Starting phenix.real_space_refine on Fri Jun 13 16:01:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xq5_38566/06_2025/8xq5_38566.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xq5_38566/06_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_38566/06_2025/8xq5_38566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xq5_38566/06_2025/8xq5_38566.map" model { file = "/net/cci-nas-00/data/ceres_data/8xq5_38566/06_2025/8xq5_38566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xq5_38566/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.00, per 1000 atoms: 0.59 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: 3.49 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: 1.56 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: 5.17 Time building geometry restraints manager: 4.16 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: 0.08 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 34.780 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.740 ------------------------------------------------------------------------------- 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 : 1.543 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: 0.3103 time to fit residues: 264.2796 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 : 2.147 ------------------------------------------------------------------------------- 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 = 0.115075 restraints weight = 23872.760| |-----------------------------------------------------------------------------| 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: 0.3199 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.8698 (m) cc_final: 0.8428 (p) REVERT: A 175 VAL cc_start: 0.8502 (p) cc_final: 0.8164 (m) REVERT: A 217 LEU cc_start: 0.8660 (mt) cc_final: 0.8345 (mm) REVERT: A 233 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7775 (tm-30) REVERT: A 263 GLN cc_start: 0.8065 (mt0) cc_final: 0.7770 (mt0) REVERT: A 267 TYR cc_start: 0.8604 (t80) cc_final: 0.8344 (t80) REVERT: A 284 LYS cc_start: 0.8759 (mmtm) cc_final: 0.8525 (mmmm) REVERT: A 346 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7492 (mt-10) REVERT: A 443 GLU cc_start: 0.8047 (tp30) cc_final: 0.7711 (tp30) REVERT: A 444 ASN cc_start: 0.8750 (t0) cc_final: 0.8383 (t0) REVERT: A 500 ARG cc_start: 0.8375 (mmm-85) cc_final: 0.8063 (tpp80) REVERT: A 511 MET cc_start: 0.9053 (tmm) cc_final: 0.8828 (tmm) REVERT: A 580 GLU cc_start: 0.7725 (tp30) cc_final: 0.7250 (tp30) REVERT: A 581 GLU cc_start: 0.7023 (tp30) cc_final: 0.6336 (tp30) REVERT: A 584 LEU cc_start: 0.8455 (mm) cc_final: 0.7657 (mm) REVERT: A 586 MET cc_start: 0.8738 (ttm) cc_final: 0.8432 (ttp) REVERT: A 588 LYS cc_start: 0.8459 (tttm) cc_final: 0.8137 (tttm) REVERT: A 592 ILE cc_start: 0.8672 (mt) cc_final: 0.8251 (mm) REVERT: A 613 GLN cc_start: 0.7687 (mt0) cc_final: 0.7337 (mt0) REVERT: A 614 HIS cc_start: 0.7773 (m-70) cc_final: 0.7229 (m-70) REVERT: A 617 VAL cc_start: 0.8007 (t) cc_final: 0.7775 (m) REVERT: A 641 TYR cc_start: 0.7953 (m-10) cc_final: 0.7556 (m-80) REVERT: A 643 TRP cc_start: 0.7742 (t-100) cc_final: 0.7293 (t-100) REVERT: A 828 LYS cc_start: 0.8433 (mmmt) cc_final: 0.8143 (mmmt) REVERT: A 832 GLN cc_start: 0.8848 (tp40) cc_final: 0.8554 (tp40) REVERT: A 841 LYS cc_start: 0.8342 (mtpt) cc_final: 0.7992 (mtpt) REVERT: A 847 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7552 (mm-30) REVERT: A 858 VAL cc_start: 0.8370 (p) cc_final: 0.7913 (p) REVERT: A 866 GLU cc_start: 0.8147 (tp30) cc_final: 0.7818 (tp30) REVERT: A 870 ILE cc_start: 0.8502 (mt) cc_final: 0.8215 (mm) REVERT: A 878 VAL cc_start: 0.8924 (t) cc_final: 0.8699 (t) REVERT: A 900 GLN cc_start: 0.8714 (tp40) cc_final: 0.8490 (tp-100) REVERT: A 921 LEU cc_start: 0.8310 (mm) cc_final: 0.8018 (mp) REVERT: A 931 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7745 (mm-30) REVERT: A 932 LEU cc_start: 0.8484 (tt) cc_final: 0.8246 (tp) REVERT: A 948 ILE cc_start: 0.8389 (mt) cc_final: 0.8071 (tt) REVERT: A 958 LYS cc_start: 0.8581 (ttpt) cc_final: 0.8209 (ttpt) REVERT: A 999 PHE cc_start: 0.8073 (m-80) cc_final: 0.7670 (m-80) REVERT: A 1003 SER cc_start: 0.8373 (t) cc_final: 0.8086 (m) REVERT: A 1045 MET cc_start: 0.8518 (ttm) cc_final: 0.8222 (tpp) REVERT: A 1063 VAL cc_start: 0.8326 (t) cc_final: 0.8107 (p) REVERT: A 1077 ILE cc_start: 0.8662 (mm) cc_final: 0.8326 (mm) REVERT: A 1100 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8487 (p) REVERT: A 1103 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8109 (mm) REVERT: A 1104 MET cc_start: 0.7875 (tpt) cc_final: 0.7476 (tpp) REVERT: A 1107 MET cc_start: 0.6934 (tmm) cc_final: 0.6208 (tmm) REVERT: A 1122 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7421 (mm-30) REVERT: B 91 SER cc_start: 0.8739 (m) cc_final: 0.8516 (p) REVERT: B 140 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8246 (mp10) REVERT: B 154 MET cc_start: 0.8464 (tpp) cc_final: 0.7991 (mmm) REVERT: B 197 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7784 (mt-10) REVERT: B 214 VAL cc_start: 0.8757 (t) cc_final: 0.8376 (p) REVERT: B 250 LYS cc_start: 0.8288 (mmmm) cc_final: 0.8079 (mttm) REVERT: B 265 VAL cc_start: 0.8471 (p) cc_final: 0.8243 (p) REVERT: B 267 TYR cc_start: 0.8470 (t80) cc_final: 0.8116 (t80) REVERT: B 300 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7793 (mt-10) REVERT: B 392 TYR cc_start: 0.8604 (t80) cc_final: 0.8375 (t80) REVERT: B 443 GLU cc_start: 0.7956 (tp30) cc_final: 0.7587 (tp30) REVERT: B 444 ASN cc_start: 0.8846 (t0) cc_final: 0.8463 (t0) REVERT: B 476 THR cc_start: 0.8818 (t) cc_final: 0.8555 (m) REVERT: B 485 ASP cc_start: 0.8232 (t0) cc_final: 0.8024 (t0) REVERT: B 486 ILE cc_start: 0.8578 (mm) cc_final: 0.8282 (mm) REVERT: B 520 ASP cc_start: 0.8167 (p0) cc_final: 0.7901 (p0) REVERT: B 579 MET cc_start: 0.7410 (tpt) cc_final: 0.7169 (tpt) REVERT: B 580 GLU cc_start: 0.7931 (tp30) cc_final: 0.7219 (tp30) REVERT: B 581 GLU cc_start: 0.7157 (tp30) cc_final: 0.6406 (tp30) REVERT: B 584 LEU cc_start: 0.8408 (mm) cc_final: 0.7920 (mm) REVERT: B 586 MET cc_start: 0.8796 (ttm) cc_final: 0.8465 (ttm) REVERT: B 587 LEU cc_start: 0.8781 (mt) cc_final: 0.8545 (mt) REVERT: B 588 LYS cc_start: 0.8328 (tttm) cc_final: 0.7890 (tttm) REVERT: B 592 ILE cc_start: 0.8596 (mt) cc_final: 0.8227 (mm) REVERT: B 620 ASP cc_start: 0.7568 (t70) cc_final: 0.7170 (t70) REVERT: B 621 GLU cc_start: 0.7119 (mp0) cc_final: 0.6384 (mp0) REVERT: B 624 GLN cc_start: 0.7556 (pt0) cc_final: 0.7267 (pt0) REVERT: B 828 LYS cc_start: 0.8552 (mmtt) cc_final: 0.8243 (mmtt) REVERT: B 835 LEU cc_start: 0.8690 (tp) cc_final: 0.8432 (tt) REVERT: B 837 TYR cc_start: 0.8318 (OUTLIER) cc_final: 0.7828 (t80) REVERT: B 839 VAL cc_start: 0.8829 (t) cc_final: 0.8529 (t) REVERT: B 845 ILE cc_start: 0.8718 (mm) cc_final: 0.8452 (mt) REVERT: B 866 GLU cc_start: 0.8352 (tp30) cc_final: 0.7946 (tp30) REVERT: B 870 ILE cc_start: 0.8644 (mm) cc_final: 0.8329 (mm) REVERT: B 878 VAL cc_start: 0.8845 (t) cc_final: 0.8585 (t) REVERT: B 879 VAL cc_start: 0.8974 (p) cc_final: 0.8774 (t) REVERT: B 921 LEU cc_start: 0.8364 (mm) cc_final: 0.8034 (mp) REVERT: B 926 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7658 (mm-30) REVERT: B 931 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7742 (mm-30) REVERT: B 932 LEU cc_start: 0.8420 (tt) cc_final: 0.8195 (tp) REVERT: B 972 PHE cc_start: 0.8426 (t80) cc_final: 0.8190 (t80) REVERT: B 999 PHE cc_start: 0.8246 (m-80) cc_final: 0.7798 (m-80) REVERT: B 1003 SER cc_start: 0.8555 (t) cc_final: 0.8223 (m) REVERT: B 1045 MET cc_start: 0.8481 (ttm) cc_final: 0.8190 (tpp) REVERT: B 1058 THR cc_start: 0.8517 (p) cc_final: 0.8298 (p) REVERT: B 1064 GLN cc_start: 0.8439 (mt0) cc_final: 0.8178 (mt0) REVERT: B 1077 ILE cc_start: 0.8623 (mm) cc_final: 0.8315 (mm) REVERT: B 1088 TYR cc_start: 0.7633 (t80) cc_final: 0.7241 (t80) REVERT: B 1104 MET cc_start: 0.8340 (tpp) cc_final: 0.8095 (tpp) REVERT: B 1122 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7436 (mm-30) REVERT: B 1145 VAL cc_start: 0.8459 (t) cc_final: 0.8213 (p) outliers start: 62 outliers final: 33 residues processed: 576 average time/residue: 0.2782 time to fit residues: 232.9330 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 : 1.829 ------------------------------------------------------------------------------- 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: 0.9980 chunk 189 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 186 optimal weight: 0.6980 chunk 46 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.133557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.114511 restraints weight = 23572.683| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.17 r_work: 0.3363 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15404 Z= 0.147 Angle : 0.587 10.219 20912 Z= 0.302 Chirality : 0.040 0.184 2526 Planarity : 0.004 0.038 2600 Dihedral : 4.633 53.821 2096 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.75 % Allowed : 23.76 % Favored : 71.48 % 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: 1.12 (0.19), residues: 1938 helix: 1.42 (0.14), residues: 1420 sheet: -0.32 (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 0.006 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 856 Details of bonding type rmsd hydrogen bonds : bond 0.04538 ( 1166) hydrogen bonds : angle 4.21075 ( 3447) covalent geometry : bond 0.00310 (15404) covalent geometry : angle 0.58735 (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: 75 poor density : 539 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.8655 (m) cc_final: 0.8368 (p) REVERT: A 137 VAL cc_start: 0.8788 (p) cc_final: 0.8582 (t) REVERT: A 140 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8192 (mp10) REVERT: A 175 VAL cc_start: 0.8507 (p) cc_final: 0.8177 (m) REVERT: A 217 LEU cc_start: 0.8693 (mt) cc_final: 0.8403 (mm) REVERT: A 233 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7707 (tm-30) REVERT: A 263 GLN cc_start: 0.8063 (mt0) cc_final: 0.7745 (mt0) REVERT: A 267 TYR cc_start: 0.8601 (t80) cc_final: 0.8270 (t80) REVERT: A 284 LYS cc_start: 0.8739 (mmtm) cc_final: 0.8512 (mmmm) REVERT: A 291 SER cc_start: 0.8625 (t) cc_final: 0.8364 (p) REVERT: A 335 ASN cc_start: 0.8581 (t0) cc_final: 0.8293 (t0) REVERT: A 346 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7476 (mt-10) REVERT: A 395 ILE cc_start: 0.8208 (tt) cc_final: 0.7656 (pt) REVERT: A 425 MET cc_start: 0.8527 (ttm) cc_final: 0.8257 (mtm) REVERT: A 443 GLU cc_start: 0.8048 (tp30) cc_final: 0.7727 (tp30) REVERT: A 444 ASN cc_start: 0.8721 (t0) cc_final: 0.8372 (t0) REVERT: A 500 ARG cc_start: 0.8366 (mmm-85) cc_final: 0.8142 (tpp80) REVERT: A 511 MET cc_start: 0.8984 (tmm) cc_final: 0.8710 (tmm) REVERT: A 580 GLU cc_start: 0.7817 (tp30) cc_final: 0.7114 (tp30) REVERT: A 584 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7378 (mm) REVERT: A 586 MET cc_start: 0.8589 (ttm) cc_final: 0.8353 (ttp) REVERT: A 588 LYS cc_start: 0.8586 (tttm) cc_final: 0.8258 (tttm) REVERT: A 592 ILE cc_start: 0.8740 (mt) cc_final: 0.8318 (mm) REVERT: A 609 ARG cc_start: 0.7870 (mtp-110) cc_final: 0.7623 (mtp-110) REVERT: A 613 GLN cc_start: 0.7704 (mt0) cc_final: 0.7469 (mt0) REVERT: A 614 HIS cc_start: 0.7760 (m-70) cc_final: 0.7368 (m-70) REVERT: A 641 TYR cc_start: 0.8037 (m-80) cc_final: 0.7696 (m-80) REVERT: A 643 TRP cc_start: 0.7835 (t-100) cc_final: 0.7221 (t-100) REVERT: A 644 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8229 (mt) REVERT: A 810 MET cc_start: 0.7322 (ppp) cc_final: 0.6957 (tmm) REVERT: A 828 LYS cc_start: 0.8479 (mmmt) cc_final: 0.8194 (mmmt) REVERT: A 832 GLN cc_start: 0.8762 (tp40) cc_final: 0.8480 (tp40) REVERT: A 837 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.7847 (t80) REVERT: A 838 ASP cc_start: 0.8326 (t0) cc_final: 0.7949 (t0) REVERT: A 839 VAL cc_start: 0.8862 (t) cc_final: 0.8662 (t) REVERT: A 841 LYS cc_start: 0.8430 (mtpt) cc_final: 0.8081 (mtpp) REVERT: A 847 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7625 (mm-30) REVERT: A 850 VAL cc_start: 0.8891 (p) cc_final: 0.8682 (m) REVERT: A 866 GLU cc_start: 0.8236 (tp30) cc_final: 0.7820 (tp30) REVERT: A 868 LYS cc_start: 0.7825 (mmtp) cc_final: 0.7494 (ttmm) REVERT: A 870 ILE cc_start: 0.8510 (mt) cc_final: 0.8079 (mm) REVERT: A 878 VAL cc_start: 0.8921 (t) cc_final: 0.8662 (t) REVERT: A 900 GLN cc_start: 0.8642 (tp40) cc_final: 0.8424 (tp-100) REVERT: A 921 LEU cc_start: 0.8293 (mm) cc_final: 0.8029 (mp) REVERT: A 926 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7511 (mp0) REVERT: A 931 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7834 (mm-30) REVERT: A 932 LEU cc_start: 0.8492 (tt) cc_final: 0.8241 (tp) REVERT: A 948 ILE cc_start: 0.8409 (mt) cc_final: 0.8088 (tt) REVERT: A 958 LYS cc_start: 0.8603 (ttpt) cc_final: 0.8176 (ttpt) REVERT: A 972 PHE cc_start: 0.8434 (t80) cc_final: 0.8094 (t80) REVERT: A 976 ARG cc_start: 0.7964 (tpp80) cc_final: 0.7700 (ttm170) REVERT: A 999 PHE cc_start: 0.8154 (m-80) cc_final: 0.7685 (m-80) REVERT: A 1003 SER cc_start: 0.8458 (t) cc_final: 0.8185 (m) REVERT: A 1058 THR cc_start: 0.8550 (p) cc_final: 0.8289 (p) REVERT: A 1063 VAL cc_start: 0.8442 (t) cc_final: 0.8156 (p) REVERT: A 1064 GLN cc_start: 0.8387 (mt0) cc_final: 0.8180 (mt0) REVERT: A 1077 ILE cc_start: 0.8758 (mm) cc_final: 0.8442 (mm) REVERT: A 1100 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8516 (m) REVERT: A 1103 ILE cc_start: 0.8529 (mm) cc_final: 0.8150 (mm) REVERT: A 1104 MET cc_start: 0.7841 (tpt) cc_final: 0.7476 (tpp) REVERT: A 1107 MET cc_start: 0.7068 (tmm) cc_final: 0.6094 (tmm) REVERT: A 1122 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7695 (tp30) REVERT: B 91 SER cc_start: 0.8738 (m) cc_final: 0.8491 (p) REVERT: B 140 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8198 (mp10) REVERT: B 154 MET cc_start: 0.8493 (tpp) cc_final: 0.8200 (tpp) REVERT: B 155 ASP cc_start: 0.8433 (t0) cc_final: 0.8033 (t0) REVERT: B 160 MET cc_start: 0.8169 (mmt) cc_final: 0.7932 (mmm) REVERT: B 190 ASN cc_start: 0.7782 (p0) cc_final: 0.7454 (p0) REVERT: B 197 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7723 (mt-10) REVERT: B 214 VAL cc_start: 0.8703 (t) cc_final: 0.8496 (p) REVERT: B 217 LEU cc_start: 0.8698 (mt) cc_final: 0.8463 (mm) REVERT: B 233 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7747 (tm-30) REVERT: B 238 ASP cc_start: 0.7348 (m-30) cc_final: 0.7056 (m-30) REVERT: B 267 TYR cc_start: 0.8485 (t80) cc_final: 0.8182 (t80) REVERT: B 296 ASP cc_start: 0.7559 (p0) cc_final: 0.6933 (p0) REVERT: B 300 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7744 (mt-10) REVERT: B 386 PHE cc_start: 0.8332 (t80) cc_final: 0.8118 (t80) REVERT: B 392 TYR cc_start: 0.8627 (t80) cc_final: 0.8305 (t80) REVERT: B 443 GLU cc_start: 0.7948 (tp30) cc_final: 0.7554 (tp30) REVERT: B 444 ASN cc_start: 0.8763 (t0) cc_final: 0.8424 (t0) REVERT: B 476 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8559 (m) REVERT: B 485 ASP cc_start: 0.8289 (t0) cc_final: 0.8054 (t0) REVERT: B 486 ILE cc_start: 0.8529 (mm) cc_final: 0.8188 (mm) REVERT: B 517 PHE cc_start: 0.8384 (m-10) cc_final: 0.8081 (m-10) REVERT: B 520 ASP cc_start: 0.8011 (p0) cc_final: 0.7662 (p0) REVERT: B 579 MET cc_start: 0.7405 (tpt) cc_final: 0.7160 (tpt) REVERT: B 580 GLU cc_start: 0.7942 (tp30) cc_final: 0.7512 (tp30) REVERT: B 581 GLU cc_start: 0.7215 (tp30) cc_final: 0.6529 (tp30) REVERT: B 585 ARG cc_start: 0.8154 (ttm-80) cc_final: 0.7707 (ttm110) REVERT: B 586 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8633 (ttp) REVERT: B 587 LEU cc_start: 0.8798 (mt) cc_final: 0.8525 (mt) REVERT: B 588 LYS cc_start: 0.8418 (tttm) cc_final: 0.7992 (tttm) REVERT: B 592 ILE cc_start: 0.8693 (mt) cc_final: 0.8345 (mm) REVERT: B 620 ASP cc_start: 0.7666 (t70) cc_final: 0.7225 (t70) REVERT: B 621 GLU cc_start: 0.7267 (mp0) cc_final: 0.6584 (mp0) REVERT: B 646 ARG cc_start: 0.7120 (ptp-170) cc_final: 0.6920 (ptp-170) REVERT: B 828 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8301 (mmtt) REVERT: B 835 LEU cc_start: 0.8741 (tp) cc_final: 0.8527 (tt) REVERT: B 837 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7727 (t80) REVERT: B 839 VAL cc_start: 0.8868 (t) cc_final: 0.8604 (t) REVERT: B 845 ILE cc_start: 0.8834 (mm) cc_final: 0.8511 (mt) REVERT: B 866 GLU cc_start: 0.8366 (tp30) cc_final: 0.7818 (tp30) REVERT: B 870 ILE cc_start: 0.8605 (mm) cc_final: 0.8204 (mm) REVERT: B 878 VAL cc_start: 0.8849 (t) cc_final: 0.8570 (t) REVERT: B 879 VAL cc_start: 0.8981 (p) cc_final: 0.8771 (t) REVERT: B 911 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7766 (mp0) REVERT: B 921 LEU cc_start: 0.8354 (mm) cc_final: 0.8045 (mp) REVERT: B 972 PHE cc_start: 0.8496 (t80) cc_final: 0.8249 (t80) REVERT: B 999 PHE cc_start: 0.8215 (m-80) cc_final: 0.7767 (m-80) REVERT: B 1003 SER cc_start: 0.8704 (t) cc_final: 0.8444 (m) REVERT: B 1045 MET cc_start: 0.8554 (ttm) cc_final: 0.8295 (tpp) REVERT: B 1058 THR cc_start: 0.8559 (p) cc_final: 0.8301 (p) REVERT: B 1077 ILE cc_start: 0.8752 (mm) cc_final: 0.8466 (mm) REVERT: B 1104 MET cc_start: 0.8211 (tpp) cc_final: 0.8007 (tpp) REVERT: B 1105 GLU cc_start: 0.8560 (tp30) cc_final: 0.8184 (tm-30) REVERT: B 1145 VAL cc_start: 0.8512 (t) cc_final: 0.8258 (p) outliers start: 75 outliers final: 40 residues processed: 578 average time/residue: 0.2879 time to fit residues: 244.2813 Evaluate side-chains 573 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 524 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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 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: 0.0980 chunk 189 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 188 optimal weight: 0.9980 chunk 111 optimal weight: 0.0970 chunk 12 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.134596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.115439 restraints weight = 23465.378| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.17 r_work: 0.3378 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15404 Z= 0.127 Angle : 0.562 8.279 20912 Z= 0.288 Chirality : 0.040 0.210 2526 Planarity : 0.004 0.033 2600 Dihedral : 4.534 55.628 2096 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.82 % Allowed : 24.52 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.72 (0.14), residues: 1416 sheet: -0.09 (0.57), residues: 96 loop : -1.17 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.000 HIS A 292 PHE 0.014 0.001 PHE B 289 TYR 0.016 0.001 TYR B 280 ARG 0.007 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 1166) hydrogen bonds : angle 4.08195 ( 3447) covalent geometry : bond 0.00264 (15404) covalent geometry : angle 0.56213 (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 621 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 545 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.8643 (m) cc_final: 0.8350 (p) REVERT: A 137 VAL cc_start: 0.8744 (p) cc_final: 0.8506 (t) REVERT: A 140 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8082 (mp10) REVERT: A 175 VAL cc_start: 0.8489 (p) cc_final: 0.8169 (m) REVERT: A 195 PHE cc_start: 0.7861 (t80) cc_final: 0.7592 (t80) REVERT: A 217 LEU cc_start: 0.8688 (mt) cc_final: 0.8411 (mm) REVERT: A 233 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7711 (tm-30) REVERT: A 267 TYR cc_start: 0.8586 (t80) cc_final: 0.8289 (t80) REVERT: A 284 LYS cc_start: 0.8744 (mmtm) cc_final: 0.8517 (mmmm) REVERT: A 291 SER cc_start: 0.8587 (t) cc_final: 0.8334 (p) REVERT: A 335 ASN cc_start: 0.8550 (t0) cc_final: 0.8247 (t0) REVERT: A 346 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7452 (mt-10) REVERT: A 395 ILE cc_start: 0.8164 (tt) cc_final: 0.7656 (pt) REVERT: A 443 GLU cc_start: 0.7989 (tp30) cc_final: 0.7701 (tp30) REVERT: A 444 ASN cc_start: 0.8779 (t0) cc_final: 0.8415 (t0) REVERT: A 494 MET cc_start: 0.8614 (tpp) cc_final: 0.7934 (tpp) REVERT: A 500 ARG cc_start: 0.8375 (mmm-85) cc_final: 0.8158 (tpp80) REVERT: A 510 ASN cc_start: 0.8485 (t0) cc_final: 0.8210 (t0) REVERT: A 580 GLU cc_start: 0.7945 (tp30) cc_final: 0.7603 (tp30) REVERT: A 581 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7186 (pp20) REVERT: A 583 ARG cc_start: 0.8158 (ttp-170) cc_final: 0.7912 (ttp-170) REVERT: A 584 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8168 (mm) REVERT: A 588 LYS cc_start: 0.8578 (tttm) cc_final: 0.8242 (tttm) REVERT: A 592 ILE cc_start: 0.8756 (mt) cc_final: 0.8321 (mm) REVERT: A 609 ARG cc_start: 0.7808 (mtp-110) cc_final: 0.7534 (mtp-110) REVERT: A 613 GLN cc_start: 0.7682 (mt0) cc_final: 0.7360 (mt0) REVERT: A 614 HIS cc_start: 0.7752 (m-70) cc_final: 0.7218 (m-70) REVERT: A 641 TYR cc_start: 0.8005 (m-80) cc_final: 0.7542 (m-80) REVERT: A 643 TRP cc_start: 0.7825 (t-100) cc_final: 0.7173 (t-100) REVERT: A 810 MET cc_start: 0.7307 (ppp) cc_final: 0.6931 (tmm) REVERT: A 828 LYS cc_start: 0.8457 (mmmt) cc_final: 0.8221 (mmmt) REVERT: A 832 GLN cc_start: 0.8760 (tp40) cc_final: 0.8471 (tp40) REVERT: A 837 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.7803 (t80) REVERT: A 841 LYS cc_start: 0.8446 (mtpt) cc_final: 0.8083 (mtpp) REVERT: A 847 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7709 (mm-30) REVERT: A 850 VAL cc_start: 0.8934 (p) cc_final: 0.8706 (m) REVERT: A 864 LEU cc_start: 0.8053 (tp) cc_final: 0.7835 (tp) REVERT: A 866 GLU cc_start: 0.8209 (tp30) cc_final: 0.7826 (tp30) REVERT: A 878 VAL cc_start: 0.8921 (t) cc_final: 0.8685 (t) REVERT: A 900 GLN cc_start: 0.8631 (tp40) cc_final: 0.8403 (tp-100) REVERT: A 921 LEU cc_start: 0.8313 (mm) cc_final: 0.8065 (mp) REVERT: A 926 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7455 (mp0) REVERT: A 932 LEU cc_start: 0.8463 (tt) cc_final: 0.8200 (tp) REVERT: A 958 LYS cc_start: 0.8597 (ttpt) cc_final: 0.8162 (ttpt) REVERT: A 999 PHE cc_start: 0.8065 (m-80) cc_final: 0.7683 (m-80) REVERT: A 1003 SER cc_start: 0.8478 (t) cc_final: 0.8168 (m) REVERT: A 1058 THR cc_start: 0.8551 (p) cc_final: 0.8299 (p) REVERT: A 1063 VAL cc_start: 0.8471 (t) cc_final: 0.8132 (p) REVERT: A 1077 ILE cc_start: 0.8782 (mm) cc_final: 0.8510 (mm) REVERT: A 1098 ILE cc_start: 0.9106 (tp) cc_final: 0.8793 (tt) REVERT: A 1100 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8540 (m) REVERT: A 1103 ILE cc_start: 0.8544 (mm) cc_final: 0.8237 (mm) REVERT: A 1104 MET cc_start: 0.7869 (tpt) cc_final: 0.7481 (tpp) REVERT: A 1107 MET cc_start: 0.7177 (tmm) cc_final: 0.6308 (tmm) REVERT: A 1122 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7652 (tp30) REVERT: B 91 SER cc_start: 0.8680 (m) cc_final: 0.8446 (p) REVERT: B 109 LEU cc_start: 0.8488 (mp) cc_final: 0.8287 (mp) REVERT: B 140 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8083 (mp10) REVERT: B 160 MET cc_start: 0.8435 (mmt) cc_final: 0.8194 (mmm) REVERT: B 190 ASN cc_start: 0.7715 (p0) cc_final: 0.7383 (p0) REVERT: B 197 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7752 (mt-10) REVERT: B 214 VAL cc_start: 0.8683 (t) cc_final: 0.8474 (p) REVERT: B 217 LEU cc_start: 0.8733 (mt) cc_final: 0.8336 (mp) REVERT: B 233 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7693 (tm-30) REVERT: B 238 ASP cc_start: 0.7293 (m-30) cc_final: 0.6990 (m-30) REVERT: B 267 TYR cc_start: 0.8466 (t80) cc_final: 0.8220 (t80) REVERT: B 300 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7594 (mt-10) REVERT: B 319 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7987 (mp) REVERT: B 335 ASN cc_start: 0.8604 (t0) cc_final: 0.8281 (t0) REVERT: B 383 MET cc_start: 0.7369 (tpp) cc_final: 0.7130 (mmt) REVERT: B 392 TYR cc_start: 0.8614 (t80) cc_final: 0.8393 (t80) REVERT: B 443 GLU cc_start: 0.7914 (tp30) cc_final: 0.7529 (tp30) REVERT: B 444 ASN cc_start: 0.8821 (t0) cc_final: 0.8466 (t0) REVERT: B 476 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8552 (m) REVERT: B 485 ASP cc_start: 0.8281 (t0) cc_final: 0.8008 (t0) REVERT: B 486 ILE cc_start: 0.8528 (mm) cc_final: 0.8177 (mm) REVERT: B 517 PHE cc_start: 0.8365 (m-10) cc_final: 0.8076 (m-10) REVERT: B 520 ASP cc_start: 0.8064 (p0) cc_final: 0.7789 (p0) REVERT: B 579 MET cc_start: 0.7472 (tpt) cc_final: 0.7213 (tpt) REVERT: B 580 GLU cc_start: 0.7998 (tp30) cc_final: 0.7560 (tp30) REVERT: B 581 GLU cc_start: 0.7283 (tp30) cc_final: 0.6605 (tp30) REVERT: B 585 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7741 (ttm170) REVERT: B 588 LYS cc_start: 0.8387 (tttm) cc_final: 0.7955 (tttm) REVERT: B 590 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8140 (mt-10) REVERT: B 592 ILE cc_start: 0.8694 (mt) cc_final: 0.8328 (mm) REVERT: B 617 VAL cc_start: 0.7926 (t) cc_final: 0.7263 (m) REVERT: B 620 ASP cc_start: 0.7627 (t70) cc_final: 0.7184 (t70) REVERT: B 621 GLU cc_start: 0.7341 (mp0) cc_final: 0.6593 (mp0) REVERT: B 644 LEU cc_start: 0.8390 (mt) cc_final: 0.8160 (mp) REVERT: B 828 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8295 (mmtt) REVERT: B 835 LEU cc_start: 0.8725 (tp) cc_final: 0.8513 (tt) REVERT: B 837 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7813 (t80) REVERT: B 839 VAL cc_start: 0.8854 (t) cc_final: 0.8587 (t) REVERT: B 841 LYS cc_start: 0.8462 (mtpt) cc_final: 0.8117 (mtpp) REVERT: B 845 ILE cc_start: 0.8786 (mm) cc_final: 0.8460 (mt) REVERT: B 850 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8621 (m) REVERT: B 866 GLU cc_start: 0.8320 (tp30) cc_final: 0.8017 (tp30) REVERT: B 870 ILE cc_start: 0.8597 (mm) cc_final: 0.8286 (mm) REVERT: B 878 VAL cc_start: 0.8846 (t) cc_final: 0.8575 (t) REVERT: B 879 VAL cc_start: 0.8974 (p) cc_final: 0.8753 (t) REVERT: B 911 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7766 (mp0) REVERT: B 921 LEU cc_start: 0.8318 (mm) cc_final: 0.8037 (mp) REVERT: B 926 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7278 (mm-30) REVERT: B 972 PHE cc_start: 0.8487 (t80) cc_final: 0.8239 (t80) REVERT: B 976 ARG cc_start: 0.7731 (ttm-80) cc_final: 0.7185 (ttm170) REVERT: B 999 PHE cc_start: 0.8147 (m-80) cc_final: 0.7714 (m-80) REVERT: B 1003 SER cc_start: 0.8710 (t) cc_final: 0.8484 (m) REVERT: B 1045 MET cc_start: 0.8521 (ttm) cc_final: 0.8280 (tpp) REVERT: B 1058 THR cc_start: 0.8576 (p) cc_final: 0.8329 (p) REVERT: B 1072 ASP cc_start: 0.7763 (t70) cc_final: 0.7040 (t70) REVERT: B 1077 ILE cc_start: 0.8740 (mm) cc_final: 0.8473 (mm) REVERT: B 1098 ILE cc_start: 0.9068 (tp) cc_final: 0.8800 (tt) REVERT: B 1104 MET cc_start: 0.8175 (tpp) cc_final: 0.7934 (tpp) REVERT: B 1122 GLU cc_start: 0.7970 (tp30) cc_final: 0.7765 (tp30) REVERT: B 1145 VAL cc_start: 0.8521 (t) cc_final: 0.8247 (p) outliers start: 76 outliers final: 47 residues processed: 582 average time/residue: 0.2779 time to fit residues: 235.3043 Evaluate side-chains 591 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 534 time to evaluate : 1.751 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 173 optimal weight: 0.5980 chunk 191 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 59 optimal weight: 20.0000 chunk 144 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 140 optimal weight: 0.0870 overall best weight: 0.6560 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.133860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.114787 restraints weight = 23679.537| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.17 r_work: 0.3368 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3058 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= 0.140 Angle : 0.561 8.800 20912 Z= 0.289 Chirality : 0.040 0.200 2526 Planarity : 0.004 0.034 2600 Dihedral : 4.475 56.194 2096 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.13 % Allowed : 24.84 % Favored : 70.03 % 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: 1.65 (0.20), residues: 1938 helix: 1.82 (0.14), residues: 1420 sheet: -0.04 (0.57), residues: 96 loop : -1.11 (0.30), residues: 422 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 0.015 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 0.04368 ( 1166) hydrogen bonds : angle 4.05207 ( 3447) covalent geometry : bond 0.00297 (15404) covalent geometry : angle 0.56066 (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 627 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 546 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.8652 (m) cc_final: 0.8350 (p) REVERT: A 137 VAL cc_start: 0.8764 (p) cc_final: 0.8520 (t) REVERT: A 140 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7982 (mp10) REVERT: A 175 VAL cc_start: 0.8505 (p) cc_final: 0.8180 (m) REVERT: A 195 PHE cc_start: 0.7869 (t80) cc_final: 0.7563 (t80) REVERT: A 218 LYS cc_start: 0.8435 (ttmp) cc_final: 0.8210 (ttmp) REVERT: A 233 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7595 (tm-30) REVERT: A 267 TYR cc_start: 0.8571 (t80) cc_final: 0.8310 (t80) REVERT: A 284 LYS cc_start: 0.8710 (mmtm) cc_final: 0.8483 (mmmm) REVERT: A 291 SER cc_start: 0.8577 (t) cc_final: 0.8317 (p) REVERT: A 335 ASN cc_start: 0.8558 (t0) cc_final: 0.8261 (t0) REVERT: A 346 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7455 (mt-10) REVERT: A 395 ILE cc_start: 0.8184 (tt) cc_final: 0.7835 (pt) REVERT: A 443 GLU cc_start: 0.7965 (tp30) cc_final: 0.7669 (tp30) REVERT: A 444 ASN cc_start: 0.8800 (t0) cc_final: 0.8461 (t0) REVERT: A 462 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.8009 (mt) REVERT: A 500 ARG cc_start: 0.8355 (mmm-85) cc_final: 0.8148 (tpp80) REVERT: A 583 ARG cc_start: 0.8242 (ttp-170) cc_final: 0.7662 (mtp180) REVERT: A 588 LYS cc_start: 0.8605 (tttm) cc_final: 0.8274 (tttm) REVERT: A 592 ILE cc_start: 0.8797 (mt) cc_final: 0.8376 (mm) REVERT: A 609 ARG cc_start: 0.7775 (mtp-110) cc_final: 0.7503 (mtp-110) REVERT: A 613 GLN cc_start: 0.7746 (mt0) cc_final: 0.7484 (mt0) REVERT: A 614 HIS cc_start: 0.7721 (m-70) cc_final: 0.7508 (m-70) REVERT: A 624 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7493 (pp30) REVERT: A 641 TYR cc_start: 0.7999 (m-80) cc_final: 0.7530 (m-80) REVERT: A 647 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8192 (pttm) REVERT: A 810 MET cc_start: 0.7309 (ppp) cc_final: 0.6919 (tmm) REVERT: A 828 LYS cc_start: 0.8410 (mmmt) cc_final: 0.8182 (mmmt) REVERT: A 832 GLN cc_start: 0.8755 (tp40) cc_final: 0.8459 (tp40) REVERT: A 837 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.7813 (t80) REVERT: A 838 ASP cc_start: 0.8338 (t0) cc_final: 0.8010 (t0) REVERT: A 841 LYS cc_start: 0.8446 (mtpt) cc_final: 0.8123 (mtpp) REVERT: A 847 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7630 (mm-30) REVERT: A 850 VAL cc_start: 0.8916 (p) cc_final: 0.8684 (m) REVERT: A 864 LEU cc_start: 0.8123 (tp) cc_final: 0.7885 (tp) REVERT: A 865 ARG cc_start: 0.7216 (mmm160) cc_final: 0.6995 (mmm160) REVERT: A 866 GLU cc_start: 0.8280 (tp30) cc_final: 0.7868 (tp30) REVERT: A 871 SER cc_start: 0.8279 (t) cc_final: 0.7743 (p) REVERT: A 878 VAL cc_start: 0.8898 (t) cc_final: 0.8656 (t) REVERT: A 921 LEU cc_start: 0.8357 (mm) cc_final: 0.8126 (mp) REVERT: A 932 LEU cc_start: 0.8481 (tt) cc_final: 0.8219 (tp) REVERT: A 958 LYS cc_start: 0.8597 (ttpt) cc_final: 0.8226 (ttpt) REVERT: A 974 LYS cc_start: 0.9049 (ttpt) cc_final: 0.8832 (tppt) REVERT: A 986 GLU cc_start: 0.8199 (tt0) cc_final: 0.7945 (tt0) REVERT: A 999 PHE cc_start: 0.8110 (m-80) cc_final: 0.7760 (m-80) REVERT: A 1003 SER cc_start: 0.8588 (t) cc_final: 0.8282 (m) REVERT: A 1045 MET cc_start: 0.8616 (mmm) cc_final: 0.8394 (mmm) REVERT: A 1058 THR cc_start: 0.8538 (p) cc_final: 0.8295 (p) REVERT: A 1063 VAL cc_start: 0.8561 (t) cc_final: 0.8237 (p) REVERT: A 1077 ILE cc_start: 0.8794 (mm) cc_final: 0.8542 (mm) REVERT: A 1098 ILE cc_start: 0.9090 (tp) cc_final: 0.8779 (tt) REVERT: A 1100 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8555 (m) REVERT: A 1103 ILE cc_start: 0.8505 (mm) cc_final: 0.8300 (mm) REVERT: A 1104 MET cc_start: 0.7903 (tpt) cc_final: 0.7585 (tpp) REVERT: A 1107 MET cc_start: 0.7243 (tmm) cc_final: 0.6408 (tmm) REVERT: A 1122 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7620 (tp30) REVERT: A 1166 LEU cc_start: 0.7753 (tp) cc_final: 0.7514 (tp) REVERT: B 91 SER cc_start: 0.8650 (m) cc_final: 0.8446 (p) REVERT: B 109 LEU cc_start: 0.8479 (mp) cc_final: 0.8276 (mp) REVERT: B 140 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8061 (mp10) REVERT: B 154 MET cc_start: 0.8520 (tpp) cc_final: 0.7964 (tpp) REVERT: B 155 ASP cc_start: 0.8416 (t0) cc_final: 0.8033 (t0) REVERT: B 160 MET cc_start: 0.8485 (mmt) cc_final: 0.8245 (mmm) REVERT: B 190 ASN cc_start: 0.7725 (p0) cc_final: 0.7411 (p0) REVERT: B 197 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7760 (mt-10) REVERT: B 214 VAL cc_start: 0.8702 (t) cc_final: 0.8489 (p) REVERT: B 217 LEU cc_start: 0.8728 (mt) cc_final: 0.8334 (mp) REVERT: B 233 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7656 (tm-30) REVERT: B 238 ASP cc_start: 0.7329 (m-30) cc_final: 0.7024 (m-30) REVERT: B 267 TYR cc_start: 0.8446 (t80) cc_final: 0.8198 (t80) REVERT: B 319 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8003 (mp) REVERT: B 335 ASN cc_start: 0.8578 (t0) cc_final: 0.8246 (t0) REVERT: B 383 MET cc_start: 0.7359 (tpp) cc_final: 0.7061 (mmt) REVERT: B 443 GLU cc_start: 0.7919 (tp30) cc_final: 0.7522 (tp30) REVERT: B 444 ASN cc_start: 0.8865 (t0) cc_final: 0.8470 (t0) REVERT: B 476 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8561 (m) REVERT: B 486 ILE cc_start: 0.8532 (mm) cc_final: 0.8269 (mm) REVERT: B 517 PHE cc_start: 0.8302 (m-10) cc_final: 0.8011 (m-10) REVERT: B 520 ASP cc_start: 0.8063 (p0) cc_final: 0.7835 (p0) REVERT: B 579 MET cc_start: 0.7495 (tpt) cc_final: 0.7234 (tpt) REVERT: B 580 GLU cc_start: 0.8026 (tp30) cc_final: 0.7226 (tp30) REVERT: B 581 GLU cc_start: 0.7326 (tp30) cc_final: 0.6608 (tp30) REVERT: B 584 LEU cc_start: 0.8482 (mm) cc_final: 0.7830 (mm) REVERT: B 585 ARG cc_start: 0.8207 (ttm-80) cc_final: 0.7672 (ttm110) REVERT: B 588 LYS cc_start: 0.8423 (tttm) cc_final: 0.8001 (tttm) REVERT: B 590 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8216 (mt-10) REVERT: B 592 ILE cc_start: 0.8706 (mt) cc_final: 0.8336 (mm) REVERT: B 617 VAL cc_start: 0.7945 (t) cc_final: 0.7288 (m) REVERT: B 620 ASP cc_start: 0.7677 (t70) cc_final: 0.7356 (t70) REVERT: B 621 GLU cc_start: 0.7346 (mp0) cc_final: 0.6626 (mp0) REVERT: B 828 LYS cc_start: 0.8640 (mmtt) cc_final: 0.8269 (mmtt) REVERT: B 835 LEU cc_start: 0.8744 (tp) cc_final: 0.8535 (tt) REVERT: B 837 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.7824 (t80) REVERT: B 839 VAL cc_start: 0.8888 (t) cc_final: 0.8647 (t) REVERT: B 841 LYS cc_start: 0.8507 (mtpt) cc_final: 0.8194 (mtpp) REVERT: B 845 ILE cc_start: 0.8861 (mm) cc_final: 0.8558 (mt) REVERT: B 850 VAL cc_start: 0.8891 (p) cc_final: 0.8647 (m) REVERT: B 870 ILE cc_start: 0.8631 (mm) cc_final: 0.8331 (mm) REVERT: B 879 VAL cc_start: 0.8959 (p) cc_final: 0.8733 (t) REVERT: B 921 LEU cc_start: 0.8335 (mm) cc_final: 0.8077 (mp) REVERT: B 926 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7366 (mm-30) REVERT: B 972 PHE cc_start: 0.8535 (t80) cc_final: 0.8284 (t80) REVERT: B 974 LYS cc_start: 0.9036 (ttpt) cc_final: 0.8708 (tppt) REVERT: B 976 ARG cc_start: 0.7756 (ttm-80) cc_final: 0.7467 (ttm110) REVERT: B 999 PHE cc_start: 0.8157 (m-80) cc_final: 0.7761 (m-80) REVERT: B 1045 MET cc_start: 0.8516 (ttm) cc_final: 0.8288 (mmm) REVERT: B 1058 THR cc_start: 0.8578 (p) cc_final: 0.8369 (p) REVERT: B 1098 ILE cc_start: 0.9060 (tp) cc_final: 0.8791 (tt) REVERT: B 1145 VAL cc_start: 0.8559 (t) cc_final: 0.8289 (p) outliers start: 81 outliers final: 53 residues processed: 584 average time/residue: 0.2927 time to fit residues: 248.9464 Evaluate side-chains 594 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 531 time to evaluate : 1.716 ------------------------------------------------------------------------------- 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 462 ILE 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 915 GLU 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 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 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 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 626 ILE Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 837 TYR 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 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: 0.9980 chunk 192 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 148 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 GLN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS B 165 GLN B 981 HIS B1120 HIS B1154 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.132875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.114019 restraints weight = 23505.336| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.12 r_work: 0.3358 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15404 Z= 0.157 Angle : 0.581 7.833 20912 Z= 0.299 Chirality : 0.041 0.235 2526 Planarity : 0.004 0.032 2600 Dihedral : 4.488 56.359 2096 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 5.51 % Allowed : 25.79 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.20), residues: 1938 helix: 1.79 (0.14), residues: 1422 sheet: 0.02 (0.57), residues: 96 loop : -1.06 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.005 0.001 HIS B 981 PHE 0.026 0.001 PHE A 625 TYR 0.018 0.001 TYR A 280 ARG 0.005 0.000 ARG A 903 Details of bonding type rmsd hydrogen bonds : bond 0.04500 ( 1166) hydrogen bonds : angle 4.07935 ( 3447) covalent geometry : bond 0.00338 (15404) covalent geometry : angle 0.58081 (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 624 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 537 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.8673 (m) cc_final: 0.8360 (p) REVERT: A 129 ASP cc_start: 0.6360 (OUTLIER) cc_final: 0.5973 (p0) REVERT: A 137 VAL cc_start: 0.8701 (p) cc_final: 0.8416 (t) REVERT: A 140 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7924 (mp10) REVERT: A 175 VAL cc_start: 0.8535 (p) cc_final: 0.8210 (m) REVERT: A 176 VAL cc_start: 0.8748 (p) cc_final: 0.8537 (t) REVERT: A 195 PHE cc_start: 0.7872 (t80) cc_final: 0.7588 (t80) REVERT: A 218 LYS cc_start: 0.8420 (ttmp) cc_final: 0.8185 (ttmp) REVERT: A 233 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7535 (tm-30) REVERT: A 267 TYR cc_start: 0.8606 (t80) cc_final: 0.8363 (t80) REVERT: A 284 LYS cc_start: 0.8684 (mmtm) cc_final: 0.8455 (mmmm) REVERT: A 335 ASN cc_start: 0.8578 (t0) cc_final: 0.8293 (t0) REVERT: A 346 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7407 (mt-10) REVERT: A 395 ILE cc_start: 0.8164 (tt) cc_final: 0.7841 (pt) REVERT: A 443 GLU cc_start: 0.7940 (tp30) cc_final: 0.7636 (tp30) REVERT: A 444 ASN cc_start: 0.8812 (t0) cc_final: 0.8481 (t0) REVERT: A 494 MET cc_start: 0.8769 (tpp) cc_final: 0.8334 (tpp) REVERT: A 500 ARG cc_start: 0.8282 (mmm-85) cc_final: 0.8077 (tpp80) REVERT: A 588 LYS cc_start: 0.8639 (tttm) cc_final: 0.8314 (tttm) REVERT: A 592 ILE cc_start: 0.8799 (mt) cc_final: 0.8391 (mm) REVERT: A 609 ARG cc_start: 0.7781 (mtp-110) cc_final: 0.7482 (mtp-110) REVERT: A 613 GLN cc_start: 0.7796 (mt0) cc_final: 0.7507 (mt0) REVERT: A 624 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7183 (pp30) REVERT: A 643 TRP cc_start: 0.7823 (t-100) cc_final: 0.7233 (t-100) REVERT: A 647 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8120 (pttm) REVERT: A 810 MET cc_start: 0.7288 (ppp) cc_final: 0.6906 (tmm) REVERT: A 828 LYS cc_start: 0.8416 (mmmt) cc_final: 0.8081 (mmmt) REVERT: A 832 GLN cc_start: 0.8744 (tp40) cc_final: 0.8438 (tp-100) REVERT: A 837 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.7722 (t80) REVERT: A 841 LYS cc_start: 0.8453 (mtpt) cc_final: 0.8162 (mtpp) REVERT: A 845 ILE cc_start: 0.8877 (mm) cc_final: 0.8669 (mt) REVERT: A 847 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7758 (mm-30) REVERT: A 850 VAL cc_start: 0.8890 (p) cc_final: 0.8681 (m) REVERT: A 857 MET cc_start: 0.7630 (tmm) cc_final: 0.7368 (tpp) REVERT: A 864 LEU cc_start: 0.8116 (tp) cc_final: 0.7897 (tp) REVERT: A 865 ARG cc_start: 0.7289 (mmm160) cc_final: 0.7071 (mmm160) REVERT: A 866 GLU cc_start: 0.8266 (tp30) cc_final: 0.7898 (tp30) REVERT: A 868 LYS cc_start: 0.7851 (mmtp) cc_final: 0.7279 (mmmm) REVERT: A 871 SER cc_start: 0.8287 (t) cc_final: 0.7678 (p) REVERT: A 878 VAL cc_start: 0.8893 (t) cc_final: 0.8650 (t) REVERT: A 921 LEU cc_start: 0.8350 (mm) cc_final: 0.8127 (mp) REVERT: A 958 LYS cc_start: 0.8639 (ttpt) cc_final: 0.8264 (ttpt) REVERT: A 974 LYS cc_start: 0.9009 (ttpt) cc_final: 0.8749 (tppt) REVERT: A 976 ARG cc_start: 0.7821 (tpp80) cc_final: 0.7559 (ttm170) REVERT: A 986 GLU cc_start: 0.8198 (tt0) cc_final: 0.7946 (tt0) REVERT: A 1003 SER cc_start: 0.8669 (t) cc_final: 0.8401 (m) REVERT: A 1045 MET cc_start: 0.8637 (mmm) cc_final: 0.8412 (mmm) REVERT: A 1058 THR cc_start: 0.8585 (p) cc_final: 0.8346 (p) REVERT: A 1063 VAL cc_start: 0.8530 (t) cc_final: 0.8184 (p) REVERT: A 1073 MET cc_start: 0.8648 (mmm) cc_final: 0.8429 (mmm) REVERT: A 1077 ILE cc_start: 0.8830 (mm) cc_final: 0.8598 (mm) REVERT: A 1098 ILE cc_start: 0.9112 (tp) cc_final: 0.8806 (tt) REVERT: A 1100 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8584 (m) REVERT: A 1103 ILE cc_start: 0.8597 (mm) cc_final: 0.8350 (mm) REVERT: A 1104 MET cc_start: 0.7947 (tpt) cc_final: 0.7569 (tpp) REVERT: A 1107 MET cc_start: 0.7422 (tmm) cc_final: 0.6326 (tmm) REVERT: A 1122 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7558 (tp30) REVERT: A 1166 LEU