cc_start: 0.8540 (mm) cc_final: 0.8184 (mm) REVERT: B 517 PHE cc_start: 0.8361 (m-10) cc_final: 0.8057 (m-10) REVERT: B 520 ASP cc_start: 0.8054 (p0) cc_final: 0.7777 (p0) REVERT: B 579 MET cc_start: 0.7433 (tpt) cc_final: 0.7175 (tpt) REVERT: B 580 GLU cc_start: 0.7964 (tp30) cc_final: 0.7525 (tp30) REVERT: B 581 GLU cc_start: 0.7240 (tp30) cc_final: 0.6566 (tp30) REVERT: B 585 ARG cc_start: 0.8095 (ttm-80) cc_final: 0.7708 (ttm170) REVERT: B 587 LEU cc_start: 0.8778 (mt) cc_final: 0.8523 (mt) REVERT: B 588 LYS cc_start: 0.8397 (tttm) cc_final: 0.7963 (tttm) REVERT: B 590 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8116 (mt-10) REVERT: B 592 ILE cc_start: 0.8670 (mt) cc_final: 0.8296 (mm) REVERT: B 617 VAL cc_start: 0.7934 (t) cc_final: 0.7311 (m) REVERT: B 620 ASP cc_start: 0.7612 (t70) cc_final: 0.7178 (t70) REVERT: B 621 GLU cc_start: 0.7347 (mp0) cc_final: 0.6612 (mp0) REVERT: B 644 LEU cc_start: 0.8410 (mt) cc_final: 0.8187 (mp) REVERT: B 828 LYS cc_start: 0.8622 (mmtt) cc_final: 0.8274 (mmtt) REVERT: B 832 GLN cc_start: 0.8701 (tp40) cc_final: 0.8438 (tp40) REVERT: B 835 LEU cc_start: 0.8736 (tp) cc_final: 0.8517 (tt) REVERT: B 837 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.7802 (t80) REVERT: B 839 VAL cc_start: 0.8844 (t) cc_final: 0.8565 (t) REVERT: B 841 LYS cc_start: 0.8410 (mtpt) cc_final: 0.8052 (mtpp) REVERT: B 845 ILE cc_start: 0.8772 (mm) cc_final: 0.8445 (mt) REVERT: B 850 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8620 (m) REVERT: B 866 GLU cc_start: 0.8314 (tp30) cc_final: 0.7988 (tp30) REVERT: B 870 ILE cc_start: 0.8581 (mm) cc_final: 0.8264 (mm) REVERT: B 878 VAL cc_start: 0.8831 (t) cc_final: 0.8558 (t) REVERT: B 879 VAL cc_start: 0.8970 (p) cc_final: 0.8751 (t) REVERT: B 921 LEU cc_start: 0.8298 (mm) cc_final: 0.8018 (mp) REVERT: B 926 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7311 (mm-30) REVERT: B 976 ARG cc_start: 0.7756 (ttm-80) cc_final: 0.7220 (ttm170) REVERT: B 999 PHE cc_start: 0.8142 (m-80) cc_final: 0.7714 (m-80) REVERT: B 1003 SER cc_start: 0.8694 (t) cc_final: 0.8472 (m) REVERT: B 1045 MET cc_start: 0.8505 (ttm) cc_final: 0.8248 (tpp) REVERT: B 1058 THR cc_start: 0.8573 (p) cc_final: 0.8326 (p) REVERT: B 1072 ASP cc_start: 0.7770 (t70) cc_final: 0.7054 (t70) REVERT: B 1077 ILE cc_start: 0.8734 (mm) cc_final: 0.8460 (mm) REVERT: B 1098 ILE cc_start: 0.9069 (tp) cc_final: 0.8795 (tt) REVERT: B 1104 MET cc_start: 0.8172 (tpp) cc_final: 0.7909 (tpp) REVERT: B 1145 VAL cc_start: 0.8509 (t) cc_final: 0.8257 (p) outliers start: 75 outliers final: 43 residues processed: 581 average time/residue: 0.2723 time to fit residues: 229.5627 Evaluate side-chains 586 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 533 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 880 LYS Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1146 ILE Chi-restraints excluded: chain B residue 1161 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 173 optimal weight: 0.0030 chunk 191 optimal weight: 4.9990 chunk 160 optimal weight: 0.7980 chunk 166 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS A 624 GLN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS B1154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.134033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.114888 restraints weight = 23659.175| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.18 r_work: 0.3369 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15404 Z= 0.144 Angle : 0.567 8.881 20912 Z= 0.291 Chirality : 0.040 0.243 2526 Planarity : 0.004 0.034 2600 Dihedral : 4.469 56.128 2096 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.88 % Allowed : 25.67 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.20), residues: 1938 helix: 1.85 (0.14), residues: 1408 sheet: -0.01 (0.57), residues: 96 loop : -1.22 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.003 0.000 HIS A 292 PHE 0.014 0.001 PHE B 289 TYR 0.017 0.001 TYR B 280 ARG 0.006 0.001 ARG A 990 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 1166) hydrogen bonds : angle 4.05206 ( 3447) covalent geometry : bond 0.00307 (15404) covalent geometry : angle 0.56728 (20912) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 538 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.8648 (m) cc_final: 0.8347 (p) REVERT: A 137 VAL cc_start: 0.8755 (p) cc_final: 0.8525 (t) REVERT: A 140 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8060 (mp10) REVERT: A 175 VAL cc_start: 0.8525 (p) cc_final: 0.8192 (m) REVERT: A 195 PHE cc_start: 0.7894 (t80) cc_final: 0.7585 (t80) REVERT: A 231 GLU cc_start: 0.8144 (tt0) cc_final: 0.7896 (mt-10) REVERT: A 233 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7656 (tm-30) REVERT: A 267 TYR cc_start: 0.8578 (t80) cc_final: 0.8306 (t80) REVERT: A 284 LYS cc_start: 0.8707 (mmtm) cc_final: 0.8481 (mmmm) REVERT: A 291 SER cc_start: 0.8595 (t) cc_final: 0.8329 (p) REVERT: A 346 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7457 (mt-10) REVERT: A 395 ILE cc_start: 0.8196 (tt) cc_final: 0.7812 (pt) REVERT: A 443 GLU cc_start: 0.7988 (tp30) cc_final: 0.7691 (tp30) REVERT: A 444 ASN cc_start: 0.8794 (t0) cc_final: 0.8472 (t0) REVERT: A 500 ARG cc_start: 0.8369 (mmm-85) cc_final: 0.8156 (tpp80) REVERT: A 580 GLU cc_start: 0.7965 (tp30) cc_final: 0.7507 (tp30) REVERT: A 583 ARG cc_start: 0.8254 (ttp-170) cc_final: 0.7978 (ttp-170) REVERT: A 584 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8087 (mm) REVERT: A 588 LYS cc_start: 0.8596 (tttm) cc_final: 0.8254 (tttm) REVERT: A 592 ILE cc_start: 0.8781 (mt) cc_final: 0.8353 (mm) REVERT: A 609 ARG cc_start: 0.7796 (mtp-110) cc_final: 0.7502 (mtp-110) REVERT: A 613 GLN cc_start: 0.7753 (mt0) cc_final: 0.7487 (mt0) REVERT: A 614 HIS cc_start: 0.7713 (m-70) cc_final: 0.7496 (m-70) REVERT: A 624 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7446 (pp30) REVERT: A 641 TYR cc_start: 0.8022 (m-80) cc_final: 0.7535 (m-80) REVERT: A 643 TRP cc_start: 0.7815 (t-100) cc_final: 0.7201 (t-100) REVERT: A 647 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8133 (pttm) REVERT: A 810 MET cc_start: 0.7290 (ppp) cc_final: 0.6902 (tmm) REVERT: A 828 LYS cc_start: 0.8407 (mmmt) cc_final: 0.8177 (mmmt) REVERT: A 832 GLN cc_start: 0.8751 (tp40) cc_final: 0.8447 (tp40) REVERT: A 837 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7726 (t80) REVERT: A 841 LYS cc_start: 0.8456 (mtpt) cc_final: 0.8125 (mtpp) REVERT: A 847 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7619 (mm-30) REVERT: A 850 VAL cc_start: 0.8910 (p) cc_final: 0.8675 (m) REVERT: A 864 LEU cc_start: 0.8096 (tp) cc_final: 0.7849 (tp) REVERT: A 865 ARG cc_start: 0.7204 (mmm160) cc_final: 0.6981 (mmm160) REVERT: A 866 GLU cc_start: 0.8286 (tp30) cc_final: 0.7887 (tp30) REVERT: A 871 SER cc_start: 0.8264 (t) cc_final: 0.7736 (p) REVERT: A 878 VAL cc_start: 0.8900 (t) cc_final: 0.8659 (t) REVERT: A 921 LEU cc_start: 0.8357 (mm) cc_final: 0.8110 (mp) REVERT: A 926 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7445 (mp0) REVERT: A 932 LEU cc_start: 0.8478 (tt) cc_final: 0.8207 (tp) REVERT: A 958 LYS cc_start: 0.8592 (ttpt) cc_final: 0.8171 (ttpt) REVERT: A 976 ARG cc_start: 0.7888 (tpp80) cc_final: 0.7592 (ttm170) REVERT: A 999 PHE cc_start: 0.8121 (m-80) cc_final: 0.7770 (m-80) REVERT: A 1003 SER cc_start: 0.8580 (t) cc_final: 0.8253 (m) REVERT: A 1045 MET cc_start: 0.8625 (mmm) cc_final: 0.8397 (mmm) REVERT: A 1058 THR cc_start: 0.8546 (p) cc_final: 0.8289 (p) REVERT: A 1063 VAL cc_start: 0.8559 (t) cc_final: 0.8236 (p) REVERT: A 1077 ILE cc_start: 0.8768 (mm) cc_final: 0.8514 (mm) REVERT: A 1098 ILE cc_start: 0.9104 (tp) cc_final: 0.8782 (tt) REVERT: A 1100 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8577 (m) REVERT: A 1103 ILE cc_start: 0.8547 (mm) cc_final: 0.8287 (mm) REVERT: A 1104 MET cc_start: 0.7931 (tpt) cc_final: 0.7608 (tpp) REVERT: A 1105 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8108 (tm-30) REVERT: A 1107 MET cc_start: 0.7246 (tmm) cc_final: 0.6232 (tmm) REVERT: A 1122 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7653 (tp30) REVERT: A 1166 LEU cc_start: 0.7774 (tp) cc_final: 0.7497 (tp) REVERT: B 91 SER cc_start: 0.8672 (m) cc_final: 0.8431 (p) REVERT: B 109 LEU cc_start: 0.8491 (mp) cc_final: 0.8289 (mp) REVERT: B 140 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8063 (mp10) REVERT: B 160 MET cc_start: 0.8469 (mmt) cc_final: 0.8231 (mmm) REVERT: B 190 ASN cc_start: 0.7729 (p0) cc_final: 0.7409 (p0) REVERT: B 214 VAL cc_start: 0.8688 (t) cc_final: 0.8479 (p) REVERT: B 217 LEU cc_start: 0.8730 (mt) cc_final: 0.8334 (mp) REVERT: B 238 ASP cc_start: 0.7288 (m-30) cc_final: 0.6974 (m-30) REVERT: B 267 TYR cc_start: 0.8453 (t80) cc_final: 0.8224 (t80) REVERT: B 319 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.8000 (mp) REVERT: B 335 ASN cc_start: 0.8558 (t0) cc_final: 0.8253 (t0) REVERT: B 392 TYR cc_start: 0.8602 (t80) cc_final: 0.8376 (t80) REVERT: B 443 GLU cc_start: 0.7921 (tp30) cc_final: 0.7525 (tp30) REVERT: B 444 ASN cc_start: 0.8876 (t0) cc_final: 0.8493 (t0) REVERT: B 476 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8563 (m) REVERT: B 485 ASP cc_start: 0.8252 (t0) cc_final: 0.7996 (t0) REVERT: B 486 ILE cc_start: 0.8534 (mm) cc_final: 0.8183 (mm) REVERT: B 517 PHE cc_start: 0.8300 (m-10) cc_final: 0.8002 (m-10) REVERT: B 520 ASP cc_start: 0.8044 (p0) cc_final: 0.7821 (p0) REVERT: B 579 MET cc_start: 0.7475 (tpt) cc_final: 0.7213 (tpt) REVERT: B 580 GLU cc_start: 0.7991 (tp30) cc_final: 0.7543 (tp30) REVERT: B 581 GLU cc_start: 0.7286 (tp30) cc_final: 0.6576 (tp30) REVERT: B 585 ARG cc_start: 0.8169 (ttm-80) cc_final: 0.7623 (ttm110) REVERT: B 587 LEU cc_start: 0.8791 (mt) cc_final: 0.8557 (mt) REVERT: B 588 LYS cc_start: 0.8407 (tttm) cc_final: 0.7991 (tttm) REVERT: B 592 ILE cc_start: 0.8728 (mt) cc_final: 0.8360 (mm) REVERT: B 617 VAL cc_start: 0.7955 (t) cc_final: 0.7295 (m) REVERT: B 620 ASP cc_start: 0.7705 (t70) cc_final: 0.7383 (t70) REVERT: B 621 GLU cc_start: 0.7334 (mp0) cc_final: 0.6602 (mp0) REVERT: B 828 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8281 (mmtt) REVERT: B 832 GLN cc_start: 0.8713 (tp40) cc_final: 0.8471 (tp40) REVERT: B 835 LEU cc_start: 0.8755 (tp) cc_final: 0.8541 (tt) REVERT: B 837 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.7823 (t80) REVERT: B 839 VAL cc_start: 0.8881 (t) cc_final: 0.8637 (t) REVERT: B 841 LYS cc_start: 0.8474 (mtpt) cc_final: 0.8162 (mtpp) REVERT: B 845 ILE cc_start: 0.8843 (mm) cc_final: 0.8498 (mt) REVERT: B 850 VAL cc_start: 0.8895 (p) cc_final: 0.8647 (m) REVERT: B 866 GLU cc_start: 0.8331 (tp30) cc_final: 0.7697 (tm-30) REVERT: B 870 ILE cc_start: 0.8620 (mm) cc_final: 0.8126 (mm) REVERT: B 879 VAL cc_start: 0.8964 (p) cc_final: 0.8747 (t) REVERT: B 911 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7830 (mp0) REVERT: B 921 LEU cc_start: 0.8346 (mm) cc_final: 0.8071 (mp) REVERT: B 976 ARG cc_start: 0.7785 (ttm-80) cc_final: 0.7091 (ttm170) REVERT: B 991 GLU cc_start: 0.7632 (tp30) cc_final: 0.7287 (tp30) REVERT: B 999 PHE cc_start: 0.8157 (m-80) cc_final: 0.7761 (m-80) REVERT: B 1045 MET cc_start: 0.8510 (ttm) cc_final: 0.8296 (tpp) REVERT: B 1058 THR cc_start: 0.8584 (p) cc_final: 0.8344 (p) REVERT: B 1072 ASP cc_start: 0.7699 (t70) cc_final: 0.6733 (t70) REVERT: B 1098 ILE cc_start: 0.9075 (tp) cc_final: 0.8788 (tt) REVERT: B 1104 MET cc_start: 0.8179 (tpp) cc_final: 0.7874 (tpp) REVERT: B 1145 VAL cc_start: 0.8560 (t) cc_final: 0.8295 (p) outliers start: 77 outliers final: 53 residues processed: 575 average time/residue: 0.2668 time to fit residues: 222.1253 Evaluate side-chains 589 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 526 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1146 ILE Chi-restraints excluded: chain B residue 1161 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 184 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 GLN B 157 HIS B 165 GLN B 981 HIS B1154 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.132897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113917 restraints weight = 23525.452| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.14 r_work: 0.3358 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15404 Z= 0.156 Angle : 0.578 9.072 20912 Z= 0.297 Chirality : 0.041 0.250 2526 Planarity : 0.004 0.031 2600 Dihedral : 4.484 56.303 2096 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.45 % Allowed : 25.79 % Favored : 68.76 % 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: 1.68 (0.20), residues: 1938 helix: 1.82 (0.14), residues: 1422 sheet: 0.05 (0.57), residues: 96 loop : -1.08 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.004 0.001 HIS B 981 PHE 0.031 0.001 PHE A 625 TYR 0.018 0.001 TYR A 280 ARG 0.006 0.001 ARG A 903 Details of bonding type rmsd hydrogen bonds : bond 0.04479 ( 1166) hydrogen bonds : angle 4.07489 ( 3447) covalent geometry : bond 0.00337 (15404) covalent geometry : angle 0.57807 (20912) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 532 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.8649 (m) cc_final: 0.8334 (p) REVERT: A 129 ASP cc_start: 0.6364 (OUTLIER) cc_final: 0.5981 (p0) REVERT: A 137 VAL cc_start: 0.8693 (p) cc_final: 0.8407 (t) REVERT: A 140 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7986 (mp10) REVERT: A 175 VAL cc_start: 0.8529 (p) cc_final: 0.8202 (m) REVERT: A 176 VAL cc_start: 0.8745 (p) cc_final: 0.8533 (t) REVERT: A 195 PHE cc_start: 0.7928 (t80) cc_final: 0.7653 (t80) REVERT: A 217 LEU cc_start: 0.8625 (mt) cc_final: 0.8395 (mm) REVERT: A 231 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7927 (mt-10) REVERT: A 233 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7569 (tm-30) REVERT: A 263 GLN cc_start: 0.7990 (mt0) cc_final: 0.7672 (mt0) REVERT: A 267 TYR cc_start: 0.8605 (t80) cc_final: 0.8375 (t80) REVERT: A 284 LYS cc_start: 0.8711 (mmtm) cc_final: 0.8473 (mmmm) REVERT: A 346 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7451 (mt-10) REVERT: