Starting phenix.real_space_refine on Wed Aug 5 22:12:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gzn_51728/08_2026/9gzn_51728.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gzn_51728/08_2026/9gzn_51728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gzn_51728/08_2026/9gzn_51728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gzn_51728/08_2026/9gzn_51728.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gzn_51728/08_2026/9gzn_51728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gzn_51728/08_2026/9gzn_51728.map" } resolution = 3.5 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= -0.001 sd= 0.035 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: 6 Type Number sf(0) Gaussians P 57 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 7247 2.51 5 N 2082 2.21 5 O 2187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11637 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7928 Classifications: {'peptide': 1000} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 64, 'TRANS': 935} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "N" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 518 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "T" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 508 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "B" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2597 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 21, 'TRANS': 304} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 41 Chain: "R" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'GTP': 1} Classifications: {'RNA': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.60, per 1000 atoms: 0.22 Number of scatterers: 11637 At special positions: 0 Unit cell: (101.7, 135, 114.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 57 15.00 Mg 1 11.99 O 2187 8.00 N 2082 7.00 C 7247 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 684.7 milliseconds 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2516 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 11 sheets defined 58.7% alpha, 6.3% beta 12 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 220 through 237 removed outlier: 3.850A pdb=" N LEU A 227 " --> pdb=" O GLN A 223 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 252 removed outlier: 3.765A pdb=" N ALA A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 4.173A pdb=" N LYS A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 275 removed outlier: 3.522A pdb=" N TYR A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 291 removed outlier: 3.781A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.561A pdb=" N TYR A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 327 Processing helix chain 'A' and resid 329 through 335 removed outlier: 3.801A pdb=" N LEU A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 352 Processing helix chain 'A' and resid 392 through 410 Processing helix chain 'A' and resid 424 through 461 Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'A' and resid 497 through 521 Processing helix chain 'A' and resid 521 through 534 removed outlier: 3.891A pdb=" N ALA A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 556 Processing helix chain 'A' and resid 568 through 587 removed outlier: 3.573A pdb=" N THR A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 635 removed outlier: 3.559A pdb=" N VAL A 628 " --> pdb=" O HIS A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 686 Processing helix chain 'A' and resid 688 through 691 Processing helix chain 'A' and resid 692 through 704 Processing helix chain 'A' and resid 711 through 724 removed outlier: 3.591A pdb=" N ALA A 723 " --> pdb=" O GLN A 719 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 789 Processing helix chain 'A' and resid 818 through 824 Processing helix chain 'A' and resid 837 through 850 Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 867 through 877 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 893 through 907 removed outlier: 3.556A pdb=" N ASN A 903 " --> pdb=" O MET A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 912 Processing helix chain 'A' and resid 925 through 936 Processing helix chain 'A' and resid 937 through 944 Processing helix chain 'A' and resid 954 through 974 removed outlier: 3.663A pdb=" N GLY A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 981 removed outlier: 3.610A pdb=" N GLN A 979 " --> pdb=" O MET A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 998 removed outlier: 4.062A pdb=" N VAL A 990 " --> pdb=" O THR A 986 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLN A 992 " --> pdb=" O LYS A 988 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N