Starting phenix.real_space_refine on Thu Sep 18 07:58:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xq5_38566/09_2025/8xq5_38566.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xq5_38566/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xq5_38566/09_2025/8xq5_38566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xq5_38566/09_2025/8xq5_38566.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xq5_38566/09_2025/8xq5_38566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xq5_38566/09_2025/8xq5_38566.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'PHE:plan': 6, 'GLU:plan': 4, 'ASN:plan1': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'TRP: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: {'PHE:plan': 6, 'GLU:plan': 4, 'ASN:plan1': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 107 Time building chain proxies: 3.25, per 1000 atoms: 0.21 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: 1.26 Conformation dependent library (CDL) restraints added in 698.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.55 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: 2.80 Time building geometry restraints manager: 1.71 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: 0.02 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.220 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.930 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (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 ARG 0.021 0.001 ARG A 499 TYR 0.036 0.002 TYR A 984 PHE 0.045 0.003 PHE B1032 TRP 0.020 0.002 TRP A 419 HIS 0.006 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00499 (15404) covalent geometry : angle 1.03156 (20912) hydrogen bonds : bond 0.11327 ( 1166) hydrogen bonds : angle 6.06311 ( 3447) *********************** 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 : 0.522 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: 0.7248 (tp30) REVERT: A 581 GLU cc_start: 0.6968 (tp30) cc_final: 0.6254 (tp30) REVERT: A 583 ARG cc_start: 0.7773 (ttt-90) cc_final: 0.7292 (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: 0.8525 (mt) REVERT: A 588 LYS cc_start: 0.8279 (tttm) cc_final: 0.7979 (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: 0.7608 (tpp80) REVERT: A 613 GLN cc_start: 0.7652 (mt0) cc_final: 0.7298 (mt0) REVERT: A 617 VAL cc_start: 0.7913 (t) cc_final: 0.7618 (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: 0.7552 (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: 0.7334 (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: 0.8130 (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: 0.7890 (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: 0.8259 (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: 0.8337 (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: 0.7054 (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: 0.6262 (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: 0.7622 (tttm) REVERT: B 592 ILE cc_start: 0.8536 (mt) cc_final: 0.8097 (mm) REVERT: B 595 TRP cc_start: 0.8498 (m100) cc_final: 0.8065 (m100) REVERT: B 612 VAL cc_start: 0.7709 (t) cc_final: 0.7509 (p) REVERT: B 621 GLU cc_start: 0.7146 (mp0) cc_final: 0.6600 (mp0) REVERT: B 624 GLN cc_start: 0.7375 (pt0) cc_final: 0.7047 (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: 0.8532 (t) REVERT: B 845 ILE cc_start: 0.8551 (mm) cc_final: 0.8291 (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: 0.8532 (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: 0.7396 (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: 0.1322 time to fit residues: 112.9132 Evaluate side-chains 534 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 526 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 886 GLN A 900 GLN A 908 HIS A 981 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 HIS B 832 GLN B 886 GLN B 908 HIS B1135 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.133919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.114716 restraints weight = 23800.987| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.20 r_work: 0.3359 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1858 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= 0.159 Angle : 0.614 7.845 20912 Z= 0.319 Chirality : 0.041 0.203 2526 Planarity : 0.005 0.044 2600 Dihedral : 5.089 54.302 2106 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.87 % Allowed : 23.51 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.19), residues: 1938 helix: 0.92 (0.13), residues: 1400 sheet: -0.33 (0.56), residues: 96 loop : -1.42 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 903 TYR 0.018 0.001 TYR B 984 PHE 0.016 0.002 PHE A1176 TRP 0.012 0.001 TRP A 353 HIS 0.005 0.001 HIS B 981 Details of bonding type rmsd covalent geometry : bond 0.00335 (15404) covalent geometry : angle 0.61396 (20912) hydrogen bonds : bond 0.04757 ( 1166) hydrogen bonds : angle 4.40032 ( 3447) *********************** 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 590 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 529 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.8701 (m) cc_final: 0.8412 (p) REVERT: A 175 VAL cc_start: 0.8486 (p) cc_final: 0.8110 (m) REVERT: A 217 LEU cc_start: 0.8660 (mt) cc_final: 0.8346 (mm) REVERT: A 233 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7769 (tm-30) REVERT: A 263 GLN cc_start: 0.8060 (mt0) cc_final: 0.7770 (mt0) REVERT: A 267 TYR cc_start: 0.8602 (t80) cc_final: 0.8339 (t80) REVERT: A 284 LYS cc_start: 0.8747 (mmtm) cc_final: 0.8515 (mmmm) REVERT: A 346 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7491 (mt-10) REVERT: A 443 GLU cc_start: 0.8063 (tp30) cc_final: 0.7724 (tp30) REVERT: A 444 ASN cc_start: 0.8755 (t0) cc_final: 0.8382 (t0) REVERT: A 500 ARG cc_start: 0.8373 (mmm-85) cc_final: 0.8134 (tpp80) REVERT: A 511 MET cc_start: 0.9068 (tmm) cc_final: 0.8832 (tmm) REVERT: A 580 GLU cc_start: 0.7727 (tp30) cc_final: 0.7248 (tp30) REVERT: A 581 GLU cc_start: 0.7058 (tp30) cc_final: 0.6354 (tp30) REVERT: A 583 ARG cc_start: 0.7929 (ttt-90) cc_final: 0.7582 (ttp-170) REVERT: A 584 LEU cc_start: 0.8468 (mm) cc_final: 0.7669 (mm) REVERT: A 586 MET cc_start: 0.8740 (ttm) cc_final: 0.8439 (ttp) REVERT: A 588 LYS cc_start: 0.8476 (tttm) cc_final: 0.8152 (tttm) REVERT: A 592 ILE cc_start: 0.8687 (mt) cc_final: 0.8264 (mm) REVERT: A 613 GLN cc_start: 0.7691 (mt0) cc_final: 0.7339 (mt0) REVERT: A 614 HIS cc_start: 0.7770 (m-70) cc_final: 0.7272 (m-70) REVERT: A 617 VAL cc_start: 0.8000 (t) cc_final: 0.7764 (m) REVERT: A 632 LYS cc_start: 0.8506 (mtpp) cc_final: 0.8240 (mtmm) REVERT: A 641 TYR cc_start: 0.7958 (m-10) cc_final: 0.7575 (m-80) REVERT: A 643 TRP cc_start: 0.7745 (t-100) cc_final: 0.7349 (t-100) REVERT: A 828 LYS cc_start: 0.8434 (mmmt) cc_final: 0.8144 (mmmt) REVERT: A 832 GLN cc_start: 0.8861 (tp40) cc_final: 0.8553 (tp40) REVERT: A 841 LYS cc_start: 0.8353 (mtpt) cc_final: 0.8001 (mtpt) REVERT: A 847 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7564 (mm-30) REVERT: A 858 VAL cc_start: 0.8379 (p) cc_final: 0.7926 (p) REVERT: A 866 GLU cc_start: 0.8159 (tp30) cc_final: 0.7825 (tp30) REVERT: A 868 LYS cc_start: 0.7889 (mmtp) cc_final: 0.7539 (ttmm) REVERT: A 870 ILE cc_start: 0.8515 (mt) cc_final: 0.8222 (mm) REVERT: A 878 VAL cc_start: 0.8918 (t) cc_final: 0.8684 (t) REVERT: A 900 GLN cc_start: 0.8715 (tp40) cc_final: 0.8494 (tp-100) REVERT: A 921 LEU cc_start: 0.8319 (mm) cc_final: 0.8027 (mp) REVERT: A 931 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7775 (mm-30) REVERT: A 932 LEU cc_start: 0.8490 (tt) cc_final: 0.8255 (tp) REVERT: A 948 ILE cc_start: 0.8401 (mt) cc_final: 0.8076 (tt) REVERT: A 958 LYS cc_start: 0.8582 (ttpt) cc_final: 0.8215 (ttpt) REVERT: A 968 LYS cc_start: 0.8039 (mppt) cc_final: 0.7837 (mmmm) REVERT: A 999 PHE cc_start: 0.8093 (m-80) cc_final: 0.7672 (m-80) REVERT: A 1003 SER cc_start: 0.8386 (t) cc_final: 0.8073 (m) REVERT: A 1045 MET cc_start: 0.8522 (ttm) cc_final: 0.8219 (tpp) REVERT: A 1063 VAL cc_start: 0.8324 (t) cc_final: 0.8102 (p) REVERT: A 1072 ASP cc_start: 0.7734 (t0) cc_final: 0.7502 (t0) REVERT: A 1077 ILE cc_start: 0.8667 (mm) cc_final: 0.8343 (mm) REVERT: A 1100 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8483 (p) REVERT: A 1103 ILE cc_start: 0.8524 (mm) cc_final: 0.8089 (mm) REVERT: A 1104 MET cc_start: 0.7891 (tpt) cc_final: 0.7463 (tpp) REVERT: A 1107 MET cc_start: 0.6989 (tmm) cc_final: 0.6252 (tmm) REVERT: A 1122 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7418 (mm-30) REVERT: B 91 SER cc_start: 0.8741 (m) cc_final: 0.8512 (p) REVERT: B 140 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8237 (mp10) REVERT: B 190 ASN cc_start: 0.7726 (p0) cc_final: 0.7368 (p0) REVERT: B 197 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7766 (mt-10) REVERT: B 214 VAL cc_start: 0.8758 (t) cc_final: 0.8377 (p) REVERT: B 231 GLU cc_start: 0.8189 (tt0) cc_final: 0.7922 (mt-10) REVERT: B 250 LYS cc_start: 0.8293 (mmmm) cc_final: 0.8079 (mttm) REVERT: B 267 TYR cc_start: 0.8475 (t80) cc_final: 0.8114 (t80) REVERT: B 300 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7790 (mt-10) REVERT: B 392 TYR cc_start: 0.8614 (t80) cc_final: 0.8372 (t80) REVERT: B 443 GLU cc_start: 0.7965 (tp30) cc_final: 0.7603 (tp30) REVERT: B 444 ASN cc_start: 0.8847 (t0) cc_final: 0.8461 (t0) REVERT: B 476 THR cc_start: 0.8816 (t) cc_final: 0.8547 (m) REVERT: B 485 ASP cc_start: 0.8242 (t0) cc_final: 0.8042 (t0) REVERT: B 486 ILE cc_start: 0.8556 (mm) cc_final: 0.8238 (mm) REVERT: B 579 MET cc_start: 0.7442 (tpt) cc_final: 0.7190 (tpt) REVERT: B 580 GLU cc_start: 0.7947 (tp30) cc_final: 0.7218 (tp30) REVERT: B 581 GLU cc_start: 0.7183 (tp30) cc_final: 0.6421 (tp30) REVERT: B 584 LEU cc_start: 0.8409 (mm) cc_final: 0.7939 (mm) REVERT: B 586 MET cc_start: 0.8784 (ttm) cc_final: 0.8456 (ttm) REVERT: B 587 LEU cc_start: 0.8783 (mt) cc_final: 0.8549 (mt) REVERT: B 588 LYS cc_start: 0.8331 (tttm) cc_final: 0.7892 (tttm) REVERT: B 592 ILE cc_start: 0.8621 (mt) cc_final: 0.8251 (mm) REVERT: B 620 ASP cc_start: 0.7589 (t70) cc_final: 0.7215 (t70) REVERT: B 621 GLU cc_start: 0.7109 (mp0) cc_final: 0.6377 (mp0) REVERT: B 624 GLN cc_start: 0.7560 (pt0) cc_final: 0.7237 (pt0) REVERT: B 828 LYS cc_start: 0.8560 (mmtt) cc_final: 0.8247 (mmtt) REVERT: B 835 LEU cc_start: 0.8693 (tp) cc_final: 0.8433 (tt) REVERT: B 837 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.7802 (t80) REVERT: B 839 VAL