A 395 ILE cc_start: 0.8142 (tt) cc_final: 0.7814 (pt) REVERT: A 443 GLU cc_start: 0.7957 (tp30) cc_final: 0.7659 (tp30) REVERT: A 500 ARG cc_start: 0.8313 (mmm-85) cc_final: 0.8108 (tpp80) REVERT: A 583 ARG cc_start: 0.8271 (ttp-170) cc_final: 0.8049 (ttp-170) REVERT: A 588 LYS cc_start: 0.8624 (tttm) cc_final: 0.8291 (tttm) REVERT: A 592 ILE cc_start: 0.8790 (mt) cc_final: 0.8374 (mm) REVERT: A 609 ARG cc_start: 0.7781 (mtp-110) cc_final: 0.7497 (mtp-110) REVERT: A 613 GLN cc_start: 0.7777 (mt0) cc_final: 0.7499 (mt0) REVERT: A 624 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7238 (pp30) REVERT: A 643 TRP cc_start: 0.7820 (t-100) cc_final: 0.7235 (t-100) REVERT: A 647 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8194 (pttm) REVERT: A 810 MET cc_start: 0.7273 (ppp) cc_final: 0.6893 (tmm) REVERT: A 828 LYS cc_start: 0.8430 (mmmt) cc_final: 0.8087 (mmmt) REVERT: A 832 GLN cc_start: 0.8763 (tp40) cc_final: 0.8452 (tp-100) REVERT: A 837 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.7751 (t80) REVERT: A 841 LYS cc_start: 0.8470 (mtpt) cc_final: 0.8174 (mtpp) REVERT: A 845 ILE cc_start: 0.8868 (mm) cc_final: 0.8655 (mt) REVERT: A 847 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7673 (mm-30) REVERT: A 850 VAL cc_start: 0.8890 (p) cc_final: 0.8680 (m) REVERT: A 864 LEU cc_start: 0.8142 (tp) cc_final: 0.7927 (tp) REVERT: A 865 ARG cc_start: 0.7285 (mmm160) cc_final: 0.7045 (mmm160) REVERT: A 866 GLU cc_start: 0.8271 (tp30) cc_final: 0.7911 (tp30) REVERT: A 867 LEU cc_start: 0.8286 (mt) cc_final: 0.8053 (mm) REVERT: A 868 LYS cc_start: 0.7840 (mmtp) cc_final: 0.7095 (mmtp) REVERT: A 871 SER cc_start: 0.8299 (t) cc_final: 0.7685 (p) REVERT: A 878 VAL cc_start: 0.8900 (t) cc_final: 0.8654 (t) REVERT: A 921 LEU cc_start: 0.8371 (mm) cc_final: 0.8144 (mp) REVERT: A 932 LEU cc_start: 0.8538 (tt) cc_final: 0.8295 (tp) REVERT: A 958 LYS cc_start: 0.8646 (ttpt) cc_final: 0.8266 (ttpt) REVERT: A 974 LYS cc_start: 0.9014 (ttpt) cc_final: 0.8749 (tppt) REVERT: A 976 ARG cc_start: 0.7895 (tpp80) cc_final: 0.7630 (ttm170) REVERT: A 1045 MET cc_start: 0.8669 (mmm) cc_final: 0.8449 (mmm) REVERT: A 1058 THR cc_start: 0.8553 (p) cc_final: 0.8309 (p) REVERT: A 1063 VAL cc_start: 0.8537 (t) cc_final: 0.8209 (p) REVERT: A 1067 PHE cc_start: 0.8035 (t80) cc_final: 0.7800 (t80) REVERT: A 1073 MET cc_start: 0.8683 (mmm) cc_final: 0.8463 (mmm) REVERT: A 1077 ILE cc_start: 0.8838 (mm) cc_final: 0.8592 (mm) REVERT: A 1098 ILE cc_start: 0.9100 (tp) cc_final: 0.8795 (tt) REVERT: A 1100 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8597 (m) REVERT: A 1103 ILE cc_start: 0.8586 (mm) cc_final: 0.8338 (mm) REVERT: A 1104 MET cc_start: 0.7962 (tpt) cc_final: 0.7548 (tpp) REVERT: A 1105 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8175 (tm-30) REVERT: A 1107 MET cc_start: 0.7371 (tmm) cc_final: 0.6353 (tmm) REVERT: A 1122 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7576 (tp30) REVERT: A 1166 LEU cc_start: 0.7785 (tp) cc_final: 0.7553 (tp) REVERT: B 91 SER cc_start: 0.8641 (m) cc_final: 0.8434 (p) REVERT: B 140 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8036 (mp10) REVERT: B 141 ILE cc_start: 0.8707 (mm) cc_final: 0.8392 (mt) REVERT: B 154 MET cc_start: 0.8583 (tpp) cc_final: 0.8025 (tpp) REVERT: B 155 ASP cc_start: 0.8422 (t0) cc_final: 0.8043 (t0) REVERT: B 160 MET cc_start: 0.8478 (mmt) cc_final: 0.8248 (mmm) REVERT: B 190 ASN cc_start: 0.7743 (p0) cc_final: 0.7420 (p0) REVERT: B 214 VAL cc_start: 0.8693 (t) cc_final: 0.8464 (p) REVERT: B 217 LEU cc_start: 0.8738 (mt) cc_final: 0.8323 (mp) REVERT: B 238 ASP cc_start: 0.7333 (m-30) cc_final: 0.7018 (m-30) REVERT: B 267 TYR cc_start: 0.8541 (t80) cc_final: 0.8292 (t80) REVERT: B 296 ASP cc_start: 0.7435 (p0) cc_final: 0.7126 (p0) REVERT: B 335 ASN cc_start: 0.8524 (t0) cc_final: 0.8309 (t0) REVERT: B 337 GLU cc_start: 0.7997 (mp0) cc_final: 0.7644 (mp0) REVERT: B 392 TYR cc_start: 0.8598 (t80) cc_final: 0.8397 (t80) REVERT: B 443 GLU cc_start: 0.7916 (tp30) cc_final: 0.7515 (tp30) REVERT: B 444 ASN cc_start: 0.8894 (t0) cc_final: 0.8498 (t0) REVERT: B 476 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8600 (m) REVERT: B 485 ASP cc_start: 0.8279 (t0) cc_final: 0.8024 (t0) REVERT: B 486 ILE cc_start: 0.8533 (mm) cc_final: 0.8202 (mm) REVERT: B 517 PHE cc_start: 0.8311 (m-10) cc_final: 0.8023 (m-10) REVERT: B 520 ASP cc_start: 0.7997 (p0) cc_final: 0.7759 (p0) REVERT: B 579 MET cc_start: 0.7494 (tpt) cc_final: 0.7234 (tpt) REVERT: B 580 GLU cc_start: 0.7955 (tp30) cc_final: 0.7532 (tp30) REVERT: B 581 GLU cc_start: 0.7329 (tp30) cc_final: 0.6599 (tp30) REVERT: B 585 ARG cc_start: 0.8237 (ttm-80) cc_final: 0.7701 (ttm110) REVERT: B 587 LEU cc_start: 0.8784 (mt) cc_final: 0.8568 (mt) REVERT: B 588 LYS cc_start: 0.8421 (tttm) cc_final: 0.8014 (tttm) REVERT: B 592 ILE cc_start: 0.8729 (mt) cc_final: 0.8371 (mm) REVERT: B 617 VAL cc_start: 0.7957 (t) cc_final: 0.7334 (m) REVERT: B 620 ASP cc_start: 0.7683 (t70) cc_final: 0.7409 (t70) REVERT: B 621 GLU cc_start: 0.7315 (mp0) cc_final: 0.6664 (mp0) REVERT: B 832 GLN cc_start: 0.8695 (tp40) cc_final: 0.8481 (tp40) REVERT: B 835 LEU cc_start: 0.8760 (tp) cc_final: 0.8559 (tt) REVERT: B 837 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.7820 (t80) REVERT: B 839 VAL cc_start: 0.8908 (t) cc_final: 0.8671 (t) REVERT: B 841 LYS cc_start: 0.8520 (mtpt) cc_final: 0.8220 (mtpp) REVERT: B 845 ILE cc_start: 0.8906 (mm) cc_final: 0.8608 (mt) REVERT: B 850 VAL cc_start: 0.8881 (p) cc_final: 0.8638 (m) REVERT: B 866 GLU cc_start: 0.8349 (tp30) cc_final: 0.7747 (tm-30) REVERT: B 870 ILE cc_start: 0.8650 (mm) cc_final: 0.8135 (mm) REVERT: B 879 VAL cc_start: 0.8980 (p) cc_final: 0.8749 (t) REVERT: B 921 LEU cc_start: 0.8412 (mm) cc_final: 0.8115 (mp) REVERT: B 931 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7757 (mm-30) REVERT: B 974 LYS cc_start: 0.9026 (ttpt) cc_final: 0.8655 (tppt) REVERT: B 976 ARG cc_start: 0.7768 (ttm-80) cc_final: 0.7344 (ttm-80) REVERT: B 991 GLU cc_start: 0.7687 (tp30) cc_final: 0.7352 (tp30) REVERT: B 999 PHE cc_start: 0.8180 (m-80) cc_final: 0.7778 (m-80) REVERT: B 1045 MET cc_start: 0.8495 (ttm) cc_final: 0.8265 (mmm) REVERT: B 1098 ILE cc_start: 0.9075 (tp) cc_final: 0.8808 (tt) REVERT: B 1104 MET cc_start: 0.8209 (tpp) cc_final: 0.7921 (tpp) outliers start: 86 outliers final: 57 residues processed: 574 average time/residue: 0.2849 time to fit residues: 234.8909 Evaluate side-chains 586 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 519 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 865 ARG Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1146 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 33 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 181 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 171 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 GLN B 157 HIS B 165 GLN B 981 HIS B1154 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.132528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.113657 