THR A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL A 998 " --> pdb=" O VAL A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1015 Processing helix chain 'A' and resid 1021 through 1023 No H-bonds generated for 'chain 'A' and resid 1021 through 1023' Processing helix chain 'A' and resid 1024 through 1039 removed outlier: 3.557A pdb=" N HIS A1030 " --> pdb=" O TRP A1026 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG A1034 " --> pdb=" O HIS A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1064 removed outlier: 4.067A pdb=" N MET A1064 " --> pdb=" O LEU A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1142 removed outlier: 3.641A pdb=" N GLY A1118 " --> pdb=" O LYS A1114 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A1119 " --> pdb=" O GLN A1115 " (cutoff:3.500A) Proline residue: A1120 - end of helix removed outlier: 3.750A pdb=" N LYS A1142 " --> pdb=" O HIS A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1177 removed outlier: 3.932A pdb=" N GLU A1177 " --> pdb=" O ARG A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1193 removed outlier: 3.751A pdb=" N SER A1193 " --> pdb=" O LYS A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1209 Processing helix chain 'A' and resid 1218 through 1224 Processing helix chain 'B' and resid 77 through 89 Processing helix chain 'B' and resid 107 through 117 Processing helix chain 'B' and resid 128 through 137 removed outlier: 4.514A pdb=" N HIS B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 154 removed outlier: 3.797A pdb=" N LEU B 154 " --> pdb=" O PHE B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 176 Processing helix chain 'B' and resid 199 through 213 Processing helix chain 'B' and resid 216 through 221 removed outlier: 4.007A pdb=" N PHE B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 221' Processing helix chain 'B' and resid 230 through 238 Processing helix chain 'B' and resid 248 through 258 Processing helix chain 'B' and resid 267 through 269 No H-bonds generated for 'chain 'B' and resid 267 through 269' Processing helix chain 'B' and resid 281 through 292 removed outlier: 3.516A pdb=" N ARG B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B 286 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP B 290 " --> pdb=" O ARG B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.526A pdb=" N PHE B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.789A pdb=" N HIS B 338 " --> pdb=" O THR B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 355 Processing helix chain 'B' and resid 366 through 379 Processing helix chain 'B' and resid 390 through 394 Processing sheet with id=AA1, first strand: chain 'A' and resid 411 through 415 Processing sheet with id=AA2, first strand: chain 'A' and resid 495 through 496 Processing sheet with id=AA3, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AA4, first strand: chain 'A' and resid 707 through 709 Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 800 Processing sheet with id=AA6, first strand: chain 'A' and resid 831 through 832 Processing sheet with id=AA7, first strand: chain 'A' and resid 1069 through 1071 Processing sheet with id=AA8, first strand: chain 'A' and resid 1090 through 1091 removed outlier: 3.534A pdb=" N ILE A1098 " --> pdb=" O ILE A1091 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1147 through 1149 removed outlier: 3.739A pdb=" N VAL A1147 " --> pdb=" O TRP A1154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AB2, first strand: chain 'B' and resid 144 through 148 removed outlier: 6.648A pdb=" N VAL B 120 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE B 147 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ALA B 122 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU B 99 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU B 123 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLU B 101 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU B 100 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N MET B 194 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N CYS B 102 " --> pdb=" O MET B 194 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS B 264 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLN B 300 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL B 262 " --> pdb=" O GLN B 300 " (cutoff:3.500A) 551 hydrogen bonds defined for protein. 