cc_start: 0.8819 (t) cc_final: 0.8539 (t) REVERT: B 845 ILE cc_start: 0.8718 (mm) cc_final: 0.8455 (mt) REVERT: B 866 GLU cc_start: 0.8369 (tp30) cc_final: 0.7961 (tp30) REVERT: B 870 ILE cc_start: 0.8646 (mm) cc_final: 0.8351 (mm) REVERT: B 921 LEU cc_start: 0.8377 (mm) cc_final: 0.8047 (mp) REVERT: B 931 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7760 (mm-30) REVERT: B 932 LEU cc_start: 0.8422 (tt) cc_final: 0.8200 (tp) REVERT: B 999 PHE cc_start: 0.8270 (m-80) cc_final: 0.7800 (m-80) REVERT: B 1003 SER cc_start: 0.8554 (t) cc_final: 0.8242 (m) REVERT: B 1045 MET cc_start: 0.8497 (ttm) cc_final: 0.8201 (tpp) REVERT: B 1058 THR cc_start: 0.8518 (p) cc_final: 0.8299 (p) REVERT: B 1077 ILE cc_start: 0.8619 (mm) cc_final: 0.8319 (mm) REVERT: B 1088 TYR cc_start: 0.7661 (t80) cc_final: 0.7258 (t80) REVERT: B 1104 MET cc_start: 0.8281 (tpp) cc_final: 0.8049 (tpp) REVERT: B 1122 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7445 (mm-30) REVERT: B 1145 VAL cc_start: 0.8454 (t) cc_final: 0.8214 (p) outliers start: 61 outliers final: 33 residues processed: 564 average time/residue: 0.1220 time to fit residues: 100.8623 Evaluate side-chains 545 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 509 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE 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 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 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 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 145 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 113 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 147 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 192 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 886 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.133856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.114702 restraints weight = 23858.344| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.20 r_work: 0.3363 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15404 Z= 0.143 Angle : 0.584 11.122 20912 Z= 0.299 Chirality : 0.040 0.184 2526 Planarity : 0.004 0.037 2600 Dihedral : 4.623 54.777 2096 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.75 % Allowed : 23.95 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.19), residues: 1938 helix: 1.47 (0.14), residues: 1406 sheet: -0.31 (0.56), residues: 96 loop : -1.37 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 585 TYR 0.014 0.001 TYR B 984 PHE 0.011 0.002 PHE A 348 TRP 0.011 0.001 TRP A 353 HIS 0.005 0.001 HIS B 981 Details of bonding type rmsd covalent geometry : bond 0.00295 (15404) covalent geometry : angle 0.58376 (20912) hydrogen bonds : bond 0.04480 ( 1166) hydrogen bonds : angle 4.19151 ( 3447) *********************** 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 600 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 525 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.8667 (m) cc_final: 0.8374 (p) REVERT: A 137 VAL cc_start: 0.8771 (p) cc_final: 0.8564 (t) REVERT: A 140 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8233 (mp10) REVERT: A 175 VAL cc_start: 0.8504 (p) cc_final: 0.8166 (m) REVERT: A 199 MET cc_start: 0.8357 (mmm) cc_final: 0.8054 (tmm) REVERT: A 217 LEU cc_start: 0.8680 (mt) cc_final: 0.8384 (mm) REVERT: A 233 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7715 (tm-30) REVERT: A 263 GLN cc_start: 0.8050 (mt0) cc_final: 0.7733 (mt0) REVERT: A 267 TYR cc_start: 0.8613 (t80) cc_final: 0.8287 (t80) REVERT: A 284 LYS cc_start: 0.8747 (mmtm) cc_final: 0.8515 (mmmm) REVERT: A 291 SER cc_start: 0.8642 (t) cc_final: 0.8380 (p) REVERT: A 335 ASN cc_start: 0.8549 (t0) cc_final: 0.8266 (t0) REVERT: A 346 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7474 (mt-10) REVERT: A 425 MET cc_start: 0.8518 (ttm) cc_final: 0.8243 (mtm) REVERT: A 443 GLU cc_start: 0.8069 (tp30) cc_final: 0.7744 (tp30) REVERT: A 444 ASN cc_start: 0.8721 (t0) cc_final: 0.8373 (t0) REVERT: A 500 ARG cc_start: 0.8361 (mmm-85) cc_final: 0.8137 (tpp80) REVERT: A 511 MET cc_start: 0.8990 (tmm) cc_final: 0.8735 (tmm) REVERT: A 580 GLU cc_start: 0.7734 (tp30) cc_final: 0.7126 (tp30) REVERT: A 583 ARG cc_start: 0.8201 (ttt-90) cc_final: 0.7911 (ttp-170) REVERT: A 584 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7420 (mm) REVERT: A 588 LYS cc_start: 0.8558 (tttm) cc_final: 0.8230 (tttm) REVERT: A 592 ILE cc_start: 0.8729 (mt) cc_final: 0.8298 (mm) REVERT: A 613 GLN cc_start: 0.7687 (mt0) cc_final: 0.7483 (mt0) REVERT: A 614 HIS cc_start: 0.7750 (m-70) cc_final: 0.7307 (m-70) REVERT: A 632 LYS cc_start: 0.8516 (mtpp) cc_final: 0.8261 (mtmm) REVERT: A 641 TYR cc_start: 0.8028 (m-80) cc_final: 0.7691 (m-80) REVERT: A 643 TRP cc_start: 0.7795 (t-100) cc_final: 0.7184 (t-100) REVERT: A 644 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8213 (mt) REVERT: A 810 MET cc_start: 0.7318 (ppp) cc_final: 0.6955 (tmm) REVERT: A 828 LYS cc_start: 0.8469 (mmmt) cc_final: 0.8173 (mmmt) REVERT: A 832 GLN cc_start: 0.8797 (tp40) cc_final: 0.8521 (tp40) REVERT: A 837 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7879 (t80) REVERT: A 838 ASP cc_start: 0.8292 (t0) cc_final: 0.7970 (t0) REVERT: A 841 LYS cc_start: 0.8433 (mtpt) cc_final: 0.8079 (mtpp) REVERT: A 847 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7678 (mm-30) REVERT: A 850 VAL cc_start: 0.8899 (p) cc_final: 0.8689 (m) REVERT: A 866 GLU cc_start: 0.8239 (tp30) cc_final: 0.7766 (tp30) REVERT: A 868 LYS cc_start: 0.7819 (mmtp) cc_final: 0.7472 (ttmm) REVERT: A 870 ILE cc_start: 0.8506 (mt) cc_final: 0.8064 (mm) REVERT: A 878 VAL cc_start: 0.8920 (t) cc_final: 0.8671 (t) REVERT: A 900 GLN cc_start: 0.8663 (tp40) cc_final: 0.8438 (tp-100) REVERT: A 921 LEU cc_start: 0.8300 (mm) cc_final: 0.8045 (mp) REVERT: A 926 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7492 (mp0) REVERT: A 931 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7862 (mm-30) REVERT: A 932 LEU cc_start: 0.8462 (tt) cc_final: 0.8201 (tp) REVERT: A 948 ILE cc_start: 0.8413 (mt) cc_final: 0.8095 (tt) REVERT: A 958 LYS cc_start: 0.8631 (ttpt) cc_final: 0.8231 (ttpt) REVERT: A 970 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8422 (tt) REVERT: A 999 PHE cc_start: 0.8101 (m-80) cc_final: 0.7628 (m-80) REVERT: A 1003 SER cc_start: 0.8509 (t) cc_final: 0.8198 (m) REVERT: A 1058 THR cc_start: 0.8564 (p) cc_final: 0.8307 (p) REVERT: A 1063 VAL cc_start: 0.8427 (t) cc_final: 0.8146 (p) REVERT: A 1064 GLN cc_start: 0.8370 (mt0) cc_final: 0.8164 (mt0) REVERT: A 1077 ILE cc_start: 0.8784 (mm) cc_final: 0.8469 (mm) REVERT: A 1100 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8520 (m) REVERT: A 1103 ILE cc_start: 0.8498 (mm) cc_final: 0.8155 (mm) REVERT: A 1104 MET cc_start: 0.7840 (tpt) cc_final: 0.7456 (tpp) REVERT: A 1107 MET cc_start: 0.7056 (tmm) cc_final: 0.6210 (tmm) REVERT: A 1122 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7692 (tp30) REVERT: B 91 SER cc_start: 0.8735 (m) cc_final: 0.8488 (p) REVERT: B 140 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8201 (mp10) REVERT: B 160 MET cc_start: 0.8455 (mmt) cc_final: 0.8226 (mmm) REVERT: B 190 ASN cc_start: 0.7787 (p0) cc_final: 0.7446 (p0) REVERT: B 197 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7721 (mt-10) REVERT: B 214 VAL cc_start: 0.8813 (t) cc_final: 0.8414 (p) REVERT: B 217 LEU cc_start: 0.8700 (mt) cc_final: 0.8469 (mm) REVERT: B 231 GLU cc_start: 0.8104 (tt0) cc_final: 0.7832 (mt-10) REVERT: B 238 ASP cc_start: 0.7338 (m-30) cc_final: 0.7029 (m-30) REVERT: B 267 TYR cc_start: 0.8530 (t80) cc_final: 0.8244 (t80) REVERT: B 300 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7801 (mt-10) REVERT: B 386 PHE cc_start: 0.8327 (t80) cc_final: 0.8113 (t80) REVERT: B 392 TYR cc_start: 0.8624 (t80) cc_final: 0.8300 (t80) REVERT: B 443 GLU cc_start: 0.7936 (tp30) cc_final: 0.7554 (tp30) REVERT: B 444 ASN cc_start: 0.8802 (t0) cc_final: 0.8390 (t0) REVERT: B 476 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8557 (m) REVERT: B 485 ASP cc_start: 0.8317 (t0) cc_final: 0.8081 (t0) REVERT: B 486 ILE cc_start: 0.8535 (mm) cc_final: 0.8194 (mm) REVERT: B 517 PHE cc_start: 0.8418 (m-10) cc_final: 0.8097 (m-10) REVERT: B 579 MET cc_start: 0.7416 (tpt) cc_final: 0.7179 (tpt) REVERT: B 580 GLU cc_start: 0.7930 (tp30) cc_final: 0.7481 (tp30) REVERT: B 581 GLU cc_start: 0.7259 (tp30) cc_final: 0.6550 (tp30) REVERT: B 585 ARG cc_start: 0.8165 (ttm-80) cc_final: 0.7676 (ttm110) REVERT: B 586 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8608 (ttp) REVERT: B 587 LEU cc_start: 0.8781 (mt) cc_final: 0.8526 (mt) REVERT: B 588 LYS cc_start: 0.8408 (tttm) cc_final: 0.7969 (tttm) REVERT: B 592 ILE cc_start: 0.8687 (mt) cc_final: 0.8331 (mm) REVERT: B 620 ASP cc_start: 0.7640 (t70) cc_final: 0.7180 (t70) REVERT: B 621 GLU cc_start: 0.7262 (mp0) cc_final: 0.6556 (mp0) REVERT: B 646 ARG cc_start: 0.7148 (ptp-170) cc_final: 0.6946 (ptp-170) REVERT: B 828 LYS cc_start: 0.8611 (mmtt) cc_final: 0.8276 (mmtt) REVERT: B 832 GLN cc_start: 0.8692 (tp40) cc_final: 0.8483 (tp40) REVERT: B 835 LEU cc_start: 0.8744 (tp) cc_final: 0.8515 (tt) REVERT: B 837 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.7833 (t80) REVERT: B 839 VAL cc_start: 0.8853 (t) cc_final: 0.8586 (t) REVERT: B 845 ILE cc_start: 0.8788 (mm) cc_final: 0.8463 (mt) REVERT: B 866 GLU cc_start: 0.8358 (tp30) cc_final: 0.7807 (tp30) REVERT: B 870 ILE cc_start: 0.8610 (mm) cc_final: 0.8221 (mm) REVERT: B 878 VAL cc_start: 0.8878 (t) cc_final: 0.8593 (t) REVERT: B 911 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7780 (mp0) REVERT: B 921 LEU cc_start: 0.8347 (mm) cc_final: 0.8032 (mp) REVERT: B 971 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.8105 (t0) REVERT: B 999 PHE cc_start: 0.8216 (m-80) cc_final: 0.7776 (m-80) REVERT: B 1003 SER cc_start: 0.8703 (t) cc_final: 0.8439 (m) REVERT: B 1045 MET cc_start: 0.8531 (ttm) cc_final: 0.8270 (tpp) REVERT: B 1058 THR cc_start: 0.8568 (p) cc_final: 0.8313 (p) REVERT: B 1077 ILE cc_start: 0.8735 (mm) cc_final: 0.8457 (mm) REVERT: B 1104 MET cc_start: 0.8273 (tpp) cc_final: 0.8065 (tpp) REVERT: B 1105 GLU cc_start: 0.8595 (tp30) cc_final: 0.8213 (tm-30) REVERT: B 1145 VAL cc_start: 0.8507 (t) cc_final: 0.8252 (p) outliers start: 75 outliers final: 36 residues processed: 561 average time/residue: 0.1261 time to fit residues: 103.7637 Evaluate side-chains 565 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 