Starting phenix.real_space_refine on Thu Jul 2 18:39:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oe2_70384/07_2026/9oe2_70384.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oe2_70384/07_2026/9oe2_70384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oe2_70384/07_2026/9oe2_70384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oe2_70384/07_2026/9oe2_70384.map" model { file = "/net/cci-nas-00/data/ceres_data/9oe2_70384/07_2026/9oe2_70384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oe2_70384/07_2026/9oe2_70384.cif" } resolution = 3.18 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= 0.000 sd= 0.013 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 6 5.49 5 Mg 2 5.21 5 S 49 5.16 5 C 5951 2.51 5 N 1559 2.21 5 O 1753 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9320 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 9115 Classifications: {'peptide': 1176} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 1148} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 205 Unusual residues: {' MG': 2, 'AGS': 2, 'CLR': 2, 'R1H': 1} Classifications: {'undetermined': 7, 'water': 37} Link IDs: {None: 43} Time building chain proxies: 2.08, per 1000 atoms: 0.22 Number of scatterers: 9320 At special positions: 0 Unit cell: (76.36, 122.01, 147.74, 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 49 16.00 P 6 15.00 Mg 2 11.99 O 1753 8.00 N 1559 7.00 C 5951 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: 0.78 Conformation dependent library (CDL) restraints added in 226.2 milliseconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 5 sheets defined 70.8% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.731A pdb=" N PHE A 45 " --> pdb=" O ILE A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 96 removed outlier: 4.139A pdb=" N LEU A 70 " --> pdb=" O ASN A 66 " (cutoff:3.500A) Proline residue: A 71 - end of helix removed outlier: 4.187A pdb=" N VAL A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE A 75 " --> pdb=" O PRO A 71 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 162 removed outlier: 3.559A pdb=" N LYS A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 172 through 191 removed outlier: 4.460A pdb=" N VAL A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 216 removed outlier: 3.642A pdb=" N GLY A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 265 removed outlier: 3.511A pdb=" N VAL A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix removed outlier: 3.790A pdb=" N ILE A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLY A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ALA A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 273 Processing helix chain 'A' and resid 274 through 328 removed outlier: 3.528A pdb=" N ASN A 285 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASP A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 323 " --> pdb=" O PHE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 376 removed outlier: 4.188A pdb=" N SER A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Proline residue: A 355 - end of helix removed outlier: 3.727A pdb=" N LYS A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 446 removed outlier: 3.702A pdb=" N THR A 441 " --> pdb=" O GLY A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 467 through 473 Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 501 through 512 removed outlier: 4.107A pdb=" N GLN A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 537 through 552 removed outlier: 3.722A pdb=" N ARG A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG A 552 " --> pdb=" O ARG A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 582 removed outlier: 3.533A pdb=" N LYS A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 600 removed outlier: 3.721A pdb=" N ASN A 599 " --> pdb=" O THR A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 624 Processing helix chain 'A' and resid 625 through 638 removed outlier: 3.690A pdb=" N SER A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 703 removed outlier: 3.619A pdb=" N VAL A 699 " --> pdb=" O SER A 695 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN A 703 " --> pdb=" O VAL A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 737 removed outlier: 3.695A pdb=" N GLN A 724 " --> pdb=" O ASN A 720 " (cutoff:3.500A) Proline residue: A 725 - end of helix removed outlier: 3.630A pdb=" N ILE A 735 " --> pdb=" O PHE A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 744 through 795 Processing helix chain 'A' and resid 798 through 803 removed outlier: 3.577A pdb=" N TYR A 802 " --> pdb=" O ASP A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 818 Processing helix chain 'A' and resid 822 through 827 removed outlier: 3.595A pdb=" N THR A 827 " --> pdb=" O GLN A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 852 Processing helix chain 'A' and resid 852 through 879 removed outlier: 3.613A pdb=" N THR A 856 " --> pdb=" O GLY A 852 " (cutoff:3.500A) Proline residue: A 864 - end of helix Processing helix chain 'A' and resid 880 through 888 Processing helix chain 'A' and resid 889 through 901 removed outlier: 3.688A pdb=" N ILE A 894 " --> pdb=" O GLN A 890 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN A 901 " --> pdb=" O GLU A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 909 Processing helix chain 'A' and resid 910 through 921 removed outlier: 3.538A pdb=" N LEU A 917 " --> pdb=" O LYS A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 964 removed outlier: 4.819A pdb=" N ILE A 947 " --> pdb=" O SER A 943 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N TYR A 948 " --> pdb=" O GLN A 944 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 949 " --> pdb=" O ALA A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 993 removed outlier: 3.624A pdb=" N THR A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1011 Processing helix chain 'A' and resid 1073 through 1083 removed outlier: 3.654A pdb=" N THR A1077 " --> pdb=" O GLY A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1102 No H-bonds generated for 'chain 'A' and resid 1100 through 1102' Processing helix chain 'A' and resid 1103 