restraints weight = 23572.108| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.15 r_work: 0.3350 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15404 Z= 0.156 Angle : 0.588 8.666 20912 Z= 0.301 Chirality : 0.041 0.249 2526 Planarity : 0.004 0.034 2600 Dihedral : 4.488 56.507 2096 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.20 % Allowed : 26.43 % Favored : 68.38 % 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: 1.68 (0.20), residues: 1938 helix: 1.83 (0.14), residues: 1422 sheet: 0.05 (0.57), residues: 96 loop : -1.08 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.005 0.001 HIS B 889 PHE 0.019 0.001 PHE A 625 TYR 0.018 0.001 TYR A 280 ARG 0.006 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 1166) hydrogen bonds : angle 4.06964 ( 3447) covalent geometry : bond 0.00339 (15404) covalent geometry : angle 0.58838 (20912) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 532 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.8639 (m) cc_final: 0.8311 (p) REVERT: A 129 ASP cc_start: 0.6336 (OUTLIER) cc_final: 0.5956 (p0) REVERT: A 137 VAL cc_start: 0.8681 (p) cc_final: 0.8385 (t) REVERT: A 140 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7986 (mp10) REVERT: A 175 VAL cc_start: 0.8525 (p) cc_final: 0.8209 (m) REVERT: A 176 VAL cc_start: 0.8738 (p) cc_final: 0.8534 (t) REVERT: A 195 PHE cc_start: 0.7931 (t80) cc_final: 0.7656 (t80) REVERT: A 231 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7969 (mt-10) REVERT: A 233 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7551 (tm-30) REVERT: A 263 GLN cc_start: 0.7961 (mt0) cc_final: 0.7634 (mt0) REVERT: A 267 TYR cc_start: 0.8604 (t80) cc_final: 0.8366 (t80) REVERT: A 284 LYS cc_start: 0.8704 (mmtm) cc_final: 0.8466 (mmmm) REVERT: A 346 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7433 (mt-10) REVERT: A 395 ILE cc_start: 0.8198 (tt) cc_final: 0.7842 (pt) REVERT: A 425 MET cc_start: 0.8546 (mtm) cc_final: 0.8329 (mtm) REVERT: A 443 GLU cc_start: 0.7965 (tp30) cc_final: 0.7663 (tp30) REVERT: A 500 ARG cc_start: 0.8330 (mmm-85) cc_final: 0.8126 (tpp80) REVERT: A 579 MET cc_start: 0.7518 (tmm) cc_final: 0.7271 (tmm) REVERT: A 588 LYS cc_start: 0.8674 (tttm) cc_final: 0.8331 (tttm) REVERT: A 592 ILE cc_start: 0.8800 (mt) cc_final: 0.8392 (mm) REVERT: A 609 ARG cc_start: 0.7758 (mtp-110) cc_final: 0.7471 (mtp-110) REVERT: A 613 GLN cc_start: 0.7801 (mt0) cc_final: 0.7531 (mt0) REVERT: A 624 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7554 (pp30) REVERT: A 641 TYR cc_start: 0.8072 (m-80) cc_final: 0.7611 (m-80) REVERT: A 647 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8194 (pttm) REVERT: A 810 MET cc_start: 0.7286 (ppp) cc_final: 0.6903 (tmm) REVERT: A 828 LYS cc_start: 0.8434 (mmmt) cc_final: 0.8127 (mmmt) REVERT: A 832 GLN cc_start: 0.8778 (tp40) cc_final: 0.8450 (tp-100) REVERT: A 837 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7667 (t80) REVERT: A 841 LYS cc_start: 0.8439 (mtpt) cc_final: 0.8138 (mtpp) REVERT: A 845 ILE cc_start: 0.8865 (mm) cc_final: 0.8662 (mt) REVERT: A 857 MET cc_start: 0.7635 (tmm) cc_final: 0.7407 (tpp) REVERT: A 864 LEU cc_start: 0.8149 (tp) cc_final: 0.7943 (tp) REVERT: A 865 ARG cc_start: 0.7348 (mmm160) cc_final: 0.7108 (mmm160) REVERT: A 866 GLU cc_start: 0.8240 (tp30) cc_final: 0.7889 (tp30) REVERT: A 867 LEU cc_start: 0.8288 (mt) cc_final: 0.8028 (mm) REVERT: A 868 LYS cc_start: 0.7882 (mmtp) cc_final: 0.7115 (mmtp) REVERT: A 871 SER cc_start: 0.8301 (t) cc_final: 0.7683 (p) REVERT: A 878 VAL cc_start: 0.8887 (t) cc_final: 0.8649 (t) REVERT: A 921 LEU cc_start: 0.8371 (mm) cc_final: 0.8135 (mp) REVERT: A 958 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8272 (ttpt) REVERT: A 974 LYS cc_start: 0.9000 (ttpt) cc_final: 0.8716 (tppt) REVERT: A 976 ARG cc_start: 0.7932 (tpp80) cc_final: 0.7701 (tpp80) REVERT: A 999 PHE cc_start: 0.8194 (m-80) cc_final: 0.7927 (m-10) REVERT: A 1045 MET cc_start: 0.8660 (mmm) cc_final: 0.8431 (mmm) REVERT: A 1058 THR cc_start: 0.8588 (p) cc_final: 0.8343 (p) REVERT: A 1063 VAL cc_start: 0.8566 (t) cc_final: 0.8227 (p) REVERT: A 1073 MET cc_start: 0.8685 (mmm) cc_final: 0.8469 (mmm) REVERT: A 1077 ILE cc_start: 0.8822 (mm) cc_final: 0.8580 (mm) REVERT: A 1078 ASP cc_start: 0.7760 (m-30) cc_final: 0.7449 (m-30) REVERT: A 1098 ILE cc_start: 0.9052 (tp) cc_final: 0.8802 (tt) REVERT: A 1100 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8598 (m) REVERT: A 1103 ILE cc_start: 0.8597 (mm) cc_final: 0.8342 (mm) REVERT: A 1104 MET cc_start: 0.7967 (tpt) cc_final: 0.7577 (tpp) REVERT: A 1105 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8165 (tm-30) REVERT: A 1107 MET cc_start: 0.7471 (tmm) cc_final: 0.5886 (tmm) REVERT: A 1122 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7563 (tp30) REVERT: A 1166 LEU cc_start: 0.7796 (tp) cc_final: 0.7566 (tp) REVERT: B 91 SER cc_start: 0.8662 (m) cc_final: 0.8427 (p) REVERT: B 140 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8030 (mp10) REVERT: B 141 ILE cc_start: 0.8690 (mm) cc_final: 0.8377 (mt) REVERT: B 154 MET cc_start: 0.8565 (tpp) cc_final: 0.7987 (tpp) REVERT: B 155 ASP cc_start: 0.8399 (t0) cc_final: 0.8036 (t0) REVERT: B 160 MET cc_start: 0.8468 (mmt) cc_final: 0.8233 (mmm) REVERT: B 190 ASN cc_start: 0.7770 (p0) cc_final: 0.7441 (p0) REVERT: B 214 VAL cc_start: 0.8703 (t) cc_final: 0.8478 (p) REVERT: B 217 LEU cc_start: 0.8751 (mt) cc_final: 0.8339 (mp) REVERT: B 238 ASP cc_start: 0.7371 (m-30) cc_final: 0.7032 (m-30) REVERT: B 267 TYR cc_start: 0.8526 (t80) cc_final: 0.8265 (t80) REVERT: B 335 ASN cc_start: 0.8637 (t0) cc_final: 0.8327 (t0) REVERT: B 337 GLU cc_start: 0.8033 (mp0) cc_final: 0.7626 (mp0) REVERT: B 355 MET cc_start: 0.8418 (ttp) cc_final: 0.8216 (ttp) REVERT: B 443 GLU cc_start: 0.7929 (tp30) cc_final: 0.7527 (tp30) REVERT: B 444 ASN cc_start: 0.8889 (t0) cc_final: 0.8478 (t0) REVERT: B 476 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8587 (m) REVERT: B 485 ASP cc_start: 0.8267 (t0) cc_final: 0.8025 (t0) REVERT: B 486 ILE cc_start: 0.8527 (mm) cc_final: 0.8269 (mm) REVERT: B 517 PHE cc_start: 0.8273 (m-10) cc_final: 0.7997 (m-10) REVERT: B 520 ASP cc_start: 0.7992 (p0) cc_final: 0.7761 (p0) REVERT: B 531 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7471 (tm-30) REVERT: B 579 MET cc_start: 0.7518 (tpt) cc_final: 0.7262 (tpt) REVERT: B 580 GLU cc_start: 0.7938 (tp30) cc_final: 0.7239 (tp30) REVERT: B 581 GLU cc_start: 0.7338 (tp30) cc_final: 0.6607 (tp30) REVERT: B 584 LEU cc_start: 0.8480 (mm) cc_final: 0.7911 (mm) REVERT: B 588 LYS cc_start: 0.8399 (tttm) cc_final: 0.7983 (tttm) REVERT: B 592 ILE cc_start: 0.8740 (mt) cc_final: 0.8404 (mm) REVERT: B 617 VAL cc_start: 0.7918 (t) cc_final: 0.7332 (m) REVERT: B 620 ASP cc_start: 0.7658 (t70) cc_final: 0.7393 (t70) REVERT: B 621 GLU cc_start: 0.7317 (mp0) cc_final: 0.6656 (mp0) REVERT: B 832 GLN cc_start: 0.8661 (tp40) cc_final: 0.8450 (tp40) REVERT: B 835 LEU cc_start: 0.8758 (tp) cc_final: 