518 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 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 584 LEU 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 970 ILE 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 123 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 154 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 B 157 HIS B 165 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.132967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.113925 restraints weight = 23558.057| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.16 r_work: 0.3354 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15404 Z= 0.153 Angle : 0.570 8.205 20912 Z= 0.294 Chirality : 0.041 0.230 2526 Planarity : 0.004 0.033 2600 Dihedral : 4.533 56.347 2096 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.58 % Allowed : 23.64 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.20), residues: 1938 helix: 1.67 (0.14), residues: 1420 sheet: -0.24 (0.56), residues: 96 loop : -1.18 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 161 TYR 0.018 0.001 TYR B 280 PHE 0.015 0.002 PHE B 289 TRP 0.011 0.001 TRP A 353 HIS 0.005 0.001 HIS B1120 Details of bonding type rmsd covalent geometry : bond 0.00324 (15404) covalent geometry : angle 0.57015 (20912) hydrogen bonds : bond 0.04577 ( 1166) hydrogen bonds : angle 4.10971 ( 3447) *********************** 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 617 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 529 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.8644 (m) cc_final: 0.8353 (p) REVERT: A 137 VAL cc_start: 0.8736 (p) cc_final: 0.8488 (t) REVERT: A 140 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8123 (mp10) REVERT: A 175 VAL cc_start: 0.8513 (p) cc_final: 0.8172 (m) REVERT: A 195 PHE cc_start: 0.7884 (t80) cc_final: 0.7589 (t80) REVERT: A 218 LYS cc_start: 0.8315 (ttmt) cc_final: 0.8072 (ttmp) REVERT: A 233 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7673 (tm-30) REVERT: A 267 TYR cc_start: 0.8590 (t80) cc_final: 0.8293 (t80) REVERT: A 284 LYS cc_start: 0.8711 (mmtm) cc_final: 0.8480 (mmmm) REVERT: A 291 SER cc_start: 0.8584 (t) cc_final: 0.8317 (p) REVERT: A 346 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7426 (mt-10) REVERT: A 395 ILE cc_start: 0.8163 (tt) cc_final: 0.7837 (pt) REVERT: A 443 GLU cc_start: 0.7997 (tp30) cc_final: 0.7712 (tp30) REVERT: A 444 ASN cc_start: 0.8757 (t0) cc_final: 0.8447 (t0) REVERT: A 462 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.8003 (mt) REVERT: A 500 ARG cc_start: 0.8338 (mmm-85) cc_final: 0.8133 (tpp80) REVERT: A 511 MET cc_start: 0.8876 (tmm) cc_final: 0.8505 (ttp) REVERT: A 580 GLU cc_start: 0.7903 (tp30) cc_final: 0.7612 (tp30) REVERT: A 584 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8172 (mm) REVERT: A 588 LYS cc_start: 0.8592 (tttm) cc_final: 0.8276 (tttm) REVERT: A 592 ILE cc_start: 0.8794 (mt) cc_final: 0.8365 (mm) REVERT: A 613 GLN cc_start: 0.7708 (mt0) cc_final: 0.7404 (mt0) REVERT: A 614 HIS cc_start: 0.7770 (m-70) cc_final: 0.7238 (m-70) REVERT: A 632 LYS cc_start: 0.8529 (mtpp) cc_final: 0.8183 (mtmm) REVERT: A 641 TYR cc_start: 0.8040 (m-80) cc_final: 0.7541 (m-80) REVERT: A 643 TRP cc_start: 0.7837 (t-100) cc_final: 0.7179 (t-100) REVERT: A 810 MET cc_start: 0.7307 (ppp) cc_final: 0.6937 (tmm) REVERT: A 828 LYS cc_start: 0.8442 (mmmt) cc_final: 0.8201 (mmmt) REVERT: A 832 GLN cc_start: 0.8777 (tp40) cc_final: 0.8469 (tp40) REVERT: A 837 TYR cc_start: 0.8450 (OUTLIER) cc_final: 0.7764 (t80) REVERT: A 838 ASP cc_start: 0.8251 (t0) cc_final: 0.8006 (t0) REVERT: A 841 LYS cc_start: 0.8473 (mtpt) cc_final: 0.8125 (mtpp) REVERT: A 847 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7636 (mm-30) REVERT: A 850 VAL cc_start: 0.8921 (p) cc_final: 0.8703 (m) REVERT: A 864 LEU cc_start: 0.8172 (tp) cc_final: 0.7940 (tp) REVERT: A 865 ARG cc_start: 0.7341 (mmm160) cc_final: 0.7048 (mmm160) REVERT: A 866 GLU cc_start: 0.8287 (tp30) cc_final: 0.7848 (tp30) REVERT: A 868 LYS cc_start: 0.7849 (mmtp) cc_final: 0.7202 (mmtp) REVERT: A 870 ILE cc_start: 0.8551 (mt) cc_final: 0.8144 (mm) REVERT: A 871 SER cc_start: 0.8362 (t) cc_final: 0.7814 (p) REVERT: A 878 VAL cc_start: 0.8922 (t) cc_final: 0.8670 (t) REVERT: A 921 LEU cc_start: 0.8342 (mm) cc_final: 0.8119 (mp) REVERT: A 926 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7525 (mp0) REVERT: A 932 LEU cc_start: 0.8528 (tt) cc_final: 0.8270 (tp) REVERT: A 958 LYS cc_start: 0.8619 (ttpt) cc_final: 0.8185 (ttpt) REVERT: A 999 PHE cc_start: 0.8144 (m-80) cc_final: 0.7806 (m-80) REVERT: A 1003 SER cc_start: 0.8626 (t) cc_final: 0.8284 (m) REVERT: A 1045 MET cc_start: 0.8667 (mmm) cc_final: 0.8418 (mmm) REVERT: A 1058 THR cc_start: 0.8554 (p) cc_final: 0.8295 (p) REVERT: A 1063 VAL cc_start: 0.8536 (t) cc_final: 0.8213 (p) REVERT: A 1077 ILE cc_start: 0.8829 (mm) cc_final: 0.8573 (mm) REVERT: A 1098 ILE cc_start: 0.9127 (tp) cc_final: 0.8812 (tt) REVERT: A 1100 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8555 (m) REVERT: A 1103 ILE cc_start: 0.8539 (mm) cc_final: 0.8250 (mm) REVERT: A 1104 MET cc_start: 0.7905 (tpt) cc_final: 0.7504 (tpp) REVERT: A 1107 MET cc_start: 0.7430 (tmm) cc_final: 0.6587 (tmm) REVERT: A 1122 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7637 (tp30) REVERT: B 91 SER cc_start: 0.8663 (m) cc_final: 0.8454 (p) REVERT: B 140 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8128 (mp10) REVERT: B 155 ASP cc_start: 0.8354 (t0) cc_final: 0.8088 (t0) REVERT: B 160 MET cc_start: 0.8508 (mmt) cc_final: 0.8273 (mmm) REVERT: B 190 ASN cc_start: 0.7855 (p0) cc_final: 0.7515 (p0) REVERT: B 197 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7747 (mt-10) REVERT: B 214 VAL cc_start: 0.8778 (t) cc_final: 0.8356 (p) REVERT: B 217 LEU cc_start: 0.8745 (mt) cc_final: 0.8471 (mm) REVERT: B 231 GLU cc_start: 0.8107 (tt0) cc_final: 0.7824 (mt-10) REVERT: B 238 ASP cc_start: 0.7337 (m-30) cc_final: 0.7018 (m-30) REVERT: B 267 TYR cc_start: 0.8524 (t80) cc_final: 0.8258 (t80) REVERT: B 319 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8011 (mp) REVERT: B 335 ASN cc_start: 0.8616 (t0) cc_final: 0.8312 (t0) REVERT: B 407 SER cc_start: 0.8256 (t) cc_final: 0.7913 (m) REVERT: B 443 GLU cc_start: 0.7937 (tp30) cc_final: 0.7550 (tp30) REVERT: B 444 ASN cc_start: 0.8886 (t0) cc_final: 0.8463 (t0) REVERT: B 476 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8583 (m) REVERT: B 485 ASP cc_start: 0.8285 (t0) cc_final: 0.8004 (t0) REVERT: B 486 ILE cc_start: 0.8514 (mm) cc_final: 0.8171 (mm) REVERT: B 517 PHE cc_start: 0.8373 (m-10) cc_final: 0.8070 (m-10) REVERT: B 579 MET cc_start: 0.7466 (tpt) cc_final: 0.7220 (tpt) REVERT: B 580 GLU cc_start: 0.8015 (tp30) cc_final: 0.7607 (tp30) REVERT: B 581 GLU cc_start: 0.7318 (tp30) cc_final: 0.6618 (tp30) REVERT: B 585 ARG cc_start: 0.8168 (ttm-80) cc_final: 0.7694 (ttm170) REVERT: B 588 LYS cc_start: 0.8440 (tttm) cc_final: 0.8029 (tttm) REVERT: B 590 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8268 (mt-10) REVERT: B 592 ILE cc_start: 0.8747 (mt) cc_final: 0.8410 (mm) REVERT: B 617 VAL cc_start: 0.7940 (t) cc_final: 0.7289 (m) REVERT: B 620 ASP cc_start: 0.7669 (t70) cc_final: 0.7306 (t70) REVERT: B 621 GLU cc_start: 0.7358 (mp0) cc_final: 0.6605 (mp0) REVERT: B 644 LEU cc_start: 0.8461 (mt) cc_final: 0.8239 (mp) REVERT: B 828 LYS cc_start: 0.8659 (mmtt) cc_final: 0.8268 (mmtt) REVERT: B 832 GLN cc_start: 0.8745 (tp40) cc_final: 0.8530 (tp40) REVERT: B 835 LEU cc_start: 0.8782 (tp) cc_final: 0.8544 (tt) REVERT: B 837 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.7917 (t80) REVERT: B 839 VAL cc_start: 0.8904 (t) cc_final: 0.8676 (t) REVERT: B 841 LYS cc_start: 0.8570 (mtpt) cc_final: 0.8251 (mtpp) REVERT: B 845 ILE cc_start: 0.8862 (mm) cc_final: 0.8552 (mt) REVERT: B 850 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8577 (m) REVERT: B 866 GLU cc_start: 0.8349 (tp30) cc_final: 0.8111 (tp30) REVERT: B 870 ILE cc_start: 0.8613 (mm) cc_final: 0.8320 (mm) REVERT: B 911 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7859 (mp0) REVERT: B 921 LEU cc_start: 0.8359 (mm) cc_final: 0.8089 (mp) REVERT: B 999 PHE cc_start: 0.8223 (m-80) cc_final: 0.7831 (m-80) REVERT: B 1045 MET cc_start: 0.8527 (ttm) cc_final: 0.8302 (tpp) REVERT: B 1058 THR cc_start: 0.8588 (p) cc_final: 0.8343 (p) REVERT: B 1064 GLN cc_start: 0.8563 (mt0) cc_final: 0.8358 (mt0) REVERT: B 1077 ILE cc_start: 0.8774 (mm) cc_final: 0.8520 (mm) REVERT: B 1098 ILE cc_start: 0.9070 (tp) cc_final: 0.8798 (tt) REVERT: B 1145 VAL cc_start: 0.8544 (t) cc_final: 0.8269 (p) outliers start: 88 outliers final: 50 residues processed: 573 average time/residue: 0.1269 time to fit residues: 105.9635 Evaluate side-chains 579 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 519 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 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 462 ILE 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 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 A residue 1161 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 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 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 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 915 GLU Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 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: 4.9990 chunk 16 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 54 optimal weight: 0.0870 chunk 50 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- 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 917 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.132105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.113230 restraints weight = 23544.295| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.13 r_work: 0.3348 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15404 Z= 0.170 Angle : 0.584 8.821 20912 Z= 0.301 Chirality : 0.041 0.218 2526 Planarity : 0.004 0.037 2600 Dihedral : 4.517 56.385 2096 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.94 % Allowed : 24.97 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.20), residues: 1938 helix: 1.70 (0.14), residues: 1420 sheet: -0.19 (0.56), residues: 96 loop : -1.19 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 161 TYR 0.017 0.001 TYR A 280 PHE 0.014 0.002 PHE B 289 TRP 0.010 0.001 TRP A 353 HIS 0.003 0.001 HIS B 981 Details of