1602 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1740 1.31 - 1.43: 3335 1.43 - 1.56: 6742 1.56 - 1.68: 110 1.68 - 1.81: 96 Bond restraints: 12023 Sorted by residual: bond pdb=" C3' DC T 11 " pdb=" C2' DC T 11 " ideal model delta sigma weight residual 1.516 1.649 -0.133 8.00e-03 1.56e+04 2.76e+02 bond pdb=" O3' DT T 19 " pdb=" P DA T 20 " ideal model delta sigma weight residual 1.607 1.474 0.133 1.20e-02 6.94e+03 1.23e+02 bond pdb=" C3' DT T 26 " pdb=" C2' DT T 26 " ideal model delta sigma weight residual 1.516 1.582 -0.066 8.00e-03 1.56e+04 6.85e+01 bond pdb=" C2' DA N 46 " pdb=" C1' DA N 46 " ideal model delta sigma weight residual 1.518 1.584 -0.066 1.00e-02 1.00e+04 4.36e+01 bond pdb=" O3' DC N 35 " pdb=" P DG N 36 " ideal model delta sigma weight residual 1.607 1.683 -0.076 1.20e-02 6.94e+03 3.97e+01 ... (remaining 12018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 16141 3.09 - 6.18: 320 6.18 - 9.27: 57 9.27 - 12.36: 14 12.36 - 15.45: 5 Bond angle restraints: 16537 Sorted by residual: angle pdb=" C3' DC T 9 " pdb=" O3' DC T 9 " pdb=" P DT T 10 " ideal model delta sigma weight residual 119.70 105.04 14.66 1.20e+00 6.94e-01 1.49e+02 angle pdb=" C3' DC T 11 " pdb=" O3' DC T 11 " pdb=" P DC T 12 " ideal model delta sigma weight residual 119.70 105.47 14.23 1.20e+00 6.94e-01 1.41e+02 angle pdb=" C3' DA N 46 " pdb=" O3' DA N 46 " pdb=" P DA N 47 " ideal model delta sigma weight residual 119.70 107.18 12.52 1.20e+00 6.94e-01 1.09e+02 angle pdb=" C3' DC N 34 " pdb=" O3' DC N 34 " pdb=" P DC N 35 " ideal model delta sigma weight residual 119.70 108.07 11.63 1.20e+00 6.94e-01 9.39e+01 angle pdb=" C3' DG T 15 " pdb=" O3' DG T 15 " pdb=" P DC T 16 " ideal model delta sigma weight residual 119.70 108.62 11.08 1.20e+00 6.94e-01 8.53e+01 ... (remaining 16532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.10: 6745 31.10 - 62.21: 403 62.21 - 93.31: 14 93.31 - 124.42: 4 124.42 - 155.52: 3 Dihedral angle restraints: 7169 sinusoidal: 3293 harmonic: 3876 Sorted by residual: dihedral pdb=" C4' A R 102 " pdb=" C3' A R 102 " pdb=" C2' A R 102 " pdb=" C1' A R 102 " ideal model delta sinusoidal sigma weight residual 36.34 -8.91 45.26 1 3.10e+00 1.04e-01 2.96e+02 dihedral pdb=" O4' A R 102 " pdb=" C2' A R 102 " pdb=" C1' A R 102 " pdb=" C3' A R 102 " ideal model delta sinusoidal sigma weight residual 25.59 -27.69 53.29 3 3.80e+00 6.93e-02 1.43e+02 dihedral pdb=" C4' A R 102 " pdb=" O4' A R 102 " pdb=" C1' A R 102 " pdb=" C2' A R 102 " ideal model delta sinusoidal sigma weight residual 3.88 -37.16 41.04 3 5.00e+00 4.00e-02 6.60e+01 ... (remaining 7166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 1764 0.130 - 0.259: 28 0.259 - 0.389: 9 0.389 - 0.519: 28 0.519 - 0.648: 9 Chirality restraints: 1838 Sorted by residual: chirality pdb=" P DA N 24 " pdb=" OP1 DA N 24 " pdb=" OP2 DA N 24 " pdb=" O5' DA N 24 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P DC T 11 " pdb=" OP1 DC T 11 " pdb=" OP2 DC T 11 " pdb=" O5' DC T 11 " both_signs ideal model delta sigma weight residual True 2.34 -2.93 -0.59 2.00e-01 2.50e+01 8.73e+00 chirality pdb=" P A R 102 " pdb=" OP1 A R 102 " pdb=" OP2 A R 102 " pdb=" O5' A R 102 " both_signs ideal model delta sigma weight residual True 2.17 -2.74 -0.57 2.00e-01 2.50e+01 8.07e+00 ... (remaining 1835 not shown) Planarity restraints: 1938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 517 " -0.014 2.00e-02 2.50e+03 2.91e-02 8.45e+00 pdb=" C GLN A 517 " 0.050 2.00e-02 2.50e+03 pdb=" O GLN A 517 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG A 518 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 522 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.75e+00 pdb=" C GLN A 522 " -0.048 2.00e-02 2.50e+03 pdb=" O GLN A 522 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 523 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 527 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.21e+00 pdb=" C GLN A 527 " -0.046 2.00e-02 2.50e+03 pdb=" O GLN A 527 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN A 528 " 0.016 2.00e-02 2.50e+03 ... (remaining 1935 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 23 2.45 - 3.07: 7383 3.07 - 3.68: 16946 3.68 - 4.29: 24589 4.29 - 4.90: 41416 Nonbonded interactions: 90357 Sorted by model distance: nonbonded pdb=" O2B GTP A1301 " pdb="MG MG A1302 " model vdw 1.843 2.170 nonbonded pdb=" OD1 ASP B 186 " pdb=" N ILE B 187 " model vdw 2.163 3.120 nonbonded pdb=" O GLY A 923 " pdb="MG MG A1302 " model vdw 2.217 2.170 nonbonded pdb=" O LYS B 236 " pdb=" OG SER B 251 " model vdw 2.224 3.040 nonbonded pdb=" NZ LYS B 91 " pdb=" O SER B 93 " model vdw 2.264 3.120 ... (remaining 90352 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.260 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.133 12024 Z= 0.427 Angle : 1.055 15.453 16537 Z= 0.640 Chirality : 0.085 0.648 1838 Planarity : 0.006 0.063 1938 Dihedral : 17.761 155.520 4653 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.56 % Favored : 96.29 % Rotamer: Outliers : 0.62 % Allowed : 0.79 % Favored : 98.59 % Cbeta Deviations : 0.08 % 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 are not related in a simple way. whole: 1.27 (0.23), residues: 1320 helix: 2.05 (0.20), residues: 718 sheet: -0.52 (0.55), residues: 80 loop : -0.65 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1224 TYR 0.016 0.001 TYR B 247 PHE 0.029 0.001 PHE A 497 TRP 0.023 0.001 TRP B 387 HIS 0.009 0.001 HIS A 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.42 (12023) covalent geometry : angle 1.05507 / 0.64 (16537) hydrogen bonds : bond 0.15122 / 10.40 ( 580) hydrogen bonds : angle 5.75372 / 4.14 ( 1660) Misc. bond : bond 0.05711 / 3.