0.8556 (tt) REVERT: B 837 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7846 (t80) REVERT: B 839 VAL cc_start: 0.8886 (t) cc_final: 0.8671 (t) REVERT: B 841 LYS cc_start: 0.8586 (mtpt) cc_final: 0.8273 (mtpp) REVERT: B 845 ILE cc_start: 0.8920 (mm) cc_final: 0.8629 (mt) REVERT: B 850 VAL cc_start: 0.8868 (p) cc_final: 0.8640 (m) REVERT: B 866 GLU cc_start: 0.8244 (tp30) cc_final: 0.7668 (tm-30) REVERT: B 870 ILE cc_start: 0.8647 (mm) cc_final: 0.8004 (mm) REVERT: B 871 SER cc_start: 0.8286 (t) cc_final: 0.8006 (t) REVERT: B 877 GLN cc_start: 0.8733 (tt0) cc_final: 0.8475 (tt0) REVERT: B 879 VAL cc_start: 0.8970 (p) cc_final: 0.8743 (t) REVERT: B 921 LEU cc_start: 0.8429 (mm) cc_final: 0.8144 (mp) REVERT: B 959 ASN cc_start: 0.8253 (m-40) cc_final: 0.7957 (m-40) REVERT: B 974 LYS cc_start: 0.9033 (ttpt) cc_final: 0.8627 (tppt) REVERT: B 976 ARG cc_start: 0.7759 (ttm-80) cc_final: 0.7425 (ttm110) REVERT: B 991 GLU cc_start: 0.7775 (tp30) cc_final: 0.7386 (tp30) REVERT: B 999 PHE cc_start: 0.8197 (m-80) cc_final: 0.7808 (m-80) REVERT: B 1078 ASP cc_start: 0.7802 (m-30) cc_final: 0.7524 (m-30) REVERT: B 1098 ILE cc_start: 0.9074 (tp) cc_final: 0.8801 (tt) REVERT: B 1104 MET cc_start: 0.8270 (tpp) cc_final: 0.8000 (tpp) outliers start: 82 outliers final: 62 residues processed: 570 average time/residue: 0.2781 time to fit residues: 227.8505 Evaluate side-chains 596 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 524 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1050 LYS Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1146 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 3 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 0.0570 chunk 187 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 GLN B 157 HIS B 165 GLN B 981 HIS B1154 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.132443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.113763 restraints weight = 23402.232| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.11 r_work: 0.3357 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15404 Z= 0.150 Angle : 0.599 9.024 20912 Z= 0.304 Chirality : 0.042 0.278 2526 Planarity : 0.004 0.033 2600 Dihedral : 4.510 56.644 2096 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 5.01 % Allowed : 27.19 % Favored : 67.81 % 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: 1.72 (0.20), residues: 1938 helix: 1.86 (0.14), residues: 1420 sheet: 0.06 (0.56), residues: 96 loop : -1.06 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.006 0.001 HIS B 889 PHE 0.024 0.001 PHE A 625 TYR 0.019 0.001 TYR A 280 ARG 0.006 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04496 ( 1166) hydrogen bonds : angle 4.07445 ( 3447) covalent geometry : bond 0.00324 (15404) covalent geometry : angle 0.59907 (20912) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 523 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.8627 (m) cc_final: 0.8298 (p) REVERT: A 129 ASP cc_start: 0.6353 (OUTLIER) cc_final: 0.5953 (p0) REVERT: A 137 VAL cc_start: 0.8676 (p) cc_final: 0.8372 (t) REVERT: A 140 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7957 (mp10) REVERT: A 175 VAL cc_start: 0.8533 (p) cc_final: 0.8232 (m) REVERT: A 176 VAL cc_start: 0.8756 (p) cc_final: 0.8544 (t) REVERT: A 195 PHE cc_start: 0.7905 (t80) cc_final: 0.7637 (t80) REVERT: A 231 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: A 233 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7556 (tm-30) REVERT: A 267 TYR cc_start: 0.8620 (t80) cc_final: 0.8365 (t80) REVERT: A 284 LYS cc_start: 0.8693 (mmtm) cc_final: 0.8466 (mmmm) REVERT: A 346 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7402 (mt-10) REVERT: A 395 ILE cc_start: 0.8219 (tt) cc_final: 0.7868 (pt) REVERT: A 579 MET cc_start: 0.7504 (tmm) cc_final: 0.7247 (tmm) REVERT: A 583 ARG cc_start: 0.8248 (ttp-170) cc_final: 0.7831 (mtp180) REVERT: A 588 LYS cc_start: 0.8653 (tttm) cc_final: 0.8237 (tttm) REVERT: A 592 ILE cc_start: 0.8805 (mt) cc_final: 0.8403 (mm) REVERT: A 609 ARG cc_start: 0.7723 (mtp-110) cc_final: 0.7472 (mtp-110) REVERT: A 613 GLN cc_start: 0.7786 (mt0) cc_final: 0.7528 (mt0) REVERT: A 624 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7523 (pp30) REVERT: A 633 LYS cc_start: 0.8674 (mttm) cc_final: 0.8459 (mttt) REVERT: A 641 TYR cc_start: 0.8088 (m-80) cc_final: 0.7581 (m-80) REVERT: A 810 MET cc_start: 0.7259 (ppp) cc_final: 0.6906 (tmm) REVERT: A 828 LYS cc_start: 0.8438 (mmmt) cc_final: 0.8142 (mmmt) REVERT: A 832 GLN cc_start: 0.8790 (tp40) cc_final: 0.8457 (tp-100) REVERT: A 837 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.7696 (t80) REVERT: A 841 LYS cc_start: 0.8442 (mtpt) cc_final: 0.8150 (mtpp) REVERT: A 845 ILE cc_start: 0.8879 (mm) cc_final: 0.8672 (mt) REVERT: A 847 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7825 (mm-30) REVERT: A 865 ARG cc_start: 0.7298 (mmm160) cc_final: 0.7038 (mmm160) REVERT: A 866 GLU cc_start: 0.8238 (tp30) cc_final: 0.7871 (tp30) REVERT: A 868 LYS cc_start: 0.7918 (mmtp) cc_final: 0.7205 (mmtp) REVERT: A 871 SER cc_start: 0.8272 (t) cc_final: 0.7752 (p) REVERT: A 921 LEU cc_start: 0.8408 (mm) cc_final: 0.8135 (mp) REVERT: A 958 LYS cc_start: 0.8692 (ttpt) cc_final: 0.8249 (ttpt) REVERT: A 974 LYS cc_start: 0.9009 (ttpt) cc_final: 0.8720 (tppt) REVERT: A 976 ARG cc_start: 0.7874 (tpp80) cc_final: 0.7659 (tpp80) REVERT: A 986 GLU cc_start: 0.8221 (tt0) cc_final: 0.7939 (tt0) REVERT: A 989 VAL cc_start: 0.8303 (OUTLIER) cc_final: 0.8101 (t) REVERT: A 999 PHE cc_start: 0.8189 (m-80) cc_final: 0.7944 (m-10) REVERT: A 1045 MET cc_start: 0.8665 (mmm) cc_final: 0.8458 (mmm) REVERT: A 1058 THR cc_start: 0.8584 (p) cc_final: 0.8324 (p) REVERT: A 1063 VAL cc_start: 0.8608 (t) cc_final: 0.8296 (p) REVERT: A 1073 MET cc_start: 0.8692 (mmm) cc_final: 0.8470 (mmm) REVERT: A 1077 ILE cc_start: 0.8843 (mm) cc_final: 0.8601 (mm) REVERT: A 1078 ASP cc_start: 0.7782 (m-30) cc_final: 0.7468 (m-30) REVERT: A 1098 ILE cc_start: 0.9010 (tp) cc_final: 0.8809 (tt) REVERT: A 1100 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8604 (m) REVERT: A 1103 ILE cc_start: 0.8630 (mm) cc_final: 0.8422 (mm) REVERT: A 1104 MET cc_start: 0.7968 (tpt) cc_final: 0.7592 (tpp) REVERT: A 1105 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8145 (tm-30) REVERT: A 1107 MET cc_start: 0.7486 (tmm) cc_final: 0.5988 (tmm) REVERT: A 1122 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7610 (tp30) REVERT: A 1166 LEU cc_start: 0.7887 (tp) cc_final: 0.7652 (tp) REVERT: A 1174 LEU cc_start: 0.8299 (mt) cc_final: 0.8053 (mm) REVERT: B 91 SER cc_start: 0.8652 (m) cc_final: 0.8438 (p) REVERT: B 140 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8026 (mp10) REVERT: B 141 ILE cc_start: 0.8685 (mm) cc_final: 0.8384 (mt) REVERT: B 154 MET cc_start: 0.8588 (tpp) cc_final: 0.8007 (tpp) REVERT: B 155 ASP cc_start: 0.8383 (t0) cc_final: 0.8027 (t0) REVERT: B 160 MET cc_start: 0.8451 (mmt) cc_final: 0.8214 (mmm) REVERT: B 190 ASN cc_start: 0.7745 (p0) cc_final: 