bonding type rmsd covalent geometry : bond 0.00369 (15404) covalent geometry : angle 0.58383 (20912) hydrogen bonds : bond 0.04681 ( 1166) hydrogen bonds : angle 4.11912 ( 3447) *********************** 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 601 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 523 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.8664 (m) cc_final: 0.8358 (p) REVERT: A 137 VAL cc_start: 0.8740 (p) cc_final: 0.8496 (t) REVERT: A 140 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7982 (mp10) REVERT: A 175 VAL cc_start: 0.8523 (p) cc_final: 0.8190 (m) REVERT: A 195 PHE cc_start: 0.7935 (t80) cc_final: 0.7657 (t80) REVERT: A 218 LYS cc_start: 0.8359 (ttmt) cc_final: 0.8078 (ttmp) REVERT: A 233 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7525 (tm-30) REVERT: A 267 TYR cc_start: 0.8642 (t80) cc_final: 0.8347 (t80) REVERT: A 284 LYS cc_start: 0.8682 (mmtm) cc_final: 0.8447 (mmmm) REVERT: A 346 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7408 (mt-10) REVERT: A 395 ILE cc_start: 0.8234 (tt) cc_final: 0.7922 (pt) REVERT: A 443 GLU cc_start: 0.7974 (tp30) cc_final: 0.7675 (tp30) REVERT: A 444 ASN cc_start: 0.8802 (t0) cc_final: 0.8465 (t0) REVERT: A 500 ARG cc_start: 0.8296 (mmm-85) cc_final: 0.8090 (tpp80) REVERT: A 511 MET cc_start: 0.8954 (tmm) cc_final: 0.8570 (ttp) REVERT: A 583 ARG cc_start: 0.8275 (ttp-170) cc_final: 0.7590 (mtp180) REVERT: A 588 LYS cc_start: 0.8637 (tttm) cc_final: 0.8317 (tttm) REVERT: A 592 ILE cc_start: 0.8819 (mt) cc_final: 0.8423 (mm) REVERT: A 613 GLN cc_start: 0.7780 (mt0) cc_final: 0.7520 (mt0) REVERT: A 647 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8152 (pttm) REVERT: A 810 MET cc_start: 0.7317 (ppp) cc_final: 0.6941 (tmm) REVERT: A 828 LYS cc_start: 0.8402 (mmmt) cc_final: 0.8075 (mmmt) REVERT: A 832 GLN cc_start: 0.8773 (tp40) cc_final: 0.8457 (tp-100) REVERT: A 837 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.7644 (t80) REVERT: A 841 LYS cc_start: 0.8473 (mtpt) cc_final: 0.8187 (mtpp) REVERT: A 847 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7698 (mm-30) REVERT: A 864 LEU cc_start: 0.8230 (tp) cc_final: 0.8027 (tp) REVERT: A 865 ARG cc_start: 0.7434 (mmm160) cc_final: 0.7149 (mmm160) REVERT: A 866 GLU cc_start: 0.8299 (tp30) cc_final: 0.7862 (tp30) REVERT: A 868 LYS cc_start: 0.7933 (mmtp) cc_final: 0.7262 (mmmm) REVERT: A 870 ILE cc_start: 0.8554 (mt) cc_final: 0.8153 (mm) REVERT: A 871 SER cc_start: 0.8389 (t) cc_final: 0.7767 (p) REVERT: A 878 VAL cc_start: 0.8923 (t) cc_final: 0.8690 (t) REVERT: A 921 LEU cc_start: 0.8332 (mm) cc_final: 0.8123 (mp) REVERT: A 958 LYS cc_start: 0.8643 (ttpt) cc_final: 0.8266 (ttpt) REVERT: A 974 LYS cc_start: 0.9088 (ttpt) cc_final: 0.8841 (tppt) REVERT: A 994 GLU cc_start: 0.8560 (pm20) cc_final: 0.8349 (pm20) REVERT: A 1003 SER cc_start: 0.8736 (t) cc_final: 0.8452 (m) REVERT: A 1045 MET cc_start: 0.8673 (mmm) cc_final: 0.8439 (mmm) REVERT: A 1063 VAL cc_start: 0.8549 (t) cc_final: 0.8214 (p) REVERT: A 1067 PHE cc_start: 0.8089 (t80) cc_final: 0.7853 (t80) REVERT: A 1077 ILE cc_start: 0.8867 (mm) cc_final: 0.8601 (mm) REVERT: A 1078 ASP cc_start: 0.7874 (m-30) cc_final: 0.7567 (m-30) REVERT: A 1098 ILE cc_start: 0.9116 (tp) cc_final: 0.8805 (tt) REVERT: A 1100 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8567 (m) REVERT: A 1103 ILE cc_start: 0.8634 (mm) cc_final: 0.8372 (mm) REVERT: A 1104 MET cc_start: 0.7920 (tpt) cc_final: 0.7547 (tpp) REVERT: A 1107 MET cc_start: 0.7527 (tmm) cc_final: 0.6453 (tmm) REVERT: A 1122 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7648 (tp30) REVERT: A 1138 ILE cc_start: 0.8488 (mt) cc_final: 0.8274 (mp) REVERT: A 1174 LEU cc_start: 0.8289 (mt) cc_final: 0.7975 (mm) REVERT: B 91 SER cc_start: 0.8660 (m) cc_final: 0.8441 (p) REVERT: B 140 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8074 (mp10) REVERT: B 155 ASP cc_start: 0.8383 (t0) cc_final: 0.8057 (t0) REVERT: B 160 MET cc_start: 0.8493 (mmt) cc_final: 0.8257 (mmm) REVERT: B 190 ASN cc_start: 0.7846 (p0) cc_final: 0.7495 (p0) REVERT: B 197 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7694 (mt-10) REVERT: B 214 VAL cc_start: 0.8777 (t) cc_final: 0.8354 (p) REVERT: B 217 LEU cc_start: 0.8764 (mt) cc_final: 0.8486 (mm) REVERT: B 231 GLU cc_start: 0.8098 (tt0) cc_final: 0.7819 (mt-10) REVERT: B 233 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7735 (tm-30) REVERT: B 238 ASP cc_start: 0.7355 (m-30) cc_final: 0.7039 (m-30) REVERT: B 267 TYR cc_start: 0.8550 (t80) cc_final: 0.8247 (t80) REVERT: B 407 SER cc_start: 0.8274 (t) cc_final: 0.7939 (m) REVERT: B 443 GLU cc_start: 0.7928 (tp30) cc_final: 0.7519 (tp30) REVERT: B 476 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8603 (m) REVERT: B 485 ASP cc_start: 0.8289 (t0) cc_final: 0.8043 (t0) REVERT: B 486 ILE cc_start: 0.8550 (mm) cc_final: 0.8291 (mm) REVERT: B 517 PHE cc_start: 0.8347 (m-10) cc_final: 0.8035 (m-10) REVERT: B 580 GLU cc_start: 0.8005 (tp30) cc_final: 0.7328 (tp30) REVERT: B 581 GLU cc_start: 0.7338 (tp30) cc_final: 0.6643 (tp30) REVERT: B 584 LEU cc_start: 0.8547 (mm) cc_final: 0.7876 (mm) REVERT: B 585 ARG cc_start: 0.8256 (ttm-80) cc_final: 0.7732 (ttm110) REVERT: B 586 MET cc_start: 0.8780 (ttp) cc_final: 0.8399 (ttm) REVERT: B 588 LYS cc_start: 0.8521 (tttm) cc_final: 0.8105 (tttm) REVERT: B 590 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8116 (mt-10) REVERT: B 592 ILE cc_start: 0.8772 (mt) cc_final: 0.8462 (mm) REVERT: B 617 VAL cc_start: 0.7967 (t) cc_final: 0.7329 (m) REVERT: B 620 ASP cc_start: 0.7652 (t70) cc_final: 0.7358 (t70) REVERT: B 621 GLU cc_start: 0.7372 (mp0) cc_final: 0.6661 (mp0) REVERT: B 837 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.7885 (t80) REVERT: B 839 VAL cc_start: 0.8915 (t) cc_final: 0.8695 (t) REVERT: B 841 LYS cc_start: 0.8587 (mtpt) cc_final: 0.8299 (mtpp) REVERT: B 845 ILE cc_start: 0.8932 (mm) cc_final: 0.8658 (mt) REVERT: B 850 VAL cc_start: 0.8879 (p) cc_final: 0.8646 (m) REVERT: B 865 ARG cc_start: 0.7630 (mmm160) cc_final: 0.7371 (mmm160) REVERT: B 866 GLU cc_start: 0.8375 (tp30) cc_final: 0.8151 (tp30) REVERT: B 870 ILE cc_start: 0.8658 (mm) cc_final: 0.8326 (mm) REVERT: B 921 LEU cc_start: 0.8370 (mm) cc_final: 0.8119 (mp) REVERT: B 931 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7771 (mm-30) REVERT: B 974 LYS cc_start: 0.9038 (ttpt) cc_final: 0.8667 (tppt) REVERT: B 999 PHE cc_start: 0.8219 (m-80) cc_final: 0.7827 (m-80) REVERT: B 1045 MET cc_start: 0.8527 (ttm) cc_final: 0.8288 (mmm) REVERT: B 1098 ILE cc_start: 0.9091 (tp) cc_final: 0.8819 (tt) REVERT: B 1104 MET cc_start: 0.8411 (tpp) cc_final: 0.8201 (tpp) REVERT: B 1107 MET cc_start: 0.7281 (tmm) cc_final: 0.6453 (tmm) REVERT: B 1122 GLU cc_start: 0.8019 (tp30) cc_final: 0.7630 (tp30) outliers start: 78 outliers final: 51 residues processed: 561 average time/residue: 0.1340 time to fit residues: 109.2605 Evaluate side-chains 575 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 517 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 418 THR Chi-restraints excluded: chain A residue 451 ILE 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 973 ILE Chi-restraints excluded: chain A residue 1033 GLU 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 A residue 1161 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 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 305 LEU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 599 GLU 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 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 1154 ASN 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 74 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 113 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 GLN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS B1154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.132145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.113457 restraints weight = 23532.019| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.12 r_work: 0.3352 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15404 Z= 0.155 Angle : 0.569 7.849 20912 Z= 0.294 Chirality : 0.041 0.243 2526 Planarity : 0.004 0.038 2600 Dihedral : 4.508 56.976 2096 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 5.45 % Allowed : 25.10 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.20), residues: 1938 helix: 1.77 (0.14), residues: 1420 sheet: -0.08 (0.56), residues: 96 loop : -1.12 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 161 TYR 0.018 0.001 TYR A 280 PHE 0.018 0.002 PHE A 999 TRP 0.010 0.001 TRP A 353 HIS 0.003 0.001 HIS B 981 Details of bonding type rmsd covalent geometry : bond 0.00334 (15404) covalent geometry : angle 0.56932 (20912) hydrogen bonds : bond 0.04570 ( 1166) hydrogen bonds : angle 4.08733 ( 3447) *********************** 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 606 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 520 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.8648 (m) cc_final: 0.8323 (p) REVERT: A 137 VAL cc_start: 0.8683 (p) cc_final: 0.8377 (t) REVERT: A 140 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7942 (mp10) REVERT: A 175 VAL cc_start: 0.8525 (p) cc_final: 0.8232 (m) REVERT: A 195 PHE cc_start: 0.7920 (t80) cc_final: 0.7648 (t80) REVERT: A 218 LYS cc_start: 0.8346 (ttmt) cc_final: 0.8059 (ttmp) REVERT: A 233 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7484 (tm-30) REVERT: A 267 TYR cc_start: 0.8597 (t80) cc_final: 0.8324 (t80) REVERT: A 284 LYS cc_start: 0.8668 (mmtm) cc_final: 0.8441 (mmmm) REVERT: A 346 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7382 (mt-10) REVERT: A 395 ILE cc_start: 0.8246 (tt) cc_final: 0.7972 (pt) REVERT: A 462 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.8036 (mt) REVERT: A 511 MET cc_start: 0.8941 (tmm) cc_final: 0.8499 (ttp) REVERT: A 580 GLU cc_start: 0.7982 (tp30) cc_final: 0.7737 (tp30) REVERT: A 583 ARG cc_start: 0.8225 (ttp-170) cc_final: 0.7933 (ttp-170) REVERT: A 588 LYS cc_start: 0.8681 (tttm) cc_final: 0.8348 (tttm) REVERT: A 590 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8303 (mt-10) REVERT: A 592 ILE cc_start: 0.8834 (mt) cc_final: 0.8450 (mm) REVERT: A 613 GLN cc_start: 0.7813 (mt0) cc_final: 0.7544 (mt0) REVERT: A 624 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7250 (pp30) REVERT: A 633 LYS cc_start: 0.8743 (mttm) cc_final: 0.8532 (mttt) REVERT: A 641 