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.7646 (mtt) cc_final: 0.7379 (mtt) REVERT: A 512 HIS cc_start: 0.8166 (OUTLIER) cc_final: 0.7735 (t70) REVERT: B 172 LEU cc_start: 0.8580 (tp) cc_final: 0.8201 (tt) outliers start: 7 outliers final: 4 residues processed: 128 average time/residue: 0.1012 time to fit residues: 19.2342 Evaluate side-chains 82 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 1096 GLN Chi-restraints excluded: chain A residue 1103 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 274 GLN A 493 GLN A 565 GLN ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1041 GLN ** A1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.055239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.042739 restraints weight = 60110.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.044096 restraints weight = 32306.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.045016 restraints weight = 21887.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.045640 restraints weight = 16893.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.046026 restraints weight = 14225.255| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12024 Z= 0.203 Angle : 0.666 10.026 16537 Z= 0.346 Chirality : 0.041 0.196 1838 Planarity : 0.005 0.058 1938 Dihedral : 18.511 149.956 2058 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.41 % Favored : 96.44 % Rotamer: Outliers : 1.76 % Allowed : 7.57 % Favored : 90.67 % 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 are not related in a simple way. whole: 1.53 (0.23), residues: 1320 helix: 2.36 (0.19), residues: 724 sheet: -0.47 (0.56), residues: 84 loop : -0.73 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 502 TYR 0.018 0.002 TYR A1100 PHE 0.015 0.001 PHE A 497 TRP 0.010 0.001 TRP B 387 HIS 0.011 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 (12023) covalent geometry : angle 0.66603 / 0.35 (16537) hydrogen bonds : bond 0.05328 / 3.53 ( 580) hydrogen bonds : angle 4.05813 / 2.96 ( 1660) Misc. bond : bond 0.00476 / 0.25 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.8786 (mtt) cc_final: 0.8429 (mpp) REVERT: A 323 MET cc_start: 0.9544 (tmm) cc_final: 0.9255 (tpp) REVERT: A 772 MET cc_start: 0.7947 (ppp) cc_final: 0.7693 (ppp) REVERT: B 172 LEU cc_start: 0.9606 (tp) cc_final: 0.9255 (tt) REVERT: B 227 MET cc_start: 0.9008 (mmp) cc_final: 0.8671 (mmp) outliers start: 20 outliers final: 13 residues processed: 95 average time/residue: 0.1013 time to fit residues: 14.3296 Evaluate side-chains 88 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain A residue 1096 GLN Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 394 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 107 optimal weight: 0.1980 chunk 117 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 GLN A1009 GLN A1103 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.055613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.043050 restraints weight = 59930.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.044429 restraints weight = 32093.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.045351 restraints weight = 21685.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.045996 restraints weight = 16734.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.046381 restraints weight = 14046.455| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12024 Z= 0.141 Angle : 0.588 9.343 16537 Z= 0.305 Chirality : 0.039 0.250 1838 Planarity : 0.005 0.058 1938 Dihedral : 18.340 150.553 2056 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.95 % Favored : 96.89 % Rotamer: Outliers : 0.97 % Allowed : 9.51 % Favored : 89.52 % 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 are not related in a simple way. whole: 1.72 (0.23), residues: 1320 helix: 2.51 (0.19), residues: 725 sheet: -0.40 (0.57), residues: 84 loop : -0.62 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 613 TYR 0.016 0.001 TYR A1100 PHE 0.014 0.001 PHE A 285 TRP 0.007 0.001 TRP A 892 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (12023) covalent