0.7417 (p0) REVERT: B 214 VAL cc_start: 0.8729 (t) cc_final: 0.8491 (p) REVERT: B 217 LEU cc_start: 0.8761 (mt) cc_final: 0.8349 (mp) REVERT: B 238 ASP cc_start: 0.7396 (m-30) cc_final: 0.7050 (m-30) REVERT: B 267 TYR cc_start: 0.8501 (t80) cc_final: 0.8252 (t80) REVERT: B 335 ASN cc_start: 0.8644 (t0) cc_final: 0.8371 (t0) REVERT: B 337 GLU cc_start: 0.8035 (mp0) cc_final: 0.7690 (mp0) REVERT: B 444 ASN cc_start: 0.8897 (t0) cc_final: 0.8446 (t0) REVERT: B 476 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8558 (m) REVERT: B 485 ASP cc_start: 0.8289 (t0) cc_final: 0.8046 (t0) REVERT: B 486 ILE cc_start: 0.8509 (mm) cc_final: 0.8261 (mm) REVERT: B 517 PHE cc_start: 0.8181 (m-10) cc_final: 0.7951 (m-10) REVERT: B 520 ASP cc_start: 0.7948 (p0) cc_final: 0.7711 (p0) REVERT: B 531 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7478 (tm-30) REVERT: B 579 MET cc_start: 0.7508 (tpt) cc_final: 0.7254 (tpt) REVERT: B 580 GLU cc_start: 0.7954 (tp30) cc_final: 0.7616 (tp30) REVERT: B 581 GLU cc_start: 0.7308 (tp30) cc_final: 0.6646 (tp30) REVERT: B 585 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7635 (ttm110) REVERT: B 588 LYS cc_start: 0.8414 (tttm) cc_final: 0.7990 (tttm) REVERT: B 592 ILE cc_start: 0.8729 (mt) cc_final: 0.8402 (mm) REVERT: B 617 VAL cc_start: 0.7887 (t) cc_final: 0.7295 (m) REVERT: B 621 GLU cc_start: 0.7375 (mp0) cc_final: 0.6809 (mp0) REVERT: B 832 GLN cc_start: 0.8572 (tp40) cc_final: 0.8349 (tp40) REVERT: B 835 LEU cc_start: 0.8754 (tp) cc_final: 0.8541 (tt) REVERT: B 837 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.7841 (t80) REVERT: B 839 VAL cc_start: 0.8925 (t) cc_final: 0.8695 (t) REVERT: B 841 LYS cc_start: 0.8586 (mtpt) cc_final: 0.8235 (mtpp) REVERT: B 845 ILE cc_start: 0.8926 (mm) cc_final: 0.8630 (mt) REVERT: B 850 VAL cc_start: 0.8897 (p) cc_final: 0.8650 (m) REVERT: B 865 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7232 (mmm160) REVERT: B 866 GLU cc_start: 0.8148 (tp30) cc_final: 0.7713 (tm-30) REVERT: B 870 ILE cc_start: 0.8632 (mm) cc_final: 0.8055 (mm) REVERT: B 871 SER cc_start: 0.8275 (t) cc_final: 0.8006 (t) REVERT: B 879 VAL cc_start: 0.8988 (p) cc_final: 0.8763 (t) REVERT: B 921 LEU cc_start: 0.8394 (mm) cc_final: 0.8120 (mp) REVERT: B 959 ASN cc_start: 0.8244 (m-40) cc_final: 0.7933 (m-40) REVERT: B 974 LYS cc_start: 0.9034 (ttpt) cc_final: 0.8642 (tppt) REVERT: B 976 ARG cc_start: 0.7750 (ttm-80) cc_final: 0.7300 (ttm-80) REVERT: B 991 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7201 (tp30) REVERT: B 999 PHE cc_start: 0.8182 (m-80) cc_final: 0.7809 (m-80) REVERT: B 1078 ASP cc_start: 0.7799 (m-30) cc_final: 0.7492 (m-30) REVERT: B 1098 ILE cc_start: 0.9082 (tp) cc_final: 0.8790 (tt) REVERT: B 1104 MET cc_start: 0.8307 (tpp) cc_final: 0.8063 (tpp) outliers start: 79 outliers final: 61 residues processed: 560 average time/residue: 0.2736 time to fit residues: 220.1906 Evaluate side-chains 594 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 521 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 888 GLU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1050 LYS Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 865 ARG Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 991 GLU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1146 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 70 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 128 optimal weight: 0.0870 chunk 112 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 GLN B 157 HIS B 165 GLN B 981 HIS B1154 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.132179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.113580 restraints weight = 23378.854| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.11 r_work: 0.3354 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15404 Z= 0.154 Angle : 0.611 9.177 20912 Z= 0.309 Chirality : 0.043 0.322 2526 Planarity : 0.004 0.033 2600 Dihedral : 4.516 56.677 2096 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 5.01 % Allowed : 27.63 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.20), residues: 1938 helix: 1.84 (0.14), residues: 1422 sheet: 0.16 (0.56), residues: 96 loop : -1.02 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.006 0.001 HIS B 889 PHE 0.018 0.001 PHE A 289 TYR 0.019 0.001 TYR A 280 ARG 0.006 0.000 ARG A 903 Details of bonding type rmsd hydrogen bonds : bond 0.04523 ( 1166) hydrogen bonds : angle 4.08158 ( 3447) covalent geometry : bond 0.00334 (15404) covalent geometry : angle 0.61137 (20912) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 528 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.8608 (m) cc_final: 0.8270 (p) REVERT: A 129 ASP cc_start: 0.6359 (OUTLIER) cc_final: 0.5977 (p0) REVERT: A 137 VAL cc_start: 0.8673 (p) cc_final: 0.8365 (t) REVERT: A 140 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: A 175 VAL cc_start: 0.8516 (p) cc_final: 0.8223 (m) REVERT: A 176 VAL cc_start: 0.8749 (p) cc_final: 0.8543 (t) REVERT: A 195 PHE cc_start: 0.7912 (t80) cc_final: 0.7603 (t80) REVERT: A 231 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.8005 (mt-10) REVERT: A 233 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7529 (tm-30) REVERT: A 267 TYR cc_start: 0.8614 (t80) cc_final: 0.8362 (t80) REVERT: A 284 LYS cc_start: 0.8689 (mmtm) cc_final: 0.8458 (mmmm) REVERT: A 346 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7406 (mt-10) REVERT: A 395 ILE cc_start: 0.8228 (tt) cc_final: 0.7884 (pt) REVERT: A 511 MET cc_start: 0.8917 (tmm) cc_final: 0.8604 (ttp) REVERT: A 583 ARG cc_start: 0.8225 (ttp-170) cc_final: 0.7900 (mtp180) REVERT: A 588 LYS cc_start: 0.8662 (tttm) cc_final: 0.8258 (tttm) REVERT: A 592 ILE cc_start: 0.8786 (mt) cc_final: 0.8403 (mm) REVERT: A 609 ARG cc_start: 0.7719 (mtp-110) cc_final: 0.7433 (mtp-110) REVERT: A 613 GLN cc_start: 0.7770 (mt0) cc_final: 0.7515 (mt0) REVERT: A 624 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7403 (pp30) REVERT: A 633 LYS cc_start: 0.8655 (mttm) cc_final: 0.8444 (mttt) REVERT: A 810 MET cc_start: 0.7230 (ppp) cc_final: 0.6867 (tmm) REVERT: A 832 GLN cc_start: 0.8777 (tp40) cc_final: 0.8434 (tp-100) REVERT: A 841 LYS cc_start: 0.8450 (mtpt) cc_final: 0.8135 (mtpp) REVERT: A 845 ILE cc_start: 0.8878 (mm) cc_final: 0.8676 (mt) REVERT: A 847 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7870 (mm-30) REVERT: A 865 ARG cc_start: 0.7367 (mmm160) cc_final: 0.7111 (mmm160) REVERT: A 866 GLU cc_start: 0.8277 (tp30) cc_final: 0.7917 (tp30) REVERT: A 868 LYS cc_start: 0.7937 (mmtp) cc_final: 0.7236 (mmtp) REVERT: A 871 SER cc_start: 0.8301 (t) cc_final: 0.7725 (p) REVERT: A 921 LEU cc_start: 0.8409 (mm) cc_final: 0.8138 (mp) REVERT: A 958 LYS cc_start: 0.8698 (ttpt) cc_final: 0.8248 (ttpt) REVERT: A 974 LYS cc_start: 0.8982 (ttpt) cc_final: 0.8693 (tppt) REVERT: A 976 ARG cc_start: 0.7873 (tpp80) cc_final: 0.7584 (ttm170) REVERT: A 986 GLU cc_start: 0.8247 (tt0) cc_final: 0.7924 (tt0) REVERT: A 989 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.8029 (t) REVERT: A 999 PHE cc_start: 0.8188 (m-80) cc_final: 0.7946 (m-10) REVERT: A 1058 THR cc_start: 0.8581 (p) cc_final: 0.8323 (p) REVERT: A 1063 VAL cc_start: 0.8607 (t) cc_final: 0.8283 (p) REVERT: A 1078 ASP cc_start: 0.7789 (m-30) cc_final: 0.7489 (m-30) REVERT: A 1100 THR cc_start: 0.8830 (OUTLIER) cc_final: 0.8616 (m) REVERT: A 1104 MET cc_start: 0.7977 (tpt) cc_final: 0.7612 (tpp) REVERT: A 1107 MET cc_start: 0.7463 (tmm) cc_final: 0.6004 (tmm) REVERT: A 1122 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7610 (tp30) REVERT: A 1166 LEU cc_start: 0.7890 (tp) cc_final: 0.7646 (tp) REVERT: A 1174 LEU cc_start: 0.8305 (mt) cc_final: 0.8060 (mm) REVERT: B 91 SER cc_start: 0.8670 (m) cc_final: 0.8442 (p) REVERT: B 140 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7988 (mp10) REVERT: B 141 ILE cc_start: 0.8693 (mm) cc_final: 0.8392 (mt) REVERT: B 154 MET cc_start: 0.8577 (tpp) cc_final: 0.7987 (tpp) REVERT: B 155 ASP cc_start: 0.8384 (t0) cc_final: 0.8028 (t0) REVERT: B 160 MET cc_start: 0.8470 (mmt) cc_final: 0.8220 (mmm) REVERT: B 190 ASN cc_start: 0.7758 (p0) cc_final: 0.7450 (p0) REVERT: B 214 VAL cc_start: 0.8785 (t) cc_final: 0.8559 (p) REVERT: B 217 LEU cc_start: 0.8762 (mt) cc_final: 0.8347 (mp) REVERT: B 238 ASP cc_start: 0.7402 (m-30) cc_final: 0.7066 (m-30) REVERT: B 267 TYR cc_start: 0.8507 (t80) cc_final: 0.8249 (t80) REVERT: B 335 ASN cc_start: 0.8645 (t0) cc_final: 0.8362 (t0) REVERT: B 337 GLU cc_start: 0.8067 (mp0) cc_final: 0.7707 (mp0) REVERT: B 375 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8350 (ttpt) REVERT: B 444 ASN cc_start: 0.8867 (t0) cc_final: 0.8477 (t0) REVERT: B 476 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8554 (m) REVERT: B 486 ILE cc_start: 0.8564 (mm) cc_final: 0.8294 (mm) REVERT: B 517 PHE cc_start: 0.8196 (m-10) cc_final: 0.7981 (m-10) REVERT: B 520 ASP cc_start: 0.7961 (p0) cc_final: 0.7721 (p0) REVERT: B 531 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7473 (tm-30) REVERT: B 579 MET cc_start: 0.7564 (tpt) cc_final: 0.7283 (tpt) REVERT: B 580 GLU cc_start: 0.8010 (tp30) cc_final: 0.7647 (tp30) REVERT: B 581 GLU cc_start: 0.7335 (tp30) cc_final: 0.6651 (tp30) REVERT: B 585 ARG cc_start: 0.8161 (ttm-80) cc_final: 0.7721 (ttm110) REVERT: B 588 LYS cc_start: 0.8442 (tttm) cc_final: 0.8026 (tttm) REVERT: B 591 LYS cc_start: 0.8654 (mtpp) cc_final: 0.8450 (mtpp) REVERT: B 592 ILE cc_start: 0.8695 (mt) cc_final: 0.8360 (mm) REVERT: B 621 GLU cc_start: 0.7370 (mp0) cc_final: 0.6836 (mp0) REVERT: B 832 GLN cc_start: 0.8548 (tp40) cc_final: 0.8329 (tp40) REVERT: B 837 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.7845 (t80) REVERT: B 839 VAL cc_start: 0.8921 (t) cc_final: 0.8699 (t) REVERT: B 841 LYS cc_start: 0.8557 (mtpt) cc_final: 0.8255 (mtpp) REVERT: B 845 ILE cc_start: 0.8919 (mm) cc_final: 0.8635 (mt) REVERT: B 850 VAL cc_start: 0.8918 (p) cc_final: 0.8683 (m) REVERT: B 866 GLU cc_start: 0.7985 (tp30) cc_final: 0.7656 (tm-30) REVERT: B 870 ILE cc_start: 0.8636 (mm) cc_final: 0.8028 (mm) REVERT: B 871 SER cc_start: 0.8301 (t) cc_final: 0.8016 (t) REVERT: B 879 VAL cc_start: 0.8979 (p) cc_final: 0.8765 (t) REVERT: B 921 LEU cc_start: 0.8412 (mm) cc_final: 0.8136 (mp) REVERT: B 959 ASN cc_start: 0.8229 (m-40) cc_final: 0.7925 (m-40) REVERT: B 974 LYS cc_start: 0.9010 (ttpt) cc_final: 0.8602 (tppt) REVERT: B 991 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7626 (tp30) REVERT: B 999 PHE cc_start: 0.8190 (m-80) cc_final: 0.7807 (m-80) REVERT: B 1007 LYS cc_start: 0.8728 (tttt) cc_final: 0.8249 (tttm) REVERT: B 1067 PHE cc_start: 0.7913 (t80) cc_final: 0.7665 (t80) REVERT: B 1078 ASP cc_start: 0.7880 (m-30) cc_final: 0.7561 (m-30) REVERT: B 1098 ILE cc_start: 0.9072 (tp) cc_final: 0.8789 (tt) REVERT: B 1104 MET cc_start: 0.8306 (tpp) cc_final: 0.8079 (tpp) outliers start: 79 outliers final: 62 residues processed: 565 average time/residue: 0.2773 time to fit residues: 225.9083 Evaluate side-chains 593 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 520 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1050 LYS Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 865 ARG Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 991 GLU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1146 ILE Chi-restraints excluded: chain B residue 1161 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 178 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 GLN B 157 HIS B 165 GLN B 613 GLN B 981 HIS B1154 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.132005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.113098 restraints weight = 23499.059| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.18 r_work: 0.3339 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15404 Z= 0.171 Angle : 0.628 10.630 20912 Z= 0.318 Chirality : 0.043 0.272 2526 Planarity : 0.004 0.033 2600 Dihedral : 4.556 57.146 2096 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.07 % Allowed : 27.50 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.66 (0.20), residues: 1938 helix: 1.78 (0.14), residues: 1422 sheet: 0.13 (0.55), residues: 96 loop : -1.01 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.006 0.001 HIS B 889 PHE 0.017 0.002 PHE A 289 TYR 0.019 0.001 TYR A 280 ARG 0.006 0.001 ARG A 856 Details of bonding type rmsd hydrogen bonds : bond 0.04659 ( 1166) hydrogen bonds : angle 4.11214 ( 3447) covalent geometry : bond 0.00372 (15404) covalent geometry : angle 0.62777 (20912) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 524 time to evaluate : 1.753 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: A 91 SER cc_start: 0.8618 (m) cc_final: 0.8314 (p) REVERT: A 129 ASP cc_start: 0.6468 (OUTLIER) cc_final: 0.6046 (p0) REVERT: A 137 VAL cc_start: 0.8673 (p) cc_final: 0.8377 (t) REVERT: A 140 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7970 (mp10) REVERT: A 155 ASP cc_start: 0.8255 (t0) cc_final: 0.7833 (t70) REVERT: A 176 VAL cc_start: 0.8753 (p) cc_final: 0.8539 (t) REVERT: A 195 PHE cc_start: 0.7946 (t80) cc_final: 0.7672 (t80) REVERT: A 205 MET cc_start: 0.8266 (mmm) cc_final: 0.8058 (mmt) REVERT: A 231 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8050 (mt-10) REVERT: A 233 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7539 (tm-30) REVERT: A 267 TYR cc_start: 0.8627 (t80) cc_final: 0.8364 (t80) REVERT: A 284 LYS cc_start: 0.8683 (mmtm) cc_final: 0.8448 (mmmm) REVERT: A 346 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7399 (mt-10) REVERT: A 395 ILE cc_start: 0.8220 (tt) cc_final: 0.7917 (pt) REVERT: A 579 MET cc_start: 0.7534 (tmm) cc_final: 0.7193 (tmm) REVERT: A 583 ARG cc_start: 0.8268 (ttp-170) cc_final: 0.7875 (mtp180) REVERT: A 588 LYS cc_start: 0.8684 (tttm) cc_final: 0.8318 (tttm) REVERT: A 592 ILE cc_start: 0.8821 (mt) cc_final: 0.8435 (mm) REVERT: A 609 ARG cc_start: 0.7738 (mtp-110) cc_final: 0.7424 (mtp-110) REVERT: A 613 GLN cc_start: 0.7806 (mt0) cc_final: 0.7558 (mt0) REVERT: A 624 