TYR cc_start: 0.8115 (m-80) cc_final: 0.7616 (m-80) REVERT: A 810 MET cc_start: 0.7280 (ppp) cc_final: 0.6905 (tmm) REVERT: A 828 LYS cc_start: 0.8401 (mmmt) cc_final: 0.8129 (mmmt) REVERT: A 832 GLN cc_start: 0.8782 (tp40) cc_final: 0.8441 (tp-100) REVERT: A 837 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7712 (t80) REVERT: A 841 LYS cc_start: 0.8468 (mtpt) cc_final: 0.8170 (mtpp) REVERT: A 847 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7842 (mm-30) REVERT: A 864 LEU cc_start: 0.8208 (tp) cc_final: 0.8003 (tp) REVERT: A 865 ARG cc_start: 0.7419 (mmm160) cc_final: 0.7146 (mmm160) REVERT: A 866 GLU cc_start: 0.8292 (tp30) cc_final: 0.7932 (tp30) REVERT: A 868 LYS cc_start: 0.7960 (mmtp) cc_final: 0.7092 (mmmm) REVERT: A 871 SER cc_start: 0.8379 (t) cc_final: 0.7811 (p) REVERT: A 878 VAL cc_start: 0.8928 (t) cc_final: 0.8686 (t) REVERT: A 921 LEU cc_start: 0.8338 (mm) cc_final: 0.8127 (mp) REVERT: A 958 LYS cc_start: 0.8678 (ttpt) cc_final: 0.8254 (ttpt) REVERT: A 974 LYS cc_start: 0.9059 (ttpt) cc_final: 0.8781 (tppt) REVERT: A 994 GLU cc_start: 0.8536 (pm20) cc_final: 0.8299 (pm20) REVERT: A 999 PHE cc_start: 0.8187 (m-80) cc_final: 0.7949 (m-10) REVERT: A 1058 THR cc_start: 0.8590 (p) cc_final: 0.8325 (p) REVERT: A 1063 VAL cc_start: 0.8604 (t) cc_final: 0.8286 (p) REVERT: A 1077 ILE cc_start: 0.8855 (mm) cc_final: 0.8618 (mm) REVERT: A 1078 ASP cc_start: 0.7875 (m-30) cc_final: 0.7559 (m-30) REVERT: A 1098 ILE cc_start: 0.9044 (tp) cc_final: 0.8803 (tt) REVERT: A 1100 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8576 (m) REVERT: A 1103 ILE cc_start: 0.8742 (mm) cc_final: 0.8534 (mt) REVERT: A 1104 MET cc_start: 0.7925 (tpt) cc_final: 0.7569 (tpp) REVERT: A 1107 MET cc_start: 0.7418 (tmm) cc_final: 0.6426 (tmm) REVERT: A 1122 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7667 (tp30) REVERT: B 91 SER cc_start: 0.8660 (m) cc_final: 0.8431 (p) REVERT: B 140 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8038 (mp10) REVERT: B 155 ASP cc_start: 0.8379 (t0) cc_final: 0.8058 (t0) REVERT: B 160 MET cc_start: 0.8475 (mmt) cc_final: 0.8223 (mmm) REVERT: B 190 ASN cc_start: 0.7831 (p0) cc_final: 0.7480 (p0) REVERT: B 197 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7666 (mt-10) REVERT: B 214 VAL cc_start: 0.8783 (t) cc_final: 0.8374 (p) REVERT: B 217 LEU cc_start: 0.8786 (mt) cc_final: 0.8523 (mm) REVERT: B 231 GLU cc_start: 0.8112 (tt0) cc_final: 0.7838 (mt-10) REVERT: B 233 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7697 (tm-30) REVERT: B 238 ASP cc_start: 0.7399 (m-30) cc_final: 0.7165 (m-30) REVERT: B 267 TYR cc_start: 0.8512 (t80) cc_final: 0.8213 (t80) REVERT: B 395 ILE cc_start: 0.8453 (tt) cc_final: 0.8135 (pt) REVERT: B 407 SER cc_start: 0.8264 (t) cc_final: 0.7918 (m) REVERT: B 443 GLU cc_start: 0.7930 (tp30) cc_final: 0.7545 (tp30) REVERT: B 476 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8606 (m) REVERT: B 485 ASP cc_start: 0.8308 (t0) cc_final: 0.8061 (t0) REVERT: B 486 ILE cc_start: 0.8573 (mm) cc_final: 0.8303 (mm) REVERT: B 511 MET cc_start: 0.9028 (tmm) cc_final: 0.8757 (ttp) REVERT: B 517 PHE cc_start: 0.8330 (m-10) cc_final: 0.8064 (m-10) REVERT: B 580 GLU cc_start: 0.8050 (tp30) cc_final: 0.7673 (tp30) REVERT: B 581 GLU cc_start: 0.7374 (tp30) cc_final: 0.6699 (tp30) REVERT: B 585 ARG cc_start: 0.8224 (ttm-80) cc_final: 0.7315 (ttm110) REVERT: B 586 MET cc_start: 0.8803 (ttp) cc_final: 0.8352 (ttp) REVERT: B 588 LYS cc_start: 0.8598 (tttm) cc_final: 0.8250 (tttm) REVERT: B 590 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8077 (mt-10) REVERT: B 592 ILE cc_start: 0.8791 (mt) cc_final: 0.8501 (mm) REVERT: B 617 VAL cc_start: 0.7912 (t) cc_final: 0.7270 (m) REVERT: B 621 GLU cc_start: 0.7336 (mp0) cc_final: 0.6732 (mp0) REVERT: B 837 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.7908 (t80) REVERT: B 841 LYS cc_start: 0.8593 (mtpt) cc_final: 0.8268 (mtpp) REVERT: B 845 ILE cc_start: 0.8981 (mm) cc_final: 0.8706 (mt) REVERT: B 850 VAL cc_start: 0.8866 (p) cc_final: 0.8608 (m) REVERT: B 865 ARG cc_start: 0.7598 (mmm160) cc_final: 0.7313 (mmm160) REVERT: B 870 ILE cc_start: 0.8612 (mm) cc_final: 0.8284 (mm) REVERT: B 921 LEU cc_start: 0.8421 (mm) cc_final: 0.8152 (mp) REVERT: B 959 ASN cc_start: 0.8244 (m-40) cc_final: 0.7932 (m-40) REVERT: B 974 LYS cc_start: 0.9035 (ttpt) cc_final: 0.8645 (tppt) REVERT: B 999 PHE cc_start: 0.8213 (m-80) cc_final: 0.7793 (m-80) REVERT: B 1098 ILE cc_start: 0.9092 (tp) cc_final: 0.8801 (tt) REVERT: B 1104 MET cc_start: 0.8381 (tpp) cc_final: 0.8109 (tpp) REVERT: B 1107 MET cc_start: 0.7184 (tmm) cc_final: 0.6244 (tmm) REVERT: B 1122 GLU cc_start: 0.7843 (tp30) cc_final: 0.7607 (tp30) outliers start: 86 outliers final: 59 residues processed: 564 average time/residue: 0.1355 time to fit residues: 110.6346 Evaluate side-chains 581 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 514 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 405 LEU Chi-restraints excluded: chain A residue 418 THR 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 858 VAL Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 888 GLU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1033 GLU 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 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 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 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 418 THR 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 652 ILE Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 838 ASP Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1146 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 31 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 79 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 B1154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.131455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.112848 restraints weight = 23343.685| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.12 r_work: 0.3342 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15404 Z= 0.164 Angle : 0.575 9.057 20912 Z= 0.297 Chirality : 0.042 0.252 2526 Planarity : 0.004 0.037 2600 Dihedral : 4.503 56.954 2096 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 5.13 % Allowed : 26.24 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.20), residues: 1938 helix: 1.81 (0.14), residues: 1418 sheet: -0.06 (0.56), residues: 96 loop : -1.13 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 161 TYR 0.018 0.001 TYR A 280 PHE 0.016 0.002 PHE A 625 TRP 0.010 0.001 TRP A 353 HIS 0.003 0.001 HIS B 981 Details of bonding type rmsd covalent geometry : bond 0.00355 (15404) covalent geometry : angle 0.57499 (20912) hydrogen bonds : bond 0.04625 ( 1166) hydrogen bonds : angle 4.09678 ( 3447) *********************** 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 599 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 518 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.8598 (m) cc_final: 0.8295 (p) REVERT: A 137 VAL cc_start: 0.8699 (p) cc_final: 0.8416 (t) REVERT: A 140 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7951 (mp10) REVERT: A 175 VAL cc_start: 0.8501 (p) cc_final: 0.8229 (m) REVERT: A 195 PHE cc_start: 0.7916 (t80) cc_final: 0.7645 (t80) REVERT: A 197 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7577 (mt-10) REVERT: A 218 LYS cc_start: 0.8399 (ttmt) cc_final: 0.8125 (ttmp) REVERT: A 233 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7590 (tm-30) REVERT: A 267 TYR cc_start: 0.8620 (t80) cc_final: 0.8334 (t80) REVERT: A 284 LYS cc_start: 0.8676 (mmtm) cc_final: 0.8444 (mmmm) REVERT: A 346 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7386 (mt-10) REVERT: A 395 ILE cc_start: 0.8258 (tt) cc_final: 0.7966 (pt) REVERT: A 443 GLU cc_start: 0.7976 (tp30) cc_final: 0.7677 (tp30) REVERT: A 511 MET cc_start: 0.8938 (tmm) cc_final: 0.8545 (ttp) REVERT: A 583 ARG cc_start: 0.8301 (ttp-170) cc_final: 0.8096 (ttp-170) REVERT: A 588 LYS cc_start: 0.8682 (tttm) cc_final: 0.8358 (tttm) REVERT: A 592 ILE cc_start: 0.8811 (mt) cc_final: 0.8426 (mm) REVERT: A 613 GLN cc_start: 0.7822 (mt0) cc_final: 0.7553 (mt0) REVERT: A 624 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7294 (pp30) REVERT: A 633 LYS cc_start: 0.8750 (mttm) cc_final: 0.8547 (mttt) REVERT: A 810 MET cc_start: 0.7301 (ppp) cc_final: 0.6928 (tmm) REVERT: A 832 GLN cc_start: 0.8774 (tp40) cc_final: 0.8438 (tp-100) REVERT: A 841 LYS cc_start: 0.8461 (mtpt) cc_final: 0.8137 (mtpp) REVERT: A 847 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7845 (mm-30) REVERT: A 862 LYS cc_start: 0.8016 (tppt) cc_final: 0.7760 (tppt) REVERT: A 865 ARG cc_start: 0.7418 (mmm160) cc_final: 0.7143 (mmm160) REVERT: A 866 GLU cc_start: 0.8334 (tp30) cc_final: 0.7974 (tp30) REVERT: A 868 LYS cc_start: 0.7968 (mmtp) cc_final: 0.7080 (mmmm) REVERT: A 871 SER cc_start: 0.8337 (t) cc_final: 0.7817 (p) REVERT: A 878 VAL cc_start: 0.8923 (t) cc_final: 0.8672 (t) REVERT: A 921 LEU cc_start: 0.8354 (mm) cc_final: 0.8130 (mp) REVERT: A 926 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7745 (mp0) REVERT: A 974 LYS cc_start: 0.9047 (ttpt) cc_final: 0.8742 (tppt) REVERT: A 994 GLU cc_start: 0.8579 (pm20) cc_final: 0.8329 (pm20) REVERT: A 999 PHE cc_start: 0.8208 (m-80) cc_final: 0.7945 (m-10) REVERT: A 1063 VAL cc_start: 0.8634 (t) cc_final: 0.8319 (p) REVERT: A 1073 MET cc_start: 0.8692 (mmm) cc_final: 0.8406 (tpt) REVERT: A 1077 ILE cc_start: 0.8864 (mm) cc_final: 0.8658 (mm) REVERT: A 1078 ASP cc_start: 0.7895 (m-30) cc_final: 0.7579 (m-30) REVERT: A 1098 ILE cc_start: 0.9015 (tp) cc_final: 0.8813 (tt) REVERT: A 1100 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8590 (m) REVERT: A 1104 MET cc_start: 0.7961 (tpt) cc_final: 0.7628 (tpp) REVERT: A 1107 MET cc_start: 0.7446 (tmm) cc_final: 0.6310 (tmm) REVERT: A 1122 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7668 (tp30) REVERT: B 91 SER cc_start: 0.8671 (m) cc_final: 0.8433 (p) REVERT: B 140 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8018 (mp10) REVERT: B 154 MET cc_start: 0.8559 (tpp) cc_final: 0.8033 (tpp) REVERT: B 155 ASP cc_start: 0.8337 (t0) cc_final: 0.7978 (t0) REVERT: B 160 MET cc_start: 0.8452 (mmt) cc_final: 0.8193 (mmm) REVERT: B 190 ASN cc_start: 0.7837 (p0) cc_final: 0.7479 (p0) REVERT: B 197 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7565 (mt-10) REVERT: B 214 VAL cc_start: 0.8763 (t) cc_final: 