geometry : angle 0.58798 / 0.30 (16537) hydrogen bonds : bond 0.04795 / 3.19 ( 580) hydrogen bonds : angle 3.76268 / 2.75 ( 1660) Misc. bond : bond 0.00340 / 0.18 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.8857 (mtt) cc_final: 0.8455 (mpp) REVERT: A 323 MET cc_start: 0.9556 (tmm) cc_final: 0.9285 (tpp) REVERT: A 565 GLN cc_start: 0.9059 (tp40) cc_final: 0.8837 (tp-100) REVERT: B 172 LEU cc_start: 0.9618 (tp) cc_final: 0.9287 (tt) REVERT: B 227 MET cc_start: 0.8617 (mmp) cc_final: 0.8307 (mmp) outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 0.0948 time to fit residues: 13.2222 Evaluate side-chains 81 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 394 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 70 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 125 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 565 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.054891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.042298 restraints weight = 60191.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.043635 restraints weight = 32677.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.044542 restraints weight = 22234.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.045155 restraints weight = 17275.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.045563 restraints weight = 14603.528| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12024 Z= 0.156 Angle : 0.577 13.524 16537 Z= 0.295 Chirality : 0.038 0.159 1838 Planarity : 0.005 0.056 1938 Dihedral : 18.153 147.354 2053 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.26 % Favored : 96.59 % Rotamer: Outliers : 1.50 % Allowed : 10.92 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.24), residues: 1320 helix: 2.57 (0.19), residues: 726 sheet: -0.54 (0.53), residues: 96 loop : -0.63 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 613 TYR 0.014 0.001 TYR A1100 PHE 0.014 0.001 PHE A 285 TRP 0.006 0.001 TRP B 387 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (12023) covalent geometry : angle 0.57697 / 0.30 (16537) hydrogen bonds : bond 0.04504 / 2.98 ( 580) hydrogen bonds : angle 3.64749 / 2.67 ( 1660) Misc. bond : bond 0.00239 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.8851 (mtt) cc_final: 0.8492 (mpp) REVERT: A 268 MET cc_start: 0.9449 (mtp) cc_final: 0.9135 (mtp) REVERT: A 323 MET cc_start: 0.9558 (tmm) cc_final: 0.9289 (tpp) REVERT: A 816 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9275 (mp) REVERT: A 1090 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7602 (tp-100) REVERT: B 172 LEU cc_start: 0.9619 (tp) cc_final: 0.9291 (tt) REVERT: B 227 MET cc_start: 0.8739 (mmp) cc_final: 0.8422 (mmp) outliers start: 17 outliers final: 10 residues processed: 93 average time/residue: 0.0950 time to fit residues: 13.6225 Evaluate side-chains 85 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 394 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 84 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 101 optimal weight: 20.0000 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 916 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.055002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.042399 restraints weight = 59968.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.043745 restraints weight = 32527.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.044620 restraints weight = 22164.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.045260 restraints weight = 17307.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.045640 restraints weight = 14591.287| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12024 Z= 0.135 Angle : 0.565 9.816 16537 Z= 0.288 Chirality : 0.038 0.250 1838 Planarity : 0.004 0.056 1938 Dihedral : 18.036 145.436 2053 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.03 % Favored : 96.82 % Rotamer: Outliers : 1.50 % Allowed : 12.50 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.23), residues: 1320 helix: 2.60 (0.19), residues: 726 sheet: -0.56 (0.53), residues: 96 loop : -0.64 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 613 TYR 0.012 0.001 TYR A1100 PHE 0.010 0.001 PHE A 285 TRP 0.005 0.001 TRP A1070 HIS 0.005 0.001 HIS A1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (12023) covalent geometry : angle 0.56511 / 0.29 (16537) hydrogen bonds : bond 0.04304 / 2.84 ( 580) hydrogen bonds : angle 3.54654 / 2.60 ( 1660) Misc. bond : bond 0.00159 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.8824 (mtt) cc_final: 0.8519 (mpp) REVERT: A 323 MET cc_start: 0.9554 (tmm) cc_final: 0.9280 (tpp) REVERT: A 816 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9186 (mp) REVERT: A 1090 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7568 (tp-100) REVERT: B 111 GLN cc_start: 0.9421 (tp-100) cc_final: 0.8833 (tp-100) REVERT: B 172 LEU cc_start: 0.9608 (tp) cc_final: 0.9320 (tt) REVERT: B 227 MET cc_start: 0.8701 (mmp) cc_final: 0.8238 (mmp) outliers start: 17 outliers final: 13 residues processed: 92 average time/residue: 0.1139 time to fit residues: 15.6170 Evaluate side-chains 87 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1041 GLN Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 394 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 82 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 84 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 30 optimal weight: 0.0470 chunk 127 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.055685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.042875 restraints weight = 59456.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.044225 restraints weight = 32192.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.045143 restraints weight = 21929.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.045756 restraints weight = 17074.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.046146 restraints weight = 14455.792| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12024 Z= 0.113 Angle : 0.547 8.923 16537 Z= 0.281 Chirality : 0.037 0.158 1838 Planarity : 0.004 0.056 1938 Dihedral : 17.910 144.043 2053 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.88 % Favored : 96.97 % Rotamer: Outliers : 1.58 % Allowed : 13.12 % Favored : 85.30 % 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 are not related in a simple way. whole: 1.81 (0.24), residues: 1320 helix: 2.59 (0.19), residues: 730 sheet: -0.45 (0.54), residues: 94 loop : -0.62 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 613 TYR 0.011 0.001 TYR A1100 PHE 0.011 0.001 PHE A 285 TRP 0.006 0.001 TRP B 387 HIS 0.005 0.001 HIS A1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (12023) covalent geometry : angle 0.54714 / 0.28 (16537) hydrogen bonds : bond 0.04062 / 2.70 ( 580) hydrogen bonds : angle 3.40586 / 2.49 ( 1660) Misc. bond : bond 0.00126 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.8801 (mtt) cc_final: 0.8534 (mpp) REVERT: A 306 MET cc_start: 0.9349 (mmm) cc_final: 0.9096 (tpp) REVERT: A 323 MET cc_start: 0.9556 (tmm) cc_final: 0.9270 (tpp) REVERT: A 495 GLU cc_start: 0.8649 (tp30) cc_final: 0.8440 (tm-30) REVERT: A 816 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9158 (mp) REVERT: B 172 LEU cc_start: 0.9625 (tp) cc_final: 0.9343 (tt) REVERT: B 227 MET cc_start: 0.8731 (mmp) cc_final: 0.8261 (mmp) REVERT: B 327 CYS cc_start: 0.9288 (m) cc_final: 0.9022 (m) outliers start: 18 outliers final: 12 residues processed: 91 average time/residue: 0.1073 time to fit residues: 14.7741 Evaluate side-chains 87 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1041 GLN Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 394 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 47 optimal weight: 8.9990 chunk 6 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 49 optimal weight: 0.0970 chunk 109 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 86 optimal weight: 0.0570 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.056094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.043304 restraints weight = 58915.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.044635 restraints weight = 32154.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.045545 restraints weight = 22018.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.046156 restraints weight = 17141.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.046550 restraints weight = 14514.327| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12024 Z= 0.109 Angle : 0.550 9.814 16537 Z= 0.279 Chirality : 0.036 0.157 1838 Planarity : 0.004 0.055 1938 Dihedral : 17.865 142.138 2053 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.88 % Favored : 96.97 % Rotamer: Outliers : 1.50 % Allowed : 13.64 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.24), residues: 1320 helix: 2.64 (0.19), residues: 731 sheet: -0.34 (0.53), residues: 100 loop : -0.63 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 613 TYR 0.010 0.001 TYR A1100 PHE 0.010 0.001 PHE A 285 TRP 0.008 0.001 TRP B 387 HIS 0.005 0.001 HIS A1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.11 (12023) covalent geometry : angle 0.54979 / 0.28 (16537) hydrogen bonds : bond 0.03870 / 2.56 ( 580) hydrogen bonds : angle 3.30096 / 2.41 ( 1660) Misc. bond : bond 0.00104 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.8785 (mtt) cc_final: 0.8535 (mpp) REVERT: A 268 MET cc_start: 0.9537 (mtp) cc_final: 0.9168 (mtp) REVERT: A 323 MET cc_start: 0.9549 (tmm) cc_final: 0.9271 (tpp) REVERT: B 111 GLN cc_start: 0.9373 (tp-100) cc_final: 0.8780 (tp-100) REVERT: B 167 MET cc_start: 0.7976 (tpp) cc_final: 0.7757 (tpp) REVERT: B 172 LEU cc_start: 0.9615 (tp) cc_final: 0.9324 (tt) REVERT: B 227 MET cc_start: 0.8716 (mmp) cc_final: 0.8239 (mmp) REVERT: B 327 CYS cc_start: 0.9272 (m) cc_final: 0.9016 (m) outliers start: 17 outliers final: 12 residues processed: 93 average time/residue: 0.0940 time to fit residues: 13.2729 Evaluate side-chains 88 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1041 GLN Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 394 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 127 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 65 optimal weight: 0.0010 chunk 19 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 565 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.055800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.043018 restraints weight = 58852.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.044338 restraints weight = 32218.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.045256 restraints weight = 22086.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.045856 restraints weight = 17181.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.046161 restraints weight = 14585.433| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12024 Z= 0.120 Angle : 0.569 11.418 16537 Z= 0.285 Chirality : 0.037 0.189 1838 Planarity : 0.005 0.056 1938 Dihedral : 17.819 139.853 2053 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.80 % Favored : 97.05 % Rotamer: Outliers : 1.50 % Allowed : 14.52 % Favored : 83.98 % 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 are not related in a simple way. whole: 1.87 (0.24), residues: 1320 helix: 2.65 (0.19), residues: 730 sheet: -0.36 (0.53), residues: 100 loop : -0.63 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 613 TYR 0.010 0.001 TYR B 247 PHE 0.010 0.001 PHE A 285 TRP 0.007 0.001 TRP B 387 HIS 0.017 0.001 HIS A 812 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (12023) covalent geometry : angle 0.56886 / 0.28 (16537) hydrogen bonds : bond 0.03842 / 2.53 ( 580) hydrogen bonds : angle 3.34090 / 2.43 ( 1660) Misc. bond : bond 0.00091 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.8802 (mtt) cc_final: 0.8550 (mpp) REVERT: A 268 MET cc_start: 0.9533 (mtp) cc_final: 0.9192 (mtp) REVERT: A 323 MET cc_start: 0.9553 (tmm) cc_final: 0.9280 (tpp) REVERT: A 495 GLU cc_start: 0.6962 (tm-30) cc_final: 0.6604 (tm-30) REVERT: B 111 GLN cc_start: 0.9414 (tp-100) cc_final: 0.8842 (tp-100) REVERT: B 172 LEU cc_start: 0.9612 (tp) cc_final: 0.9335 (tt) REVERT: B 227 MET cc_start: 0.8680 (mmp) cc_final: 0.8275 (mmp) REVERT: B 235 GLN cc_start: 0.9220 (mt0) cc_final: 0.8947 (mp10) REVERT: B 327 CYS cc_start: 0.9267 (m) cc_final: 0.9016 (m) outliers start: 17 outliers final: 11 residues processed: 91 average time/residue: 0.0940 time to fit residues: 12.9939 Evaluate side-chains 89 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1041 GLN Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 394 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 chunk 12 optimal weight: 0.0980 chunk 22 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 129 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.055397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.042674 restraints weight = 59368.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.043990 restraints weight = 32393.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.044906 restraints weight = 22151.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.045526 restraints weight = 17234.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.045898 restraints weight = 14541.604| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12024 Z= 0.135 Angle : 0.578 13.498 16537 Z= 0.289 Chirality : 0.037 0.166 1838 Planarity : 0.004 0.055 1938 Dihedral : 17.787 136.804 2051 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.95 % Favored : 96.89 % Rotamer: Outliers : 1.23 % Allowed : 14.79 % Favored : 83.98 % 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 are not related in a simple way. whole: 1.87 (0.24), residues: 1320 helix: 2.65 (0.19), residues: 731 sheet: -0.57 (0.53), residues: 96 loop : -0.58 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 613 TYR 0.011 0.001 TYR B 247 PHE 0.012 0.001 PHE A 285 TRP 0.007 0.001 TRP A 567 HIS 0.004 0.001 HIS A1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (12023) covalent geometry : angle 0.57811 / 0.29 (16537) hydrogen bonds : bond 