cc_start: 0.7768 (tp) cc_final: 0.7525 (tp) REVERT: B 91 SER cc_start: 0.8654 (m) cc_final: 0.8448 (p) REVERT: B 140 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8039 (mp10) REVERT: B 141 ILE cc_start: 0.8708 (mm) cc_final: 0.8394 (mt) REVERT: B 154 MET cc_start: 0.8586 (tpp) cc_final: 0.7995 (tpp) REVERT: B 155 ASP cc_start: 0.8412 (t0) cc_final: 0.8047 (t0) REVERT: B 160 MET cc_start: 0.8461 (mmt) cc_final: 0.8228 (mmm) REVERT: B 190 ASN cc_start: 0.7747 (p0) cc_final: 0.7425 (p0) REVERT: B 197 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7706 (mt-10) REVERT: B 214 VAL cc_start: 0.8743 (t) cc_final: 0.8513 (p) REVERT: B 217 LEU cc_start: 0.8739 (mt) cc_final: 0.8326 (mp) REVERT: B 233 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7629 (tm-30) REVERT: B 238 ASP cc_start: 0.7330 (m-30) cc_final: 0.7022 (m-30) REVERT: B 267 TYR cc_start: 0.8528 (t80) cc_final: 0.8271 (t80) REVERT: B 335 ASN cc_start: 0.8629 (t0) cc_final: 0.8328 (t0) REVERT: B 443 GLU cc_start: 0.7899 (tp30) cc_final: 0.7505 (tp30) REVERT: B 444 ASN cc_start: 0.8890 (t0) cc_final: 0.8498 (t0) REVERT: B 476 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8602 (m) REVERT: B 485 ASP cc_start: 0.8265 (t0) cc_final: 0.8012 (t0) REVERT: B 486 ILE cc_start: 0.8533 (mm) cc_final: 0.8201 (mm) REVERT: B 517 PHE cc_start: 0.8264 (m-10) cc_final: 0.7979 (m-10) REVERT: B 520 ASP cc_start: 0.7966 (p0) cc_final: 0.7727 (p0) REVERT: B 579 MET cc_start: 0.7550 (tpt) cc_final: 0.7259 (tpt) REVERT: B 580 GLU cc_start: 0.8023 (tp30) cc_final: 0.7587 (tp30) REVERT: B 581 GLU cc_start: 0.7354 (tp30) cc_final: 0.6673 (tp30) REVERT: B 585 ARG cc_start: 0.8267 (ttm-80) cc_final: 0.7407 (ttm110) REVERT: B 586 MET cc_start: 0.8732 (ttp) cc_final: 0.8400 (ttm) REVERT: B 588 LYS cc_start: 0.8433 (tttm) cc_final: 0.8032 (tttm) REVERT: B 590 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8095 (mt-10) REVERT: B 592 ILE cc_start: 0.8719 (mt) cc_final: 0.8386 (mm) REVERT: B 617 VAL cc_start: 0.7945 (t) cc_final: 0.7326 (m) REVERT: B 620 ASP cc_start: 0.7689 (t70) cc_final: 0.7410 (t70) REVERT: B 621 GLU cc_start: 0.7344 (mp0) cc_final: 0.6685 (mp0) REVERT: B 837 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.7819 (t80) REVERT: B 839 VAL cc_start: 0.8909 (t) cc_final: 0.8701 (t) REVERT: B 841 LYS cc_start: 0.8544 (mtpt) cc_final: 0.8235 (mtpp) REVERT: B 845 ILE cc_start: 0.8934 (mm) cc_final: 0.8673 (mt) REVERT: B 850 VAL cc_start: 0.8876 (p) cc_final: 0.8645 (m) REVERT: B 870 ILE cc_start: 0.8665 (mm) cc_final: 0.8347 (mm) REVERT: B 871 SER cc_start: 0.8265 (t) cc_final: 0.7997 (t) REVERT: B 879 VAL cc_start: 0.8973 (p) cc_final: 0.8749 (t) REVERT: B 911 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: B 921 LEU cc_start: 0.8410 (mm) cc_final: 0.8127 (mp) REVERT: B 926 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7499 (mm-30) REVERT: B 931 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7742 (mm-30) REVERT: B 974 LYS cc_start: 0.9023 (ttpt) cc_final: 0.8623 (tppt) REVERT: B 976 ARG cc_start: 0.7725 (ttm-80) cc_final: 0.7246 (ttm-80) REVERT: B 999 PHE cc_start: 0.8176 (m-80) cc_final: 0.7772 (m-80) REVERT: B 1098 ILE cc_start: 0.9094 (tp) cc_final: 0.8815 (tt) REVERT: B 1104 MET cc_start: 0.8437 (tpp) cc_final: 0.8225 (tpp) outliers start: 87 outliers final: 57 residues processed: 582 average time/residue: 0.3104 time to fit residues: 263.7577 Evaluate side-chains 595 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 528 time to evaluate : 1.860 ------------------------------------------------------------------------------- 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 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 510 ASN 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 858 VAL 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 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 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 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 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 911 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 33 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 181 optimal weight: 0.6980 chunk 45 optimal weight: 0.0670 chunk 171 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 66 optimal weight: 0.0870 chunk 69 optimal weight: 1.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 GLN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3771 r_free = 0.3771 target = 0.133788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.114877 restraints weight = 23660.087| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.15 r_work: 0.3376 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3425 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= 0.128 Angle : 0.575 9.052 20912 Z= 0.293 Chirality : 0.040 0.250 2526 Planarity : 0.004 0.034 2600 Dihedral : 4.473 57.020 2096 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.94 % Allowed : 27.06 % Favored : 68.00 % 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: 1.77 (0.20), residues: 1938 helix: 1.88 (0.14), residues: 1424 sheet: 0.07 (0.57), residues: 96 loop : -1.00 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.004 0.000 HIS B 981 PHE 0.023 0.001 PHE A 625 TYR 0.017 0.001 TYR A 280 ARG 0.007 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 1166) hydrogen bonds : angle 4.02499 ( 3447) covalent geometry : bond 0.00269 (15404) covalent geometry : angle 0.57536 (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 613 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 535 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.8674 (m) cc_final: 0.8363 (p) REVERT: A 129 ASP cc_start: 0.6310 (OUTLIER) cc_final: 0.5946 (p0) REVERT: A 137 VAL cc_start: 0.8663 (p) cc_final: 0.8358 (t) REVERT: A 140 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7952 (mp10) REVERT: A 175 VAL cc_start: 0.8494 (p) cc_final: 0.8188 (m) REVERT: A 195 PHE cc_start: 0.7845 (t80) cc_final: 0.7518 (t80) REVERT: A 218 LYS cc_start: 0.8437 (ttmp) cc_final: 0.8188 (ttmp) REVERT: A 233 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7543 (tm-30) REVERT: A 267 TYR cc_start: 0.8603 (t80) cc_final: 0.8367 (t80) REVERT: A 284 LYS cc_start: 0.8718 (mmtm) cc_final: 0.8481 (mmmm) REVERT: A 335 ASN cc_start: 0.8538 (t0) cc_final: 0.8239 (t0) REVERT: A 346 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7388 (mt-10) REVERT: A 395 ILE cc_start: 0.8139 (tt) cc_final: 0.7807 (pt) REVERT: A 425 MET cc_start: 0.8585 (mtm) cc_final: 0.8365 (mtm) REVERT: A 443 GLU cc_start: 0.7930 (tp30) cc_final: 0.7629 (tp30) REVERT: A 500 ARG cc_start: 0.8263 (mmm-85) cc_final: 0.8059 (tpp80) REVERT: A 579 MET cc_start: 0.7525 (tmm) cc_final: 0.7266 (tmm) REVERT: A 583 ARG cc_start: 0.8262 (ttp-170) cc_final: 0.7852 (mtp180) REVERT: A 586 MET cc_start: 0.8526 (ttt) cc_final: 0.8326 (ttt) REVERT: A 588 LYS cc_start: 0.8646 (tttm) cc_final: 0.8295 (tttm) REVERT: A 592 ILE cc_start: 0.8786 (mt) cc_final: 0.8393 (mm) REVERT: A 609 ARG cc_start: 0.7756 (mtp-110) cc_final: 0.7460 (mtp-110) REVERT: A 613 GLN cc_start: 0.7765 (mt0) cc_final: 0.7487 (mt0) REVERT: A 624 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7293 (pp30) REVERT: A 633 LYS cc_start: 0.8690 (mttm) cc_final: 0.8483 (mttt) REVERT: A 641 TYR cc_start: 0.8039 (m-80) cc_final: 0.7584 (m-80) REVERT: A 647 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8202 (pttm) REVERT: A 810 MET cc_start: 0.7266 (ppp) cc_final: 0.6902 (tmm) REVERT: A 828 LYS cc_start: 0.8402 (mmmt) cc_final: 0.8101 (mmmt) REVERT: A 832 GLN cc_start: 0.8737 (tp40) cc_final: 0.8409 (tp-100) REVERT: A 837 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.7755 (t80) REVERT: A 841 LYS cc_start: 0.8438 (mtpt) cc_final: 0.8142 (mtpp) REVERT: A 864 LEU cc_start: 0.8073 (tp) cc_final: 0.7852 (tp) REVERT: A 865 ARG cc_start: 0.7263 (mmm160) cc_final: 0.7010 (mmm160) REVERT: A 866 GLU cc_start: 0.8266 (tp30) cc_final: 0.7894 (tp30) REVERT: A 871 SER cc_start: 0.8241 (t) cc_final: 0.7678 (p) REVERT: A 878 VAL cc_start: 0.8888 (t) cc_final: 0.8643 (t) REVERT: A 880 LYS cc_start: 0.8801 (tttm) cc_final: 0.8548 (tttp) REVERT: A 921 LEU cc_start: 0.8336 (mm) cc_final: 0.8102 (mp) REVERT: A 958 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8258 (ttpt) REVERT: A 974 LYS cc_start: 0.8977 (ttpt) cc_final: 0.8709 (tppt) REVERT: A 976 ARG cc_start: 0.7860 (tpp80) cc_final: 0.7582 (ttm170) REVERT: A 986 GLU cc_start: 0.8211 (tt0) cc_final: 0.7909 (tt0) REVERT: A 999 PHE cc_start: 0.8149 (m-80) cc_final: 0.7923 (m-80) REVERT: A 1045 MET cc_start: 0.8650 (mmm) cc_final: 0.8422 (mmm) REVERT: A 1058 THR cc_start: 0.8583 (p) cc_final: 0.8329 (p) REVERT: A 1063 VAL cc_start: 0.8544 (t) cc_final: 0.8182 (p) REVERT: A 1073 MET cc_start: 0.8666 (mmm) cc_final: 0.8447 (mmm) REVERT: A 1077 ILE cc_start: 0.8832 (mm) cc_final: 0.8592 (mm) REVERT: A 1078 ASP cc_start: 0.7718 (m-30) cc_final: 0.7404 (m-30) REVERT: A 1098 ILE cc_start: 0.9019 (tp) cc_final: 0.8794 (tt) REVERT: A 1100 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8581 (m) REVERT: A 1104 MET cc_start: 0.7913 (tpt) cc_final: 0.7537 (tpp) REVERT: A 1107 MET cc_start: 0.7464 (tmm) cc_final: 0.5990 (tmm) REVERT: A 1122 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7588 (tp30) REVERT: A 1166 LEU cc_start: 0.7778 (tp) cc_final: 0.7523 (tp) REVERT: B 91 SER cc_start: 0.8659 (m) cc_final: 0.8434 (p) REVERT: B 109 LEU cc_start: 0.8512 (mp) cc_final: 0.8305 (mp) REVERT: B 140 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7992 (mp10) REVERT: B 141 ILE cc_start: 0.8641 (mm) cc_final: 0.8331 (mt) REVERT: B 154 MET cc_start: 0.8559 (tpp) cc_final: 0.7956 (tpp) REVERT: B 155 ASP cc_start: 0.8405 (t0) cc_final: 0.8034 (t0) REVERT: B 160 MET cc_start: 0.8432 (mmt) cc_final: 0.8203 (mmm) REVERT: B 190 ASN cc_start: 0.7730 (p0) cc_final: 0.7414 (p0) REVERT: B 197 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7585 (mt-10) REVERT: B 214 VAL cc_start: 0.8743 (t) cc_final: 0.8511 (p) REVERT: B 217 LEU cc_start: 0.8726 (mt) cc_final: 0.8325 (mp) REVERT: B 233 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7625 (tm-30) REVERT: B 238 ASP cc_start: 0.7342 (m-30) cc_final: 0.7014 (m-30) REVERT: B 267 TYR cc_start: 0.8483 (t80) cc_final: 0.8251 (t80) REVERT: B 335 ASN cc_start: 0.8562 (t0) cc_final: 0.8244 (t0) REVERT: B 443 GLU cc_start: 0.7909 (tp30) cc_final: 0.7503 (tp30) REVERT: B 444 ASN cc_start: 0.8880 (t0) cc_final: 0.8496 (t0) REVERT: B 476 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8541 (m) REVERT: B 485 ASP cc_start: 0.8271 (t0) cc_final: 0.8028 (t0) REVERT: B 486 ILE cc_start: 0.8492 (mm) cc_final: 0.8156 (mm) REVERT: B 517 PHE cc_start: 0.8206 (m-10) cc_final: 0.7973 (m-10) REVERT: B 520 ASP cc_start: 0.7938 (p0) cc_final: 0.7726 (p0) REVERT: B 579 MET cc_start: 0.7506 (tpt) cc_final: 0.7235 (tpt) REVERT: B 580 GLU cc_start: 0.7971 (tp30) cc_final: 0.7578 (tp30) REVERT: B 581 GLU cc_start: 0.7353 (tp30) cc_final: 0.6798 (tp30) REVERT: B 585 ARG cc_start: 0.8153 (ttm-80) cc_final: 0.7535 (ttm170) REVERT: B 588 LYS cc_start: 0.8462 (tttm) cc_final: 0.8048 (tttm) REVERT: B 590 GLU cc_start: 0.8588 (mt-10) cc_final: 0.7991 (mt-10) REVERT: B 592 ILE cc_start: 0.8690 (mt) cc_final: 0.8348 (mm) REVERT: B 617 VAL cc_start: 0.7848 (t) cc_final: 0.7219 (m) REVERT: B 620 ASP cc_start: 0.7665 (t70) cc_final: 0.7395 (t70) REVERT: B 621 GLU cc_start: 0.7321 (mp0) cc_final: 0.6666 (mp0) REVERT: B 837 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.7841 (t80) REVERT: B 839 VAL cc_start: 0.8940 (t) cc_final: 0.8706 (t) REVERT: B 841 LYS cc_start: 0.8526 (mtpt) cc_final: 0.8214 (mtpp) REVERT: B 845 ILE cc_start: 0.8921 (mm) cc_final: 0.8631 (mt) REVERT: B 850 VAL cc_start: 0.8836 (p) cc_final: 0.8608 (m) REVERT: B 870 ILE cc_start: 0.8622 (mm) cc_final: 0.8312 (mm) REVERT: B 871 SER cc_start: 0.8231 (t) cc_final: 0.7968 (t) REVERT: B 877 GLN cc_start: 0.8699 (tt0) cc_final: 0.8494 (tt0) REVERT: B 879 VAL cc_start: 0.8975 (p) cc_final: 0.8748 (t) REVERT: B 911 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: B 921 LEU cc_start: 0.8379 (mm) cc_final: 0.8097 (mp) REVERT: B 974 LYS cc_start: 0.9007 (ttpt) cc_final: 0.8626 (tppt) REVERT: B 976 ARG cc_start: 0.7734 (ttm-80) cc_final: 0.7283 (ttm-80) REVERT: B 999 PHE cc_start: 0.8146 (m-80) cc_final: 0.7725 (m-80) REVERT: B 1078 ASP cc_start: 0.7761 (m-30) cc_final: 0.7445 (m-30) REVERT: B 1098 ILE cc_start: 0.9071 (tp) cc_final: 0.8789 (tt) REVERT: B 1104 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8147 (tpp) outliers start: 78 outliers final: 57 residues processed: 569 average time/residue: 0.2801 time to fit residues: 230.7061 Evaluate side-chains 598 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 530 time to evaluate : 1.614 ------------------------------------------------------------------------------- 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 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 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 858 VAL 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 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 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 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 911 GLU 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 1063 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1104 MET 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: 3.9990 chunk 89 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 981 HIS B1154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.132574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113828 restraints weight = 23465.172| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.14 r_work: 0.3357 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15404 Z= 0.158 Angle : 0.604 8.139 20912 Z= 0.308 Chirality : 0.042 0.270 2526 Planarity : 0.004 0.048 2600 Dihedral : 4.488 56.675 2096 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.07 % Allowed : 27.76 % Favored : 67.17 % 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: 1.73 (0.20), residues: 1938 helix: 1.84 (0.14), residues: 1422 sheet: 0.04 (0.56), residues: 96 loop : -0.98 (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 981 PHE 0.022 0.001 PHE A 625 TYR 0.018 0.001 TYR A 280 ARG 0.009 0.001 ARG B 940 Details of bonding type rmsd hydrogen bonds : bond 0.04492 ( 1166) hydrogen bonds : angle 4.07132 ( 3447) covalent geometry : bond 0.00345 (15404) covalent geometry : angle 0.60404 (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 612 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 532 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.8637 (m) cc_final: 0.8307 (p) REVERT: A 129 ASP cc_start: 0.6372 (OUTLIER) cc_final: 0.5990 (p0) REVERT: A 137 VAL cc_start: 0.8671 (p) cc_final: 0.8369 (t) REVERT: A 140 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7957 (mp10) REVERT: A 174 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8173 (tp) REVERT: A 175 VAL cc_start: 0.8486 (p) cc_final: 0.8191 (m) REVERT: A 195 PHE cc_start: 0.7942 (t80) cc_final: 0.7648 (t80) REVERT: A 197 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7571 (mt-10) REVERT: A 218 LYS cc_start: 0.8452 (ttmp) cc_final: 0.8212 (ttmp) REVERT: A 233 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7497 (tm-30) REVERT: A 267 TYR cc_start: 0.8626 (t80) cc_final: 0.8383 (t80) REVERT: A 284 LYS cc_start: 0.8699 (mmtm) cc_final: 0.8462 (mmmm) REVERT: A 346 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7379 (mt-10) REVERT: A 395 ILE cc_start: 0.8203 (tt) cc_final: 0.7904 (pt) REVERT: A 443 GLU cc_start: 0.7953 (tp30) cc_final: 0.7664 (tp30) REVERT: A 579 MET cc_start: 0.7510 (tmm) cc_final: 0.7270 (tmm) REVERT: A 588 LYS cc_start: 0.8632 (tttm) cc_final: 0.8261 (tttm) REVERT: A 592 ILE cc_start: 0.8809 (mt) cc_final: 0.8406 (mm) REVERT: A 609 ARG cc_start: 0.7735 (mtp-110) cc_final: 0.7441 (mtp-110) REVERT: A 613 GLN cc_start: 0.7802 (mt0) cc_final: 0.7546 (mt0) REVERT: A 621 GLU cc_start: 0.7571 (mp0) cc_final: 0.7053 (mp0) REVERT: A 624 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7118 (pp30) REVERT: A 810 MET cc_start: 0.7237 (ppp) cc_final: 0.6880 (tmm) REVERT: A 832 GLN cc_start: 0.8750 (tp40) cc_final: 0.8418 (tp-100) REVERT: A 837 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7736 (t80) REVERT: A 841 LYS cc_start: 0.8448 (mtpt) cc_final: 0.8148 (mtpp) REVERT: A 845 ILE cc_start: 0.8872 (mm) cc_final: 0.8671 (mt) REVERT: A 857 MET cc_start: 0.8252 (tpp) cc_final: 0.8018 (tmm) REVERT: A 865 ARG cc_start: 0.7270 (mmm160) cc_final: 0.7025 (mmm160) REVERT: A 866 GLU cc_start: 0.8243 (tp30) cc_final: 0.7877 (tp30) REVERT: A 868 LYS cc_start: 0.7856 (mmtp) cc_final: 0.7118 (mmtp) REVERT: A 871 SER cc_start: 0.8269 (t) cc_final: 0.7690 (p) REVERT: A 878 VAL cc_start: 0.8901 (t) cc_final: 0.8656 (t) REVERT: A 921 LEU cc_start: 0.8405 (mm) cc_final: 0.8137 (mp) REVERT: A 958 LYS cc_start: 0.8690 (ttpt) cc_final: 0.8246 (ttpt) REVERT: A 972 PHE cc_start: 0.8610 (t80) cc_final: 0.8368 (t80) REVERT: A 974 LYS cc_start: 0.9006 (ttpt) cc_final: 0.8698 (tppt) REVERT: A 976 ARG cc_start: 0.7900 (tpp80) cc_final: 0.7596 (ttm170) REVERT: A 986 GLU cc_start: 0.8258 (tt0) cc_final: 0.7946 (tt0) REVERT: A 999 PHE cc_start: 0.8189 (m-80) cc_final: 0.7950 (m-80) REVERT: A 1058 THR cc_start: 0.8578 (p) cc_final: 0.8331 (p) REVERT: A 1063 VAL cc_start: 0.8623 (t) cc_final: 0.8293 (p) REVERT: A 1073 MET cc_start: 0.8680 (mmm) cc_final: 0.8473 (mmm) REVERT: A 1078 ASP cc_start: 0.7778 (m-30) cc_final: 0.7473 (m-30) REVERT: A 1100 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8616 (m) REVERT: A 1104 MET cc_start: 0.7953 (tpt) cc_final: 0.7603 (tpp) REVERT: A 1107 MET cc_start: 0.7457 (tmm) cc_final: 0.6029 (tmm) REVERT: A 1122 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7608 (tp30) REVERT: A 1166 LEU cc_start: 0.7889 (tp) cc_final: 0.7632 (tp) REVERT: A 1174 LEU cc_start: 0.8299 (mt) cc_final: 0.8050 (mm) REVERT: B 91 SER cc_start: 0.8667 (m) cc_final: 0.8443 (p) REVERT: B 140 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8002 (mp10) REVERT: B 141 ILE cc_start: 0.8692 (mm) cc_final: 0.8398 (mt) REVERT: B 154 MET cc_start: 0.8601 (tpp) cc_final: 0.8005 (tpp) REVERT: B 155 ASP cc_start: 0.8394 (t0) cc_final: 0.8034 (t0) REVERT: B 160 MET cc_start: 0.8433 (mmt) cc_final: 0.8196 (mmm) REVERT: B 190 ASN cc_start: 0.7770 (p0) cc_final: 0.7449 (p0) REVERT: B 197 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7577 (mt-10) REVERT: B 214 VAL cc_start: 0.8737 (t) cc_final: 0.8499 (p) REVERT: B 217 LEU cc_start: 0.8732 (mt) cc_final: 0.8320 (mp) REVERT: B 233 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7621 (tm-30) REVERT: B 238 ASP cc_start: 0.7403 (m-30) cc_final: 0.7067 (m-30) REVERT: B 267 TYR cc_start: 0.8532 (t80) cc_final: 0.8277 (t80) REVERT: B 300 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7805 (mt-10) REVERT: B 335 ASN cc_start: 0.8560 (t0) cc_final: 0.8250 (t0) REVERT: B 443 GLU cc_start: 0.7940 (tp30) cc_final: 0.7556 (tp30) REVERT: B 444 ASN cc_start: 0.8870 (t0) cc_final: 0.8476 (t0) REVERT: B 476 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8546 (m) REVERT: B 485 ASP cc_start: 0.8283 (t0) cc_final: 0.8040 (t0) REVERT: B 486 ILE cc_start: 0.8504 (mm) cc_final: 0.8252 (mm) REVERT: B 517 PHE cc_start: 0.8182 (m-10) cc_final: 0.7964 (m-10) REVERT: B 520 ASP cc_start: 0.7996 (p0) cc_final: 0.7765 (p0) REVERT: B 579 MET cc_start: 0.7524 (tpt) cc_final: 0.7240 (tpt) REVERT: B 580 GLU cc_start: 0.7998 (tp30) cc_final: 0.7594 (tp30) REVERT: B 586 MET cc_start: 0.8605 (ttp) cc_final: 0.8318 (ttm) REVERT: B 588 LYS cc_start: 0.8528 (tttm) cc_final: 0.8137 (tttm) REVERT: B 590 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8340 (mt-10) REVERT: B 592 ILE cc_start: 0.8699 (mt) cc_final: 0.8372 (mm) REVERT: B 617 VAL cc_start: 0.7870 (t) cc_final: 0.7241 (m) REVERT: B 620 ASP cc_start: 0.7667 (t70) cc_final: 0.7416 (t70) REVERT: B 621 GLU cc_start: 0.7365 (mp0) cc_final: 0.6720 (mp0) REVERT: B 837 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7819 (t80) REVERT: B 839 VAL cc_start: 0.8902 (t) cc_final: 0.8701 (t) REVERT: B 841 LYS cc_start: 0.8544 (mtpt) cc_final: 0.8221 (mtpp) REVERT: B 845 ILE cc_start: 0.8927 (mm) cc_final: 0.8637 (mt) REVERT: B 850 VAL cc_start: 0.8827 (p) cc_final: 0.8607 (m) REVERT: B 865 ARG cc_start: 0.7616 (mmm160) cc_final: 0.7268 (mmm160) REVERT: B 870 ILE cc_start: 0.8623 (mm) cc_final: 0.8306 (mm) REVERT: B 871 SER cc_start: 0.8244 (t) cc_final: 0.7986 (t) REVERT: B 879 VAL cc_start: 0.8953 (p) cc_final: 0.8740 (t) REVERT: B 911 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: B 921 LEU cc_start: 0.8424 (mm) cc_final: 0.8149 (mp) REVERT: B 959 ASN cc_start: 0.8237 (m-40) cc_final: 0.7928 (m-40) REVERT: B 974 LYS cc_start: 0.9027 (ttpt) cc_final: 0.8626 (tppt) REVERT: B 976 ARG cc_start: 0.7823 (ttm-80) cc_final: 0.7439 (ttm-80) REVERT: B 999 PHE cc_start: 0.8192 (m-80) cc_final: 0.7830 (m-80) REVERT: B 1078 ASP cc_start: 0.7854 (m-30) cc_final: 0.7537 (m-30) REVERT: B 1098 ILE cc_start: 0.9074 (tp) cc_final: 0.8787 (tt) REVERT: B 1104 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8167 (tpp) outliers start: 80 outliers final: 58 residues processed: 568 average time/residue: 0.2846 time to fit residues: 233.3296 Evaluate side-chains 591 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 522 time to evaluate : 1.723 ------------------------------------------------------------------------------- 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 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 418 THR 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 858 VAL 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 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 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 257 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 293 ILE 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 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 911 GLU Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 991 GLU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1104 MET 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: 1.9990 chunk 133 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 51 optimal weight: 0.1980 chunk 124 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** B1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1154 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.132805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.114228 restraints weight = 23359.835| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.11 r_work: 0.3360 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3700 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= 0.152 Angle : 0.609 9.200 20912 Z= 0.308 Chirality : 0.042 0.244 2526 Planarity : 0.004 0.035 2600 Dihedral : 4.505 56.985 2096 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.69 % Allowed : 28.45 % 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: 1.73 (0.20), residues: 1938 helix: 1.84 (0.14), residues: 1422 sheet: 0.04 (0.56), residues: 96 loop : -0.99 (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 0.015 0.001 PHE A 625 TYR 0.019 0.001 TYR A 280 ARG 0.007 0.001 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 1166) hydrogen bonds : angle 4.07082 ( 3447) covalent geometry : bond 0.00330 (15404) covalent geometry : angle 0.60871 (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 598 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 524 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8488 (m-10) cc_final: 0.8248 (m-10) REVERT: A 91 SER cc_start: 0.8602 (m) cc_final: 0.8309 (p) REVERT: A 129 ASP cc_start: 0.6367 (OUTLIER) cc_final: 0.5990 (p0) REVERT: A 137 VAL cc_start: 0.8671 (p) cc_final: 0.8367 (t) REVERT: A 140 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7943 (mp10) REVERT: A 174 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8141 (tp) REVERT: A 175 VAL cc_start: 0.8492 (p) cc_final: 0.8213 (m) REVERT: A 195 PHE cc_start: 0.7923 (t80) cc_final: 0.7628 (t80) REVERT: A 197 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7556 (mt-10) REVERT: A 205 MET cc_start: 0.8278 (mmm) cc_final: 0.8076 (mmt) REVERT: A 218 LYS cc_start: 0.8458 (ttmp) cc_final: 0.8220 (ttmp) REVERT: A 233 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7552 (tm-30) REVERT: A 267 TYR cc_start: 0.8625 (t80) cc_final: 0.8382 (t80) REVERT: A 284 LYS cc_start: 0.8686 (mmtm) cc_final: 0.8456 (mmmm) REVERT: A 346 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7361 (mt-10) REVERT: A 395 ILE cc_start: 0.8213 (tt) cc_final: 0.7902 (pt) REVERT: A 443 GLU cc_start: 0.7928 (tp30) cc_final: 0.7634 (tp30) REVERT: A 511 MET cc_start: 0.8884 (tmm) cc_final: 0.8565 (ttp) REVERT: A 580 GLU cc_start: 0.8172 (tp30) cc_final: 0.7917 (tp30) REVERT: A 588 LYS cc_start: 0.8647 (tttm) cc_final: 0.8268 (tttm) REVERT: A 592 ILE cc_start: 0.8819 (mt) cc_final: 0.8433 (mm) REVERT: A 609 ARG cc_start: 0.7800 (mtp-110) cc_final: 0.7473 (mtp-110) REVERT: A 613 GLN cc_start: 0.7803 (mt0) cc_final: 0.7550 (mt0) REVERT: A 624 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7020 (pp30) REVERT: A 810 MET cc_start: 0.7235 (ppp) cc_final: 0.6876 (tmm) REVERT: A 832 GLN cc_start: 0.8763 (tp40) cc_final: 0.8428 (tp-100) REVERT: A 837 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7765 (t80) REVERT: A 838 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8167 (t0) REVERT: A 841 LYS cc_start: 0.8430 (mtpt) cc_final: 0.8119 (mtpp) REVERT: A 845 ILE cc_start: 0.8893 (mm) cc_final: 0.8692 (mt) REVERT: A 857 MET cc_start: 0.8222 (tpp) cc_final: 0.7754 (tmm) REVERT: A 865 ARG cc_start: 0.7336 (mmm160) cc_final: 0.7095 (mmm160) REVERT: A 866 GLU cc_start: 0.8279 (tp30) cc_final: 0.7933 (tp30) REVERT: A 868 LYS cc_start: 0.7911 (mmtp) cc_final: 0.7187 (mmtp) REVERT: A 871 SER cc_start: 0.8286 (t) cc_final: 0.7675 (p) REVERT: A 921 LEU cc_start: 0.8399 (mm) cc_final: 0.8150 (mp) REVERT: A 958 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8261 (ttpt) REVERT: A 974 LYS cc_start: 0.8971 (ttpt) cc_final: 0.8661 (tppt) REVERT: A 986 GLU cc_start: 0.8244 (tt0) cc_final: 0.7934 (tt0) REVERT: A 999 PHE cc_start: 0.8181 (m-80) cc_final: 0.7940 (m-80) REVERT: A 1058 THR cc_start: 0.8579 (p) cc_final: 0.8328 (p) REVERT: A 1063 VAL cc_start: 0.8620 (t) cc_final: 0.8283 (p) REVERT: A 1073 MET cc_start: 0.8611 (mmm) cc_final: 0.8404 (mmm) REVERT: A 1078 ASP cc_start: 0.7768 (m-30) cc_final: 0.7452 (m-30) REVERT: A 1100 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8641 (m) REVERT: A 1104 MET cc_start: 0.7965 (tpt) cc_final: 0.7634 (tpp) REVERT: A 1107 MET cc_start: 0.7459 (tmm) cc_final: 0.6006 (tmm) REVERT: A 1122 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7302 (mm-30) REVERT: A 1166 LEU cc_start: 0.7917 (tp) cc_final: 0.7667 (tp) REVERT: A 1174 LEU cc_start: 0.8307 (mt) cc_final: 0.8074 (mm) REVERT: B 91 SER cc_start: 0.8668 (m) cc_final: 0.8430 (p) REVERT: B 140 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7997 (mp10) REVERT: B 141 ILE cc_start: 0.8687 (mm) cc_final: 0.8390 (mt) REVERT: B 154 MET cc_start: 0.8613 (tpp) cc_final: 0.8002 (tpp) REVERT: B 155 ASP cc_start: 0.8353 (t0) cc_final: 0.7991 (t0) REVERT: B 160 MET cc_start: 0.8419 (mmt) cc_final: 0.8174 (mmm) REVERT: B 190 ASN cc_start: 0.7758 (p0) cc_final: 0.7447 (p0) REVERT: B 214 VAL cc_start: 0.8720 (t) cc_final: 0.8477 (p) REVERT: B 217 LEU cc_start: 0.8734 (mt) cc_final: 0.8322 (mp) REVERT: B 238 ASP cc_start: 0.7364 (m-30) cc_final: 0.7022 (m-30) REVERT: B 267 TYR cc_start: 0.8519 (t80) cc_final: 0.8253 (t80) REVERT: B 335 ASN cc_start: 0.8583 (t0) cc_final: 0.8326 (t0) REVERT: B 337 GLU cc_start: 0.8049 (mp0) cc_final: 0.7665 (mp0) REVERT: B 338 LYS cc_start: 0.8467 (mtmm) cc_final: 0.8223 (mttp) REVERT: B 444 ASN cc_start: 0.8884 (t0) cc_final: 0.8452 (t0) REVERT: B 476 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8545 (m) REVERT: B 485 ASP cc_start: 0.8324 (t0) cc_final: 0.8124 (t0) REVERT: B 486 ILE cc_start: 0.8551 (mm) cc_final: 0.8281 (mm) REVERT: B 520 ASP cc_start: 0.7968 (p0) cc_final: 0.7734 (p0) REVERT: B 579 MET cc_start: 0.7484 (tpt) cc_final: 0.7198 (tpt) REVERT: B 580 GLU cc_start: 0.7981 (tp30) cc_final: 0.7571 (tp30) REVERT: B 581 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7429 (pp20) REVERT: B 588 LYS cc_start: 0.8507 (tttm) cc_final: 0.8139 (tttm) REVERT: B 592 ILE cc_start: 0.8739 (mt) cc_final: 0.8421 (mm) REVERT: B 617 VAL cc_start: 0.7861 (t) cc_final: 0.7261 (m) REVERT: B 620 ASP cc_start: 0.7676 (t70) cc_final: 0.7439 (t70) REVERT: B 621 GLU cc_start: 0.7352 (mp0) cc_final: 0.6699 (mp0) REVERT: B 837 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7842 (t80) REVERT: B 839 VAL cc_start: 0.8930 (t) cc_final: 0.8698 (t) REVERT: B 841 LYS cc_start: 0.8544 (mtpt) cc_final: 0.8234 (mtpp) REVERT: B 845 ILE cc_start: 0.8952 (mm) cc_final: 0.8680 (mt) REVERT: B 850 VAL cc_start: 0.8871 (p) cc_final: 0.8654 (m) REVERT: B 855 ASP cc_start: 0.7838 (t0) cc_final: 0.7464 (t0) REVERT: B 865 ARG cc_start: 0.7651 (mmm160) cc_final: 0.7296 (mmm160) REVERT: B 866 GLU cc_start: 0.8262 (tp30) cc_final: 0.7770 (tm-30) REVERT: B 870 ILE cc_start: 0.8604 (mm) cc_final: 0.8086 (mm) REVERT: B 871 SER cc_start: 0.8218 (t) cc_final: 0.7957 (t) REVERT: B 879 VAL cc_start: 0.8961 (p) cc_final: 0.8745 (t) REVERT: B 921 LEU cc_start: 0.8454 (mm) cc_final: 0.8179 (mp) REVERT: B 959 ASN cc_start: 0.8215 (m-40) cc_final: 0.7920 (m-40) REVERT: B 974 LYS cc_start: 0.8966 (ttpt) cc_final: 0.8573 (tppt) REVERT: B 976 ARG cc_start: 0.7838 (ttm-80) cc_final: 0.7394 (ttm-80) REVERT: B 991 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7591 (tp30) REVERT: B 999 PHE cc_start: 0.8191 (m-80) cc_final: 0.7816 (m-80) REVERT: B 1067 PHE cc_start: 0.7920 (t80) cc_final: 0.7664 (t80) REVERT: B 1078 ASP cc_start: 0.7873 (m-30) cc_final: 0.7558 (m-30) REVERT: B 1098 ILE cc_start: 0.9067 (tp) cc_final: 0.8778 (tt) REVERT: B 1104 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8187 (tpp) REVERT: B 1105 GLU cc_start: 0.8552 (tp30) cc_final: 0.7990 (mm-30) outliers start: 74 outliers final: 58 residues processed: 556 average time/residue: 0.2950 time to fit residues: 235.9643 Evaluate side-chains 591 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 521 time to evaluate : 1.695 ------------------------------------------------------------------------------- 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 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 418 THR 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 838 ASP 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 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 174 LEU 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 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 476 THR Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 599 GLU 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 