0.8341 (p) REVERT: B 217 LEU cc_start: 0.8771 (mt) cc_final: 0.8507 (mm) REVERT: B 231 GLU cc_start: 0.8097 (tt0) cc_final: 0.7819 (mt-10) REVERT: B 233 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7646 (tm-30) REVERT: B 238 ASP cc_start: 0.7446 (m-30) cc_final: 0.7213 (m-30) REVERT: B 267 TYR cc_start: 0.8518 (t80) cc_final: 0.8206 (t80) REVERT: B 395 ILE cc_start: 0.8434 (tt) cc_final: 0.8101 (pt) REVERT: B 407 SER cc_start: 0.8271 (t) cc_final: 0.7903 (m) REVERT: B 443 GLU cc_start: 0.7951 (tp30) cc_final: 0.7553 (tp30) REVERT: B 476 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8593 (m) REVERT: B 486 ILE cc_start: 0.8577 (mm) cc_final: 0.8311 (mm) REVERT: B 511 MET cc_start: 0.9036 (tmm) cc_final: 0.8775 (ttp) REVERT: B 517 PHE cc_start: 0.8323 (m-10) cc_final: 0.8064 (m-10) REVERT: B 580 GLU cc_start: 0.8076 (tp30) cc_final: 0.7655 (tp30) REVERT: B 581 GLU cc_start: 0.7422 (tp30) cc_final: 0.6813 (tp30) REVERT: B 585 ARG cc_start: 0.8219 (ttm-80) cc_final: 0.7670 (ttm110) REVERT: B 586 MET cc_start: 0.8777 (ttp) cc_final: 0.8534 (ttp) REVERT: B 588 LYS cc_start: 0.8641 (tttm) cc_final: 0.8312 (tttm) REVERT: B 592 ILE cc_start: 0.8812 (mt) cc_final: 0.8532 (mm) REVERT: B 617 VAL cc_start: 0.7876 (t) cc_final: 0.7253 (m) REVERT: B 621 GLU cc_start: 0.7315 (mp0) cc_final: 0.6736 (mp0) REVERT: B 837 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.7904 (t80) REVERT: B 841 LYS cc_start: 0.8595 (mtpt) cc_final: 0.8281 (mtpp) REVERT: B 845 ILE cc_start: 0.8968 (mm) cc_final: 0.8695 (mt) REVERT: B 850 VAL cc_start: 0.8869 (p) cc_final: 0.8640 (m) REVERT: B 865 ARG cc_start: 0.7619 (mmm160) cc_final: 0.7332 (mmm160) REVERT: B 870 ILE cc_start: 0.8635 (mm) cc_final: 0.8312 (mm) REVERT: B 921 LEU cc_start: 0.8486 (mm) cc_final: 0.8231 (mp) REVERT: B 926 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7667 (mm-30) REVERT: B 940 ARG cc_start: 0.8447 (ttm-80) cc_final: 0.8127 (ttm-80) REVERT: B 959 ASN cc_start: 0.8227 (m-40) cc_final: 0.7937 (m-40) REVERT: B 971 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7932 (t0) REVERT: B 974 LYS cc_start: 0.9013 (ttpt) cc_final: 0.8579 (tppt) REVERT: B 999 PHE cc_start: 0.8229 (m-80) cc_final: 0.7822 (m-80) REVERT: B 1067 PHE cc_start: 0.7911 (t80) cc_final: 0.7686 (t80) REVERT: B 1078 ASP cc_start: 0.7905 (m-30) cc_final: 0.7592 (m-30) REVERT: B 1098 ILE cc_start: 0.9081 (tp) cc_final: 0.8786 (tt) REVERT: B 1104 MET cc_start: 0.8468 (tpp) cc_final: 0.8125 (tpp) REVERT: B 1107 MET cc_start: 0.7145 (tmm) cc_final: 0.6345 (tmm) REVERT: B 1122 GLU cc_start: 0.7856 (tp30) cc_final: 0.7625 (tp30) outliers start: 81 outliers final: 61 residues processed: 560 average time/residue: 0.1368 time to fit residues: 111.1482 Evaluate side-chains 575 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 507 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 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 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 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 1048 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain B residue 79 VAL 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 174 LEU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 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 418 THR 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 652 ILE Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 838 ASP 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 980 LEU Chi-restraints excluded: chain B residue 995 SER Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1146 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 91 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 B1154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.131707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.113103 restraints weight = 23503.248| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.12 r_work: 0.3346 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3685 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= 0.157 Angle : 0.591 9.696 20912 Z= 0.303 Chirality : 0.042 0.283 2526 Planarity : 0.004 0.029 2600 Dihedral : 4.493 55.891 2096 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.75 % Allowed : 27.19 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.20), residues: 1938 helix: 1.82 (0.14), residues: 1418 sheet: -0.09 (0.55), residues: 96 loop : -1.08 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 161 TYR 0.020 0.001 TYR B1125 PHE 0.017 0.001 PHE B 972 TRP 0.011 0.001 TRP B 635 HIS 0.003 0.000 HIS B 981 Details of bonding type rmsd covalent geometry : bond 0.00338 (15404) covalent geometry : angle 0.59134 (20912) hydrogen bonds : bond 0.04584 ( 1166) hydrogen bonds : angle 4.09091 ( 3447) *********************** 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 592 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 517 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.8599 (m) cc_final: 0.8299 (p) REVERT: A 129 ASP cc_start: 0.6472 (OUTLIER) cc_final: 0.6060 (p0) REVERT: A 137 VAL cc_start: 0.8704 (p) cc_final: 0.8407 (t) REVERT: A 140 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7970 (mp10) REVERT: A 175 VAL cc_start: 0.8515 (p) cc_final: 0.8254 (m) REVERT: A 195 PHE cc_start: 0.7936 (t80) cc_final: 0.7655 (t80) REVERT: A 218 LYS cc_start: 0.8420 (ttmt) cc_final: 0.8139 (ttmp) REVERT: A 233 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7569 (tm-30) REVERT: A 267 TYR cc_start: 0.8613 (t80) cc_final: 0.8329 (t80) REVERT: A 284 LYS cc_start: 0.8673 (mmtm) cc_final: 0.8447 (mmmm) REVERT: A 346 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7366 (mt-10) REVERT: A 395 ILE cc_start: 0.8315 (tt) cc_final: 0.8017 (pt) REVERT: A 511 MET cc_start: 0.8912 (tmm) cc_final: 0.8622 (tmm) REVERT: A 579 MET cc_start: 0.7569 (tmm) cc_final: 0.7274 (tmm) REVERT: A 580 GLU cc_start: 0.8154 (tp30) cc_final: 0.7920 (tp30) REVERT: A 583 ARG cc_start: 0.8281 (ttp-170) cc_final: 0.8080 (ttp-170) REVERT: A 588 LYS cc_start: 0.8654 (tttm) cc_final: 0.8258 (tttm) REVERT: A 592 ILE cc_start: 0.8810 (mt) cc_final: 0.8432 (mm) REVERT: A 613 GLN cc_start: 0.7808 (mt0) cc_final: 0.7552 (mt0) REVERT: A 624 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7248 (pp30) REVERT: A 633 LYS cc_start: 0.8712 (mttm) cc_final: 0.8511 (mttt) REVERT: A 810 MET cc_start: 0.7311 (ppp) cc_final: 0.6950 (tmm) REVERT: A 832 GLN cc_start: 0.8761 (tp40) cc_final: 0.8436 (tp-100) REVERT: A 841 LYS cc_start: 0.8454 (mtpt) cc_final: 0.8127 (mtpp) REVERT: A 865 ARG cc_start: 0.7423 (mmm160) cc_final: 0.7113 (mmm160) REVERT: A 866 GLU cc_start: 0.8321 (tp30) cc_final: 0.8007 (tp30) REVERT: A 868 LYS cc_start: 0.7966 (mmtp) cc_final: 0.7086 (mmmm) REVERT: A 871 SER cc_start: 0.8313 (t) cc_final: 0.7742 (p) REVERT: A 878 VAL cc_start: 0.8925 (t) cc_final: 0.8674 (t) REVERT: A 921 LEU cc_start: 0.8403 (mm) cc_final: 0.8157 (mp) REVERT: A 974 LYS cc_start: 0.9031 (ttpt) cc_final: 0.8728 (tppt) REVERT: A 986 GLU cc_start: 0.8219 (tt0) cc_final: 0.7940 (tt0) REVERT: A 994 GLU cc_start: 0.8581 (pm20) cc_final: 0.8326 (pm20) REVERT: A 999 PHE cc_start: 0.8199 (m-80) cc_final: 0.7937 (m-10) REVERT: A 1063 VAL cc_start: 0.8633 (t) cc_final: 0.8309 (p) REVERT: A 1073 MET cc_start: 0.8694 (mmm) cc_final: 0.8411 (tpt) REVERT: A 1077 ILE cc_start: 0.8876 (mm) cc_final: 0.8667 (mm) REVERT: A 1078 ASP cc_start: 0.7884 (m-30) cc_final: 0.7558 (m-30) REVERT: A 1100 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8601 (m) REVERT: A 1104 MET cc_start: 0.7975 (tpt) cc_final: 0.7749 (tpp) REVERT: A 1107 MET cc_start: 0.7357 (tmm) cc_final: 0.6526 (tmm) REVERT: A 1122 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7657 (tp30) REVERT: B 91 SER cc_start: 0.8677 (m) cc_final: 0.8440 (p) REVERT: B 140 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7991 (mp10) REVERT: B 154 MET cc_start: 0.8584 (tpp) cc_final: 0.8033 (tpp) REVERT: B 155 ASP cc_start: 0.8324 (t0) cc_final: 0.7963 (t0) REVERT: B 160 MET cc_start: 0.8445 (mmt) cc_final: 0.8201 (mmm) REVERT: B 190 ASN cc_start: 0.7822 (p0) cc_final: 0.7466 (p0) REVERT: B 197 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7578 (mt-10) REVERT: B 214 VAL cc_start: 0.8771 (t) cc_final: 0.8356 (p) REVERT: B 217 LEU cc_start: 0.8774 (mt) cc_final: 0.8511 (mm) REVERT: B 231 GLU cc_start: 0.8079 (tt0) cc_final: 0.7806 (mt-10) REVERT: B 233 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7715 (tm-30) REVERT: B 238 ASP cc_start: 0.7432 (m-30) cc_final: 0.7101 (m-30) REVERT: B 267 TYR cc_start: 0.8515 (t80) cc_final: 0.8208 (t80) REVERT: B 300 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7725 (mt-10) REVERT: B 335 ASN cc_start: 0.8615 (t0) cc_final: 0.8292 (t0) REVERT: B 383 MET cc_start: 0.7360 (tpp) cc_final: 0.7114 (tpp) REVERT: B 395 ILE cc_start: 0.8451 (tt) cc_final: 0.8112 (pt) REVERT: B 407 SER cc_start: 0.8282 (t) cc_final: 0.7982 (p) REVERT: B 443 GLU cc_start: 0.7921 (tp30) cc_final: 0.7527 (tp30) REVERT: B 476 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8569 (m) REVERT: B 486 ILE cc_start: 0.8437 (mm) cc_final: 0.8219 (mm) REVERT: B 511 MET cc_start: 0.9022 (tmm) cc_final: 0.8753 (ttp) REVERT: B 517 PHE cc_start: 0.8307 (m-10) cc_final: 0.8062 (m-10) REVERT: B 579 MET cc_start: 0.7591 (tpt) cc_final: 0.7309 (tpt) REVERT: B 580 GLU cc_start: 0.8063 (tp30) cc_final: 0.7639 (tp30) REVERT: B 581 GLU cc_start: 0.7447 (tp30) cc_final: 0.6854 (tp30) REVERT: B 585 ARG cc_start: 0.8235 (ttm-80) cc_final: 0.7522 (ttm110) REVERT: B 588 LYS cc_start: 0.8631 (tttm) cc_final: 0.8310 (tttm) REVERT: B 590 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8107 (mt-10) REVERT: B 592 ILE cc_start: 0.8816 (mt) cc_final: 0.8541 (mm) REVERT: B 617 VAL cc_start: 0.7863 (t) cc_final: 0.7265 (m) REVERT: B 621 GLU cc_start: 0.7309 (mp0) cc_final: 0.6736 (mp0) REVERT: B 644 LEU cc_start: 0.8368 (mt) cc_final: 0.8130 (mp) REVERT: B 837 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.7805 (t80) REVERT: B 841 LYS cc_start: 0.8568 (mtpt) cc_final: 0.8260 (mtpp) REVERT: B 845 ILE cc_start: 0.8977 (mm) cc_final: 0.8720 (mt) REVERT: B 850 VAL cc_start: 0.8852 (p) cc_final: 0.8631 (m) REVERT: B 865 ARG cc_start: 0.7641 (mmm160) cc_final: 0.7363 (mmm160) REVERT: B 870 ILE cc_start: 0.8651 (mm) cc_final: 0.8333 (mm) REVERT: B 871 SER cc_start: 0.8292 (t) cc_final: 0.8018 (t) REVERT: B 921 LEU cc_start: 0.8473 (mm) cc_final: 0.8226 (mp) REVERT: B 