0.03951 / 2.60 ( 580) hydrogen bonds : angle 3.41834 / 2.49 ( 1660) Misc. bond : bond 0.00085 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.8797 (mtt) cc_final: 0.8552 (mpp) REVERT: A 268 MET cc_start: 0.9512 (mtp) cc_final: 0.9203 (mtp) REVERT: A 323 MET cc_start: 0.9543 (tmm) cc_final: 0.9266 (tpp) REVERT: B 172 LEU cc_start: 0.9614 (tp) cc_final: 0.9345 (tt) REVERT: B 227 MET cc_start: 0.8674 (mmp) cc_final: 0.8279 (mmp) REVERT: B 235 GLN cc_start: 0.9193 (mt0) cc_final: 0.8931 (mp10) REVERT: B 327 CYS cc_start: 0.9257 (m) cc_final: 0.9014 (m) outliers start: 14 outliers final: 12 residues processed: 89 average time/residue: 0.0994 time to fit residues: 13.4182 Evaluate side-chains 89 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1041 GLN Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 394 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 29 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.055851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.043039 restraints weight = 59003.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.044387 restraints weight = 32394.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.045299 restraints weight = 22108.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.045904 restraints weight = 17200.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.046304 restraints weight = 14597.322| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12024 Z= 0.114 Angle : 0.586 14.915 16537 Z= 0.290 Chirality : 0.037 0.167 1838 Planarity : 0.005 0.057 1938 Dihedral : 17.705 136.262 2051 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.03 % Favored : 96.82 % Rotamer: Outliers : 1.14 % Allowed : 14.96 % Favored : 83.89 % 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 are not related in a simple way. whole: 1.89 (0.24), residues: 1320 helix: 2.67 (0.19), residues: 730 sheet: -0.56 (0.53), residues: 96 loop : -0.57 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 613 TYR 0.010 0.001 TYR B 247 PHE 0.012 0.001 PHE A 285 TRP 0.006 0.001 TRP B 387 HIS 0.005 0.001 HIS A1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (12023) covalent geometry : angle 0.58601 / 0.29 (16537) hydrogen bonds : bond 0.03798 / 2.51 ( 580) hydrogen bonds : angle 3.32489 / 2.42 ( 1660) Misc. bond : bond 0.00090 / 0.05 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.8796 (mtt) cc_final: 0.8568 (mpp) REVERT: A 323 MET cc_start: 0.9534 (tmm) cc_final: 0.9254 (tpp) REVERT: B 111 GLN cc_start: 0.9369 (tp-100) cc_final: 0.8829 (tp-100) REVERT: B 172 LEU cc_start: 0.9605 (tp) cc_final: 0.9365 (tt) REVERT: B 227 MET cc_start: 0.8717 (mmp) cc_final: 0.8257 (mmp) REVERT: B 235 GLN cc_start: 0.9192 (mt0) cc_final: 0.8922 (mp10) REVERT: B 327 CYS cc_start: 0.9264 (m) cc_final: 0.9011 (m) outliers start: 13 outliers final: 12 residues processed: 89 average time/residue: 0.1003 time to fit residues: 13.5192 Evaluate side-chains 89 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1041 GLN Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 394 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 135 optimal weight: 0.0570 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.056163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.043380 restraints weight = 58932.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.044721 restraints weight = 32025.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.045640 restraints weight = 21885.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.046274 restraints weight = 16986.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.046650 restraints weight = 14309.677| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12024 Z= 0.112 Angle : 0.586 15.279 16537 Z= 0.289 Chirality : 0.037 0.193 1838 Planarity : 0.005 0.056 1938 Dihedral : 17.626 135.058 2051 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.95 % Favored : 96.89 % Rotamer: Outliers : 1.23 % Allowed : 14.88 % Favored : 83.89 % 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 are not related in a simple way. whole: 2.02 (0.24), residues: 1320 helix: 2.78 (0.19), residues: 723 sheet: -0.43 (0.51), residues: 102 loop : -0.47 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 613 TYR 0.010 0.001 TYR A 264 PHE 0.012 0.001 PHE A 285 TRP 0.008 0.001 TRP B 387 HIS 0.007 0.001 HIS A 812 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (12023) covalent geometry : angle 0.58600 / 0.29 (16537) hydrogen bonds : bond 0.03640 / 2.39 ( 580) hydrogen bonds : angle 3.27042 / 2.38 ( 1660) Misc. bond : bond 0.00088 / 0.05 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1902.83 seconds wall clock time: 33 minutes 36.76 seconds (2016.76 seconds total)