915 GLU Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 991 GLU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1104 MET 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: 4.9990 chunk 137 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 166 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 90 optimal weight: 0.0370 chunk 172 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 877 GLN B 981 HIS ** B1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1154 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.133039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.114049 restraints weight = 23503.092| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.19 r_work: 0.3349 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3838 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= 0.149 Angle : 0.624 9.417 20912 Z= 0.315 Chirality : 0.043 0.428 2526 Planarity : 0.004 0.031 2600 Dihedral : 4.522 58.160 2096 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.63 % Allowed : 28.14 % Favored : 67.24 % 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: 1.73 (0.20), residues: 1938 helix: 1.83 (0.14), residues: 1424 sheet: 0.07 (0.55), residues: 96 loop : -0.94 (0.31), residues: 418 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 0.020 0.001 PHE A 289 TYR 0.019 0.001 TYR A 280 ARG 0.006 0.001 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 1166) hydrogen bonds : angle 4.07813 ( 3447) covalent geometry : bond 0.00322 (15404) covalent geometry : angle 0.62439 (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 603 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 530 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8492 (m-10) cc_final: 0.8256 (m-10) REVERT: A 91 SER cc_start: 0.8618 (m) cc_final: 0.8323 (p) REVERT: A 129 ASP cc_start: 0.6436 (OUTLIER) cc_final: 0.6020 (p0) REVERT: A 137 VAL cc_start: 0.8645 (p) cc_final: 0.8347 (t) REVERT: A 140 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7897 (mp10) REVERT: A 175 VAL cc_start: 0.8489 (p) cc_final: 0.8213 (m) REVERT: A 195 PHE cc_start: 0.7894 (t80) cc_final: 0.7591 (t80) REVERT: A 205 MET cc_start: 0.8261 (mmm) cc_final: 0.8056 (mmt) REVERT: A 218 LYS cc_start: 0.8447 (ttmp) cc_final: 0.8207 (ttmp) REVERT: A 233 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7629 (tm-30) REVERT: A 267 TYR cc_start: 0.8626 (t80) cc_final: 0.8378 (t80) REVERT: A 284 LYS cc_start: 0.8682 (mmtm) cc_final: 0.8445 (mmmm) REVERT: A 346 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7382 (mt-10) REVERT: A 395 ILE cc_start: 0.8187 (tt) cc_final: 0.7885 (pt) REVERT: A 511 MET cc_start: 0.8923 (tmm) cc_final: 0.8600 (ttp) REVERT: A 579 MET cc_start: 0.7537 (tmm) cc_final: 0.7216 (tmm) REVERT: A 583 ARG cc_start: 0.8145 (ttp-170) cc_final: 0.7773 (ttp-170) REVERT: A 588 LYS cc_start: 0.8655 (tttm) cc_final: 0.8230 (tttm) REVERT: A 592 ILE cc_start: 0.8775 (mt) cc_final: 0.8388 (mm) REVERT: A 609 ARG cc_start: 0.7773 (mtp-110) cc_final: 0.7413 (mtp-110) REVERT: A 613 GLN cc_start: 0.7791 (mt0) cc_final: 0.7530 (mt0) REVERT: A 621 GLU cc_start: 0.7675 (mp0) cc_final: 0.7240 (mp0) REVERT: A 624 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7428 (pp30) REVERT: A 810 MET cc_start: 0.7249 (ppp) cc_final: 0.6872 (tmm) REVERT: A 832 GLN cc_start: 0.8719 (tp40) cc_final: 0.8379 (tp-100) REVERT: A 837 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7733 (t80) REVERT: A 841 LYS cc_start: 0.8446 (mtpt) cc_final: 0.8128 (mtpp) REVERT: A 865 ARG cc_start: 0.7400 (mmm160) cc_final: 0.7140 (mmm160) REVERT: A 866 GLU cc_start: 0.8281 (tp30) cc_final: 0.7906 (tp30) REVERT: A 868 LYS cc_start: 0.7946 (mmtp) cc_final: 0.7266 (mmtp) REVERT: A 871 SER cc_start: 0.8262 (t) cc_final: 0.7755 (p) REVERT: A 878 VAL cc_start: 0.8904 (t) cc_final: 0.8648 (t) REVERT: A 921 LEU cc_start: 0.8377 (mm) cc_final: 0.8128 (mp) REVERT: A 974 LYS cc_start: 0.8968 (ttpt) cc_final: 0.8659 (tppt) REVERT: A 986 GLU cc_start: 0.8310 (tt0) cc_final: 0.7983 (tt0) REVERT: A 999 PHE cc_start: 0.8221 (m-80) cc_final: 0.7932 (m-10) REVERT: A 1058 THR cc_start: 0.8574 (p) cc_final: 0.8312 (p) REVERT: A 1063 VAL cc_start: 0.8625 (t) cc_final: 0.8285 (p) REVERT: A 1073 MET cc_start: 0.8614 (mmm) cc_final: 0.8394 (mmm) REVERT: A 1078 ASP cc_start: 0.7801 (m-30) cc_final: 0.7467 (m-30) REVERT: A 1104 MET cc_start: 0.8002 (tpt) cc_final: 0.7681 (tpp) REVERT: A 1107 MET cc_start: 0.7416 (tmm) cc_final: 0.6004 (tmm) REVERT: A 1122 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7277 (mm-30) REVERT: A 1166 LEU cc_start: 0.7938 (tp) cc_final: 0.7697 (tp) REVERT: B 91 SER cc_start: 0.8710 (m) cc_final: 0.8472 (p) REVERT: B 140 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8020 (mp10) REVERT: B 141 ILE cc_start: 0.8695 (mm) cc_final: 0.8392 (mt) REVERT: B 154 MET cc_start: 0.8596 (tpp) cc_final: 0.7979 (tpp) REVERT: B 155 ASP cc_start: 0.8374 (t0) cc_final: 0.7995 (t0) REVERT: B 160 MET cc_start: 0.8477 (mmt) cc_final: 0.8234 (mmm) REVERT: B 190 ASN cc_start: 0.7789 (p0) cc_final: 0.7474 (p0) REVERT: B 214 VAL cc_start: 0.8692 (t) cc_final: 0.8458 (p) REVERT: B 217 LEU cc_start: 0.8727 (mt) cc_final: 0.8313 (mp) REVERT: B 238 ASP cc_start: 0.7443 (m-30) cc_final: 0.7105 (m-30) REVERT: B 267 TYR cc_start: 0.8493 (t80) cc_final: 0.8226 (t80) REVERT: B 335 ASN cc_start: 0.8553 (t0) cc_final: 0.8277 (t0) REVERT: B 337 GLU cc_start: 0.8045 (mp0) cc_final: 0.7467 (mp0) REVERT: B 375 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8417 (ttpt) REVERT: B 419 TRP cc_start: 0.8315 (p-90) cc_final: 0.8094 (p-90) REVERT: B 444 ASN cc_start: 0.8858 (t0) cc_final: 0.8484 (t0) REVERT: B 476 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8538 (m) REVERT: B 485 ASP cc_start: 0.8350 (t0) cc_final: 0.8129 (t0) REVERT: B 486 ILE cc_start: 0.8578 (mm) cc_final: 0.8309 (mm) REVERT: B 520 ASP cc_start: 0.7982 (p0) cc_final: 0.7759 (p0) REVERT: B 531 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7411 (tm-30) REVERT: B 579 MET cc_start: 0.7541 (tpt) cc_final: 0.7298 (tpt) REVERT: B 580 GLU cc_start: 0.8027 (tp30) cc_final: 0.7631 (tp30) REVERT: B 581 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7435 (pp20) REVERT: B 588 LYS cc_start: 0.8497 (tttm) cc_final: 0.8153 (tttm) REVERT: B 592 ILE cc_start: 0.8686 (mt) cc_final: 0.8358 (mm) REVERT: B 620 ASP cc_start: 0.7631 (t70) cc_final: 0.7389 (t70) REVERT: B 621 GLU cc_start: 0.7365 (mp0) cc_final: 0.6659 (mp0) REVERT: B 837 TYR cc_start: 0.8450 (OUTLIER) cc_final: 0.7843 (t80) REVERT: B 841 LYS cc_start: 0.8570 (mtpt) cc_final: 0.8246 (mtpp) REVERT: B 845 ILE cc_start: 0.8925 (mm) cc_final: 0.8660 (mt) REVERT: B 850 VAL cc_start: 0.8837 (p) cc_final: 0.8626 (m) REVERT: B 855 ASP cc_start: 0.7890 (t0) cc_final: 0.7532 (t0) REVERT: B 865 ARG cc_start: 0.7605 (mmm160) cc_final: 0.7216 (mmm160) REVERT: B 866 GLU cc_start: 0.8102 (tp30) cc_final: 0.7783 (tm-30) REVERT: B 868 LYS cc_start: 0.8062 (mtpp) cc_final: 0.7816 (mtpp) REVERT: B 870 ILE cc_start: 0.8604 (mm) cc_final: 0.8022 (mm) REVERT: B 871 SER cc_start: 0.8237 (t) cc_final: 0.7993 (t) REVERT: B 878 VAL cc_start: 0.8863 (t) cc_final: 0.8592 (t) REVERT: B 879 VAL cc_start: 0.8981 (p) cc_final: 0.8747 (t) REVERT: B 921 LEU cc_start: 0.8466 (mm) cc_final: 0.8195 (mp) REVERT: B 959 ASN cc_start: 0.8267 (m-40) cc_final: 0.7985 (m-40) REVERT: B 974 LYS cc_start: 0.8966 (ttpt) cc_final: 0.8525 (tppt) REVERT: B 976 ARG cc_start: 0.7884 (ttm-80) cc_final: 0.7586 (ttm110) REVERT: B 991 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7655 (tp30) REVERT: B 999 PHE cc_start: 0.8219 (m-80) cc_final: 0.7841 (m-80) REVERT: B 1067 PHE cc_start: 0.7937 (t80) cc_final: 0.7691 (t80) REVERT: B 1078 ASP cc_start: 0.7849 (m-30) cc_final: 0.7549 (m-30) REVERT: B 1098 ILE cc_start: 0.9058 (tp) cc_final: 0.8760 (tt) REVERT: B 1104 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8201 (tpp) REVERT: B 1145 VAL cc_start: 0.8473 (t) cc_final: 0.8153 (p) outliers start: 73 outliers final: 54 residues processed: 560 average time/residue: 0.2871 time to fit residues: 231.3013 Evaluate side-chains 584 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 520 time to evaluate : 1.721 ------------------------------------------------------------------------------- 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 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 802 PHE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 838 ASP 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 1002 VAL Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1082 LEU 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 257 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 305 LEU 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 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 915 GLU 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 1063 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1146 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: 0.9990 chunk 13 optimal weight: 4.9990 chunk 181 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 167 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ** B1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1154 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.133219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.114779 restraints weight = 23354.907| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.11 r_work: 0.3351 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15404 Z= 0.162 Angle : 0.626 9.113 20912 Z= 0.316 Chirality : 0.043 0.277 2526 Planarity : 0.004 0.035 2600 Dihedral : 4.531 57.891 2096 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.44 % Allowed : 28.96 % Favored : 66.60 % 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: 1.69 (0.20), residues: 1938 helix: 1.80 (0.14), residues: 1422 sheet: 0.13 (0.55), residues: 96 loop : -0.96 (0.30), 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 981 PHE 0.018 0.001 PHE A 289 TYR 0.019 0.001 TYR A 280 ARG 0.009 0.001 ARG A 940 Details of bonding type rmsd hydrogen bonds : bond 0.04558 ( 1166) hydrogen bonds : angle 4.09347 ( 3447) covalent geometry : bond 0.00354 (15404) covalent geometry : angle 0.62608 (20912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9478.83 seconds wall clock time: 164 minutes 19.63 seconds (9859.63 seconds total)