940 ARG cc_start: 0.8435 (ttm-80) cc_final: 0.8131 (ttm-80) REVERT: B 959 ASN cc_start: 0.8181 (m-40) cc_final: 0.7887 (m-40) REVERT: B 971 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7915 (t0) REVERT: B 974 LYS cc_start: 0.8997 (ttpt) cc_final: 0.8604 (tppt) REVERT: B 999 PHE cc_start: 0.8210 (m-80) cc_final: 0.7824 (m-80) REVERT: B 1067 PHE cc_start: 0.7900 (t80) cc_final: 0.7682 (t80) REVERT: B 1078 ASP cc_start: 0.7908 (m-30) cc_final: 0.7606 (m-30) REVERT: B 1098 ILE cc_start: 0.9080 (tp) cc_final: 0.8788 (tt) REVERT: B 1104 MET cc_start: 0.8443 (tpp) cc_final: 0.8078 (tpp) REVERT: B 1107 MET cc_start: 0.7144 (tmm) cc_final: 0.6354 (tmm) REVERT: B 1122 GLU cc_start: 0.7814 (tp30) cc_final: 0.7570 (tp30) REVERT: B 1145 VAL cc_start: 0.8524 (t) cc_final: 0.8223 (p) outliers start: 75 outliers final: 59 residues processed: 555 average time/residue: 0.1363 time to fit residues: 109.4996 Evaluate side-chains 570 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 503 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 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 462 ILE Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 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 1048 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain B residue 79 VAL 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 174 LEU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 372 VAL 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 418 THR 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 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 980 LEU Chi-restraints excluded: chain B residue 995 SER Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1146 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 73 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 119 optimal weight: 0.0970 chunk 176 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 144 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 103 optimal weight: 0.2980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 GLN A1120 HIS B 157 HIS B1154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.133100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.114505 restraints weight = 23288.057| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.11 r_work: 0.3369 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3742 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= 0.128 Angle : 0.589 8.755 20912 Z= 0.299 Chirality : 0.041 0.305 2526 Planarity : 0.004 0.036 2600 Dihedral : 4.455 56.375 2096 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.50 % Allowed : 27.44 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.20), residues: 1938 helix: 1.90 (0.14), residues: 1426 sheet: 0.09 (0.64), residues: 76 loop : -1.02 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 161 TYR 0.019 0.001 TYR B 280 PHE 0.020 0.001 PHE A 625 TRP 0.010 0.001 TRP A 353 HIS 0.003 0.000 HIS B 981 Details of bonding type rmsd covalent geometry : bond 0.00267 (15404) covalent geometry : angle 0.58943 (20912) hydrogen bonds : bond 0.04247 ( 1166) hydrogen bonds : angle 4.02261 ( 3447) *********************** 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 602 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 531 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8479 (m-10) cc_final: 0.8252 (m-10) REVERT: A 91 SER cc_start: 0.8639 (m) cc_final: 0.8300 (p) REVERT: A 96 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8289 (tmtt) REVERT: A 129 ASP cc_start: 0.6340 (OUTLIER) cc_final: 0.5960 (p0) REVERT: A 137 VAL cc_start: 0.8656 (p) cc_final: 0.8342 (t) REVERT: A 140 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7906 (mp10) REVERT: A 175 VAL cc_start: 0.8454 (p) cc_final: 0.8203 (m) REVERT: A 195 PHE cc_start: 0.7902 (t80) cc_final: 0.7578 (t80) REVERT: A 218 LYS cc_start: 0.8410 (ttmt) cc_final: 0.8131 (ttmp) REVERT: A 233 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7501 (tm-30) REVERT: A 267 TYR cc_start: 0.8586 (t80) cc_final: 0.8323 (t80) REVERT: A 284 LYS cc_start: 0.8658 (mmtm) cc_final: 0.8426 (mmmm) REVERT: A 335 ASN cc_start: 0.8558 (t0) cc_final: 0.8267 (t0) REVERT: A 346 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7319 (mt-10) REVERT: A 355 MET cc_start: 0.8523 (ttp) cc_final: 0.8069 (ttp) REVERT: A 395 ILE cc_start: 0.8258 (tt) cc_final: 0.7988 (pt) REVERT: A 511 MET cc_start: 0.8897 (tmm) cc_final: 0.8605 (tmm) REVERT: A 579 MET cc_start: 0.7502 (tmm) cc_final: 0.7231 (tmm) REVERT: A 580 GLU cc_start: 0.8135 (tp30) cc_final: 0.7810 (tp30) REVERT: A 588 LYS cc_start: 0.8646 (tttm) cc_final: 0.8230 (tttm) REVERT: A 592 ILE cc_start: 0.8811 (mt) cc_final: 0.8417 (mm) REVERT: A 613 GLN cc_start: 0.7757 (mt0) cc_final: 0.7501 (mt0) REVERT: A 624 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7308 (pp30) REVERT: A 633 LYS cc_start: 0.8655 (mttm) cc_final: 0.8382 (mptt) REVERT: A 810 MET cc_start: 0.7280 (ppp) cc_final: 0.6901 (tmm) REVERT: A 832 GLN cc_start: 0.8771 (tp40) cc_final: 0.8431 (tp-100) REVERT: A 841 LYS cc_start: 0.8446 (mtpt) cc_final: 0.8121 (mtpp) REVERT: A 865 ARG cc_start: 0.7378 (mmm160) cc_final: 0.7056 (mmm160) REVERT: A 868 LYS cc_start: 0.7951 (mmtp) cc_final: 0.7120 (mmmm) REVERT: A 871 SER cc_start: 0.8257 (t) cc_final: 0.7725 (p) REVERT: A 878 VAL cc_start: 0.8909 (t) cc_final: 0.8666 (t) REVERT: A 921 LEU cc_start: 0.8364 (mm) cc_final: 0.8125 (mp) REVERT: A 958 LYS cc_start: 0.8709 (ttpt) cc_final: 0.8275 (ttpt) REVERT: A 974 LYS cc_start: 0.9008 (ttpt) cc_final: 0.8704 (tppt) REVERT: A 986 GLU cc_start: 0.8171 (tt0) cc_final: 0.7849 (tt0) REVERT: A 994 GLU cc_start: 0.8559 (pm20) cc_final: 0.8305 (pm20) REVERT: A 999 PHE cc_start: 0.8192 (m-80) cc_final: 0.7955 (m-10) REVERT: A 1063 VAL cc_start: 0.8642 (t) cc_final: 0.8309 (p) REVERT: A 1073 MET cc_start: 0.8703 (mmm) cc_final: 0.8424 (tpt) REVERT: A 1077 ILE cc_start: 0.8869 (mm) cc_final: 0.8647 (mm) REVERT: A 1078 ASP cc_start: 0.7883 (m-30) cc_final: 0.7555 (m-30) REVERT: A 1100 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8599 (m) REVERT: A 1104 MET cc_start: 0.7941 (tpt) cc_final: 0.7621 (tpp) REVERT: A 1107 MET cc_start: 0.7300 (tmm) cc_final: 0.5954 (tmm) REVERT: A 1122 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7290 (mm-30) REVERT: B 91 SER cc_start: 0.8674 (m) cc_final: 0.8434 (p) REVERT: B 140 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7968 (mp10) REVERT: B 154 MET cc_start: 0.8541 (tpp) cc_final: 0.8000 (tpp) REVERT: B 155 ASP cc_start: 0.8284 (t0) cc_final: 0.7960 (t0) REVERT: B 160 MET cc_start: 0.8434 (mmt) cc_final: 0.8189 (mmm) REVERT: B 190 ASN cc_start: 0.7772 (p0) cc_final: 0.7416 (p0) REVERT: B 197 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7580 (mt-10) REVERT: B 214 VAL cc_start: 0.8754 (t) cc_final: 0.8333 (p) REVERT: B 217 LEU cc_start: 0.8732 (mt) cc_final: 0.8331 (mp) REVERT: B 231 GLU cc_start: 0.8072 (tt0) cc_final: 0.7793 (mt-10) REVERT: B 238 ASP cc_start: 0.7404 (m-30) cc_final: 0.7170 (m-30) REVERT: B 267 TYR cc_start: 0.8486 (t80) cc_final: 0.8188 (t80) REVERT: B 335 ASN cc_start: 0.8539 (t0) cc_final: 0.8217 (t0) REVERT: B 355 MET cc_start: 0.8388 (ttp) cc_final: 0.8107 (ttp) REVERT: B 383 MET cc_start: 0.7308 (tpp) cc_final: 0.7000 (tpp) REVERT: B 395 ILE cc_start: 0.8406 (tt) cc_final: 0.8081 (pt) REVERT: B 407 SER cc_start: 0.8234 (t) cc_final: 0.7926 (p) REVERT: B 419 TRP cc_start: 0.8271 (p-90) cc_final: 0.8056 (p-90) REVERT: B 443 GLU cc_start: 0.7918 (tp30) cc_final: 0.7524 (tp30) REVERT: B 444 ASN cc_start: 0.8847 (t0) cc_final: 0.8428 (t0) REVERT: B 476 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8544 (m) REVERT: B 486 ILE cc_start: 0.8435 (mm) cc_final: 0.8225 (mm) REVERT: B 511 MET cc_start: 0.9037 (tmm) cc_final: 0.8745 (ttp) REVERT: B 517 PHE cc_start: 0.8271 (m-10) cc_final: 0.8057 (m-10) REVERT: B 579 MET cc_start: 0.7598 (tpt) cc_final: 0.7313 (tpt) REVERT: B 580 GLU cc_start: 0.8053 (tp30) cc_final: 0.7279 (tp30) REVERT: B 581 GLU cc_start: 0.7396 (tp30) cc_final: 0.6786 (tp30) REVERT: B 584 LEU cc_start: 0.8535 (mm) cc_final: 0.7940 (mm) REVERT: B 585 ARG cc_start: 0.8193 (ttm-80) cc_final: 0.7706 (ttm110) REVERT: B 588 LYS cc_start: 0.8539 (tttm) cc_final: 0.8135 (tttm) REVERT: B 590 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8278 (mt-10) REVERT: B 592 ILE cc_start: 0.8760 (mt) cc_final: 0.8441 (mm) REVERT: B 617 VAL cc_start: 0.7821 (t) cc_final: 0.7259 (m) REVERT: B 621 GLU cc_start: 0.7295 (mp0) cc_final: 0.6698 (mp0) REVERT: B 644 LEU cc_start: 0.8323 (mt) cc_final: 0.8092 (mp) REVERT: B 837 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.7739 (t80) REVERT: B 841 LYS cc_start: 0.8536 (mtpt) cc_final: 0.8200 (mtpp) REVERT: B 845 ILE cc_start: 0.8947 (mm) cc_final: 0.8694 (mt) REVERT: B 865 ARG cc_start: 0.7605 (mmm160) cc_final: 0.7303 (mmm160) REVERT: B 870 ILE cc_start: 0.8640 (mm) cc_final: 0.8340 (mm) REVERT: B 871 SER cc_start: 0.8211 (t) cc_final: 0.7979 (t) REVERT: B 921 LEU cc_start: 0.8446 (mm) cc_final: 0.8209 (mp) REVERT: B 926 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7669 (mm-30) REVERT: B 940 ARG cc_start: 0.8409 (ttm-80) cc_final: 0.8104 (ttm-80) REVERT: B 959 ASN cc_start: 0.8158 (m-40) cc_final: 0.7867 (m-40) REVERT: B 971 ASP cc_start: 0.8237 (m-30) cc_final: 0.7935 (t70) REVERT: B 974 LYS cc_start: 0.8993 (ttpt) cc_final: 0.8592 (tppt) REVERT: B 976 ARG cc_start: 0.7670 (ttm-80) cc_final: 0.7387 (tpp80) REVERT: B 999 PHE cc_start: 0.8178 (m-80) cc_final: 0.7789 (m-80) REVERT: B 1045 MET cc_start: 0.8643 (tpp) cc_final: 0.8418 (mmm) REVERT: B 1067 PHE cc_start: 0.7877 (t80) cc_final: 0.7666 (t80) REVERT: B 1078 ASP cc_start: 0.7890 (m-30) cc_final: 0.7594 (m-30) REVERT: B 1098 ILE cc_start: 0.9040 (tp) cc_final: 0.8766 (tt) REVERT: B 1104 MET cc_start: 0.8410 (tpp) cc_final: 0.8129 (tpp) REVERT: B 1107 MET cc_start: 0.7125 (tmm) cc_final: 0.6440 (tmm) REVERT: B 1122 GLU cc_start: 0.7790 (tp30) cc_final: 0.7537 (tp30) REVERT: B 1145 VAL cc_start: 0.8486 (t) cc_final: 0.8178 (p) outliers start: 71 outliers final: 49 residues processed: 565 average time/residue: 0.1375 time to fit residues: 112.4163 Evaluate side-chains 581 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 524 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 378 VAL Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 405 LEU 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 884 LEU