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7616 (pp30) REVERT: A 633 LYS cc_start: 0.8656 (mttm) cc_final: 0.8441 (mttt) REVERT: A 810 MET cc_start: 0.7242 (ppp) cc_final: 0.6875 (tmm) REVERT: A 832 GLN cc_start: 0.8699 (tp40) cc_final: 0.8359 (tp-100) REVERT: A 841 LYS cc_start: 0.8481 (mtpt) cc_final: 0.8154 (mtpp) REVERT: A 847 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7855 (mm-30) REVERT: A 865 ARG cc_start: 0.7452 (mmm160) cc_final: 0.7216 (mmm160) REVERT: A 866 GLU cc_start: 0.8307 (tp30) cc_final: 0.8102 (tp30) REVERT: A 868 LYS cc_start: 0.7998 (mmtp) cc_final: 0.7279 (mmtp) REVERT: A 871 SER cc_start: 0.8313 (t) cc_final: 0.7724 (p) REVERT: A 921 LEU cc_start: 0.8405 (mm) cc_final: 0.8145 (mp) REVERT: A 972 PHE cc_start: 0.8459 (t80) cc_final: 0.8241 (t80) REVERT: A 974 LYS cc_start: 0.8999 (ttpt) cc_final: 0.8705 (tppt) REVERT: A 976 ARG cc_start: 0.7870 (tpp80) cc_final: 0.7654 (tpp80) REVERT: A 986 GLU cc_start: 0.8288 (tt0) cc_final: 0.7952 (tt0) REVERT: A 989 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.8029 (t) REVERT: A 999 PHE cc_start: 0.8238 (m-80) cc_final: 0.7982 (m-10) REVERT: A 1058 THR cc_start: 0.8580 (p) cc_final: 0.8318 (p) REVERT: A 1063 VAL cc_start: 0.8625 (t) cc_final: 0.8305 (p) REVERT: A 1078 ASP cc_start: 0.7871 (m-30) cc_final: 0.7542 (m-30) REVERT: A 1100 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8673 (m) REVERT: A 1104 MET cc_start: 0.8033 (tpt) cc_final: 0.7706 (tpp) REVERT: A 1107 MET cc_start: 0.7416 (tmm) cc_final: 0.5950 (tmm) REVERT: A 1122 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7598 (tp30) REVERT: A 1166 LEU cc_start: 0.7897 (tp) cc_final: 0.7523 (tp) REVERT: B 91 SER cc_start: 0.8688 (m) cc_final: 0.8456 (p) REVERT: B 140 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8050 (mp10) REVERT: B 141 ILE cc_start: 0.8684 (mm) cc_final: 0.8390 (mt) REVERT: B 154 MET cc_start: 0.8573 (tpp) cc_final: 0.7947 (tpp) REVERT: B 155 ASP cc_start: 0.8381 (t0) cc_final: 0.8011 (t0) REVERT: B 160 MET cc_start: 0.8506 (mmt) cc_final: 0.8259 (mmm) REVERT: B 190 ASN cc_start: 0.7776 (p0) cc_final: 0.7462 (p0) REVERT: B 214 VAL cc_start: 0.8822 (t) cc_final: 0.8602 (p) REVERT: B 217 LEU cc_start: 0.8764 (mt) cc_final: 0.8354 (mp) REVERT: B 238 ASP cc_start: 0.7470 (m-30) cc_final: 0.7131 (m-30) REVERT: B 267 TYR cc_start: 0.8538 (t80) cc_final: 0.8241 (t80) REVERT: B 335 ASN cc_start: 0.8634 (t0) cc_final: 0.8345 (t0) REVERT: B 375 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8417 (ttpt) REVERT: B 419 TRP cc_start: 0.8297 (p-90) cc_final: 0.8075 (p-90) REVERT: B 444 ASN cc_start: 0.8852 (t0) cc_final: 0.8459 (t0) REVERT: B 476 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8562 (m) REVERT: B 486 ILE cc_start: 0.8458 (mm) cc_final: 0.8235 (mm) REVERT: B 520 ASP cc_start: 0.7978 (p0) cc_final: 0.7737 (p0) REVERT: B 531 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7592 (tm-30) REVERT: B 579 MET cc_start: 0.7563 (tpt) cc_final: 0.7289 (tpt) REVERT: B 580 GLU cc_start: 0.8086 (tp30) cc_final: 0.7682 (tp30) REVERT: B 581 GLU cc_start: 0.7374 (tp30) cc_final: 0.6659 (tp30) REVERT: B 585 ARG cc_start: 0.8209 (ttm-80) cc_final: 0.7668 (ttm170) REVERT: B 588 LYS cc_start: 0.8460 (tttm) cc_final: 0.8063 (tttm) REVERT: B 591 LYS cc_start: 0.8685 (mtpp) cc_final: 0.8447 (mtpp) REVERT: B 592 ILE cc_start: 0.8700 (mt) cc_final: 0.8371 (mm) REVERT: B 617 VAL cc_start: 0.7872 (t) cc_final: 0.7320 (m) REVERT: B 620 ASP cc_start: 0.7658 (t70) cc_final: 0.7402 (t70) REVERT: B 621 GLU cc_start: 0.7403 (mp0) cc_final: 0.6729 (mp0) REVERT: B 832 GLN cc_start: 0.8565 (tp40) cc_final: 0.8345 (tp40) REVERT: B 837 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7876 (t80) REVERT: B 841 LYS cc_start: 0.8568 (mtpt) cc_final: 0.8268 (mtpp) REVERT: B 845 ILE cc_start: 0.8924 (mm) cc_final: 0.8653 (mt) REVERT: B 850 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8677 (m) REVERT: B 865 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7161 (mmm160) REVERT: B 866 GLU cc_start: 0.7899 (tp30) cc_final: 0.7676 (tm-30) REVERT: B 870 ILE cc_start: 0.8619 (mm) cc_final: 0.7967 (mm) REVERT: B 871 SER cc_start: 0.8293 (t) cc_final: 0.8018 (t) REVERT: B 879 VAL cc_start: 0.8982 (p) cc_final: 0.8759 (t) REVERT: B 921 LEU cc_start: 0.8462 (mm) cc_final: 0.8195 (mp) REVERT: B 959 ASN cc_start: 0.8269 (m-40) cc_final: 0.7982 (m-40) REVERT: B 974 LYS cc_start: 0.8998 (ttpt) cc_final: 0.8583 (tppt) REVERT: B 976 ARG cc_start: 0.7999 (ttm170) cc_final: 0.7773 (ttm110) REVERT: B 991 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7663 (tp30) REVERT: B 999 PHE cc_start: 0.8254 (m-80) cc_final: 0.7877 (m-80) REVERT: B 1007 LYS cc_start: 0.8777 (tttt) cc_final: 0.8270 (tttm) REVERT: B 1067 PHE cc_start: 0.7940 (t80) cc_final: 0.7696 (t80) REVERT: B 1078 ASP cc_start: 0.7854 (m-30) cc_final: 0.7567 (m-30) REVERT: B 1098 ILE cc_start: 0.9077 (tp) cc_final: 0.8780 (tt) REVERT: B 1104 MET cc_start: 0.8285 (tpp) cc_final: 0.8070 (tpp) outliers start: 80 outliers final: 58 residues processed: 561 average time/residue: 0.2887 time to fit residues: 233.6865 Evaluate side-chains 580 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 509 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 888 GLU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 865 ARG Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 991 GLU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1051 LYS Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1146 ILE Chi-restraints excluded: chain B residue 1161 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 40 optimal weight: 0.0470 chunk 13 optimal weight: 0.7980 chunk 181 optimal weight: 0.8980 chunk 150 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 167 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 GLN A1120 HIS B 157 HIS B 165 GLN B 981 HIS B1154 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.132927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.114223 restraints weight = 23454.555| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.16 r_work: 0.3355 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15404 Z= 0.142 Angle : 0.631 10.545 20912 Z= 0.316 Chirality : 0.043 0.321 2526 Planarity : 0.004 0.033 2600 Dihedral : 4.552 58.279 2096 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.50 % Allowed : 28.64 % Favored : 66.86 % 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: 1.71 (0.20), residues: 1938 helix: 1.83 (0.14), residues: 1422 sheet: 0.13 (0.55), residues: 96 loop : -1.02 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.005 0.000 HIS B 889 PHE 0.019 0.001 PHE A 625 TYR 0.019 0.001 TYR B 280 ARG 0.007 0.000 ARG A 940 Details of bonding type rmsd hydrogen bonds : bond 0.04423 ( 1166) hydrogen bonds : angle 4.08512 ( 3447) covalent geometry : bond 0.00308 (15404) covalent geometry : angle 0.63147 (20912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8745.36 seconds wall clock time: 151 minutes 43.39 seconds (9103.39 seconds total)