Chi-restraints excluded: chain A residue 888 GLU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1033 GLU 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 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 137 VAL Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 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 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 925 MET Chi-restraints excluded: chain B residue 991 GLU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1146 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 181 optimal weight: 3.9990 chunk 97 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 chunk 186 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 B1154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.132457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.113807 restraints weight = 23413.857| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.14 r_work: 0.3358 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3826 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= 0.143 Angle : 0.612 9.883 20912 Z= 0.307 Chirality : 0.042 0.271 2526 Planarity : 0.004 0.033 2600 Dihedral : 4.454 57.074 2096 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.18 % Allowed : 28.07 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.20), residues: 1938 helix: 1.89 (0.14), residues: 1424 sheet: -0.05 (0.54), residues: 96 loop : -0.98 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 940 TYR 0.019 0.001 TYR B 280 PHE 0.023 0.001 PHE B 289 TRP 0.010 0.001 TRP A 353 HIS 0.003 0.000 HIS B 981 Details of bonding type rmsd covalent geometry : bond 0.00309 (15404) covalent geometry : angle 0.61225 (20912) hydrogen bonds : bond 0.04395 ( 1166) hydrogen bonds : angle 4.03059 ( 3447) ********************** 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 583 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 517 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8480 (m-10) cc_final: 0.8258 (m-10) REVERT: A 91 SER cc_start: 0.8607 (m) cc_final: 0.8299 (p) REVERT: A 96 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8289 (tmtt) REVERT: A 129 ASP cc_start: 0.6395 (OUTLIER) cc_final: 0.6000 (p0) REVERT: A 137 VAL cc_start: 0.8650 (p) cc_final: 0.8310 (t) REVERT: A 140 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7890 (mp10) REVERT: A 195 PHE cc_start: 0.7935 (t80) cc_final: 0.7618 (t80) REVERT: A 218 LYS cc_start: 0.8434 (ttmt) cc_final: 0.8175 (ttmp) REVERT: A 233 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7606 (tm-30) REVERT: A 267 TYR cc_start: 0.8600 (t80) cc_final: 0.8327 (t80) REVERT: A 284 LYS cc_start: 0.8674 (mmtm) cc_final: 0.8442 (mmmm) REVERT: A 346 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7331 (mt-10) REVERT: A 395 ILE cc_start: 0.8274 (tt) cc_final: 0.8004 (pt) REVERT: A 580 GLU cc_start: 0.8131 (tp30) cc_final: 0.7897 (tp30) REVERT: A 583 ARG cc_start: 0.8206 (ttp-170) cc_final: 0.7957 (mtp180) REVERT: A 588 LYS cc_start: 0.8669 (tttm) cc_final: 0.8254 (tttm) REVERT: A 592 ILE cc_start: 0.8827 (mt) cc_final: 0.8436 (mm) REVERT: A 613 GLN cc_start: 0.7741 (mt0) cc_final: 0.7507 (mt0) REVERT: A 633 LYS cc_start: 0.8634 (mttm) cc_final: 0.8373 (mptt) REVERT: A 810 MET cc_start: 0.7256 (ppp) cc_final: 0.6879 (tmm) REVERT: A 832 GLN cc_start: 0.8755 (tp40) cc_final: 0.8426 (tp-100) REVERT: A 841 LYS cc_start: 0.8456 (mtpt) cc_final: 0.8121 (mtpp) REVERT: A 865 ARG cc_start: 0.7424 (mmm160) cc_final: 0.7066 (mmm160) REVERT: A 868 LYS cc_start: 0.7961 (mmtp) cc_final: 0.7340 (mmmm) REVERT: A 878 VAL cc_start: 0.8902 (t) cc_final: 0.8659 (t) REVERT: A 921 LEU cc_start: 0.8374 (mm) cc_final: 0.8137 (mp) REVERT: A 958 LYS cc_start: 0.8734 (ttpt) cc_final: 0.8287 (ttpt) REVERT: A 974 LYS cc_start: 0.9008 (ttpt) cc_final: 0.8715 (tppt) REVERT: A 986 GLU cc_start: 0.8202 (tt0) cc_final: 0.7847 (tt0) REVERT: A 994 GLU cc_start: 0.8561 (pm20) cc_final: 0.8302 (pm20) REVERT: A 999 PHE cc_start: 0.8196 (m-80) cc_final: 0.7960 (m-10) REVERT: A 1063 VAL cc_start: 0.8609 (t) cc_final: 0.8242 (p) REVERT: A 1073 MET cc_start: 0.8710 (mmm) cc_final: 0.8431 (tpt) REVERT: A 1078 ASP cc_start: 0.7899 (m-30) cc_final: 0.7581 (m-30) REVERT: A 1100 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8614 (m) REVERT: A 1104 MET cc_start: 0.7919 (tpt) cc_final: 0.7618 (tpp) REVERT: A 1107 MET cc_start: 0.7287 (tmm) cc_final: 0.6570 (tmm) REVERT: A 1122 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7582 (tp30) REVERT: B 91 SER cc_start: 0.8667 (m) cc_final: 0.8423 (p) REVERT: B 140 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7977 (mp10) REVERT: B 154 MET cc_start: 0.8574 (tpp) cc_final: 0.8015 (tpp) REVERT: B 155 ASP cc_start: 0.8319 (t0) cc_final: 0.7984 (t0) REVERT: B 160 MET cc_start: 0.8442 (mmt) cc_final: 0.8196 (mmm) REVERT: B 190 ASN cc_start: 0.7777 (p0) cc_final: 0.7421 (p0) REVERT: B 197 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7596 (mt-10) REVERT: B 214 VAL cc_start: 0.8767 (t) cc_final: 0.8356 (p) REVERT: B 217 LEU cc_start: 0.8749 (mt) cc_final: 0.8341 (mp) REVERT: B 231 GLU cc_start: 0.8047 (tt0) cc_final: 0.7769 (mt-10) REVERT: B 238 ASP cc_start: 0.7425 (m-30) cc_final: 0.7188 (m-30) REVERT: B 267 TYR cc_start: 0.8493 (t80) cc_final: 0.8196 (t80) REVERT: B 300 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7847 (mt-10) REVERT: B 335 ASN cc_start: 0.8549 (t0) cc_final: 0.8234 (t0) REVERT: B 355 MET cc_start: 0.8375 (ttp) cc_final: 0.8093 (ttp) REVERT: B 395 ILE cc_start: 0.8422 (tt) cc_final: 0.8077 (pt) REVERT: B 407 SER cc_start: 0.8240 (t) cc_final: 0.7926 (p) REVERT: B 443 GLU cc_start: 0.7916 (tp30) cc_final: 0.7529 (tp30) REVERT: B 476 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8538 (m) REVERT: B 511 MET cc_start: 0.9025 (tmm) cc_final: 0.8725 (ttp) REVERT: B 517 PHE cc_start: 0.8279 (m-10) cc_final: 0.8059 (m-10) REVERT: B 579 MET cc_start: 0.7619 (tpt) cc_final: 0.7330 (tpt) REVERT: B 580 GLU cc_start: 0.8069 (tp30) cc_final: 0.7268 (tp30) REVERT: B 581 GLU cc_start: 0.7440 (tp30) cc_final: 0.6818 (tp30) REVERT: B 584 LEU cc_start: 0.8576 (mm) cc_final: 0.8023 (mm) REVERT: B 585 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7734 (ttm110) REVERT: B 588 LYS cc_start: 0.8512 (tttm) cc_final: 0.8127 (tttm) REVERT: B 590 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8300 (mt-10) REVERT: B 592 ILE cc_start: 0.8726 (mt) cc_final: 0.8401 (mm) REVERT: B 617 VAL cc_start: 0.7841 (t) cc_final: 0.7293 (m) REVERT: B 621 GLU cc_start: 0.7307 (mp0) cc_final: 0.6710 (mp0) REVERT: B 644 LEU cc_start: 0.8245 (mt) cc_final: 0.8018 (mp) REVERT: B 837 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.7654 (t80) REVERT: B 841 LYS cc_start: 0.8527 (mtpt) cc_final: 0.8203 (mtpp) REVERT: B 845 ILE cc_start: 0.8928 (mm) cc_final: 0.8675 (mt) REVERT: B 865 ARG cc_start: 0.7664 (mmm160) cc_final: 0.7303 (mmm160) REVERT: B 866 GLU cc_start: 0.8159 (tp30) cc_final: 0.7885 (tp30) REVERT: B 870 ILE cc_start: 0.8647 (mm) cc_final: 0.8260 (mm) REVERT: B 921 LEU cc_start: 0.8458 (mm) cc_final: 0.8232 (mp) REVERT: B 940 ARG cc_start: 0.8415 (ttm-80) cc_final: 0.8100 (ttm-80) REVERT: B 959 ASN cc_start: 0.8171 (m-40) cc_final: 0.7888 (m-40) REVERT: B 971 ASP cc_start: 0.8252 (m-30) cc_final: 0.7945 (t70) REVERT: B 974 LYS cc_start: 0.8999 (ttpt) cc_final: 0.8585 (tppt) REVERT: B 976 ARG cc_start: 0.7690 (ttm-80) cc_final: 0.7406 (tpp80) REVERT: B 999 PHE cc_start: 0.8235 (m-80) cc_final: 0.7841 (m-80) REVERT: B 1045 MET cc_start: 0.8623 (tpp) cc_final: 0.8375 (mmm) REVERT: B 1050 LYS cc_start: 0.8979 (mmmm) cc_final: 0.8738 (mmmm) REVERT: B 1067 PHE cc_start: 0.7892 (t80) cc_final: 0.7681 (t80) REVERT: B 1078 ASP cc_start: 0.7988 (m-30) cc_final: 0.7684 (m-30) REVERT: B 1098 ILE cc_start: 0.9024 (tp) cc_final: 0.8740 (tt) REVERT: B 1104 MET cc_start: 0.8441 (tpp) cc_final: 0.8147 (tpp) REVERT: B 1107 MET cc_start: 0.7021 (tmm) cc_final: 0.6224 (tmm) REVERT: B 1122 GLU cc_start: 0.7827 (tp30) cc_final: 0.7562 (tp30) REVERT: B 1145 VAL cc_start: 0.8505 (t) cc_final: 0.8209 (p) outliers start: 66 outliers final: 50 residues processed: 552 average time/residue: 0.1365 time to fit residues: 109.3260 Evaluate side-chains 571 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 514 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 405 LEU 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 884 LEU Chi-restraints excluded: chain A residue 888 GLU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1033 GLU 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 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 137 VAL Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 372 VAL 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 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 925 MET Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1146 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 189 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 195 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 181 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 191 optimal weight: 5.9990 chunk 26 optimal weight: 0.0870 chunk 33 optimal weight: 0.3980 chunk 125 optimal weight: 0.1980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS B 165 GLN B 613 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 = 0.3770 r_free = 0.3770 target = 0.133915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.114945 restraints weight = 23414.298| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.19 r_work: 0.3369 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15404 Z= 0.131 Angle : 0.617 9.747 20912 Z= 0.306 Chirality : 0.042 0.253 2526 Planarity : 0.004 0.034 2600 Dihedral : 4.436 57.669 2096 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.06 % Allowed : 28.64 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.20), residues: 1938 helix: 1.92 (0.14), residues: 1426 sheet: -0.00 (0.54), residues: 96 loop : -1.02 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 161 TYR 0.018 0.001 TYR B 280 PHE 0.021 0.001 PHE B 289 TRP 0.010 0.001 TRP A 353 HIS 0.004 0.000 HIS B 981 Details of bonding type rmsd covalent geometry : bond 0.00282 (15404) covalent geometry : angle 0.61685 (20912) hydrogen bonds : bond 0.04212 ( 1166) hydrogen bonds : angle 3.98280 ( 3447) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4645.62 seconds wall clock time: 80 minutes 0.68 seconds (4800.68 seconds total)