through 1110 Processing helix chain 'A' and resid 1124 through 1131 Processing helix chain 'A' and resid 1139 through 1150 removed outlier: 3.594A pdb=" N ALA A1146 " --> pdb=" O GLU A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1159 Processing helix chain 'A' and resid 1161 through 1165 removed outlier: 3.527A pdb=" N THR A1165 " --> pdb=" O ARG A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1190 removed outlier: 3.699A pdb=" N LYS A1179 " --> pdb=" O SER A1175 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG A1181 " --> pdb=" O GLY A1177 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A1182 " --> pdb=" O GLN A1178 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG A1190 " --> pdb=" O ARG A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1220 Processing helix chain 'A' and resid 1254 through 1262 Processing helix chain 'A' and resid 1262 through 1274 Processing sheet with id=AA1, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.686A pdb=" N LEU A 557 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL A 590 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU A 559 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 428 " --> pdb=" O VAL A 589 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA A 604 " --> pdb=" O THR A 427 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ALA A 429 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE A 606 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL A 431 " --> pdb=" O PHE A 606 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE A 603 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 614 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY A 605 " --> pdb=" O VAL A 612 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 458 Processing sheet with id=AA3, first strand: chain 'A' and resid 1055 through 1057 Processing sheet with id=AA4, first strand: chain 'A' and resid 1039 through 1040 Processing sheet with id=AA5, first strand: chain 'A' and resid 1111 through 1114 removed outlier: 6.732A pdb=" N LEU A1064 " --> pdb=" O ILE A1227 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR A1063 " --> pdb=" O CYS A1240 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA A1242 " --> pdb=" O THR A1063 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ALA A1065 " --> pdb=" O ALA A1242 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL A1244 " --> pdb=" O ALA A1065 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL A1067 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU A1251 " --> pdb=" O VAL A1243 " (cutoff:3.500A) 604 hydrogen bonds defined for protein. 1782 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: 1.76 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 3032 1.37 - 1.51: 2596 1.51 - 1.66: 3736 1.66 - 1.80: 68 1.80 - 1.95: 19 Bond restraints: 9451 Sorted by residual: bond pdb=" O3B AGS A1303 " pdb=" PB AGS A1303 " ideal model delta sigma weight residual 1.673 1.588 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" O3B AGS A1304 " pdb=" PB AGS A1304 " ideal model delta sigma weight residual 1.673 1.588 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" O3A AGS A1303 " pdb=" PA AGS A1303 " ideal model delta sigma weight residual 1.664 1.589 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" O3A AGS A1304 " pdb=" PA AGS A1304 " ideal model delta sigma weight residual 1.664 1.589 0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" O3B AGS A1304 " pdb=" PG AGS A1304 " ideal model delta sigma weight residual 1.614 1.560 0.054 2.00e-02 2.50e+03 7.29e+00 ... (remaining 9446 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 12635 2.38 - 4.76: 129 4.76 - 7.15: 20 7.15 - 9.53: 10 9.53 - 11.91: 6 Bond angle restraints: 12800 Sorted by residual: angle pdb=" C4 CLR A1306 " pdb=" C3 CLR A1306 " pdb=" O1 CLR A1306 " ideal model delta sigma weight residual 111.96 100.05 11.91 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C13 R1H A1305 " pdb=" C14 R1H A1305 " pdb=" C15 R1H A1305 " ideal model delta sigma weight residual 118.22 106.36 11.86 3.00e+00 1.11e-01 1.56e+01 angle pdb=" O3A AGS A1303 " pdb=" PB AGS A1303 " pdb=" O3B AGS A1303 " ideal model delta sigma weight residual 100.38 110.93 -10.55 3.00e+00 1.11e-01 1.24e+01 angle pdb=" CA GLY A 454 " pdb=" C GLY A 454 " pdb=" O GLY A 454 " ideal model delta sigma weight residual 122.37 119.95 2.42 7.30e-01 1.88e+00 1.10e+01 angle pdb=" O1A AGS A1304 " pdb=" PA AGS A1304 " pdb=" O2A AGS A1304 " ideal model delta sigma weight residual 122.09 112.29 9.80 3.00e+00 1.11e-01 1.07e+01 ... (remaining 12795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 5496 35.19 - 70.38: 253 70.38 - 105.57: 31 105.57 - 140.77: 6 140.77 - 175.96: 6 Dihedral angle restraints: 5792 sinusoidal: 2416 harmonic: 3376 Sorted by residual: dihedral pdb=" C09 R1H A1305 " pdb=" C13 R1H A1305 " pdb=" N08 R1H A1305 " pdb=" C14 R1H A1305 " ideal model delta sinusoidal sigma weight residual 72.22 -103.74 175.96 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B AGS A1303 " pdb=" O3B AGS A1303 " pdb=" PB AGS A1303 " pdb=" PG AGS A1303 " ideal model delta sinusoidal sigma weight residual 138.55 -30.86 169.41 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C07 R1H A1305 " pdb=" C13 R1H A1305 " pdb=" N08 R1H A1305 " pdb=" C14 R1H A1305 " ideal model delta sinusoidal sigma weight residual 295.98 134.50 161.48 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 5789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1211 0.050 - 0.100: 227 0.100 - 0.150: 37 0.150 - 0.201: 1 0.201 - 0.251: 2 Chirality restraints: 1478 Sorted by residual: chirality pdb=" C3' AGS A1303 " pdb=" C2' AGS A1303 " pdb=" C4' AGS A1303 " pdb=" O3' AGS A1303 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C3' AGS A1304 " pdb=" C2' AGS A1304 " pdb=" C4' AGS A1304 " pdb=" O3' AGS A1304 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB VAL A 581 " pdb=" CA VAL A 581 " pdb=" CG1 VAL A 581 " pdb=" CG2 VAL A 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 1475 not shown) Planarity restraints: 1602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C29 R1H A1305 " -0.380 2.00e-02 2.50e+03 3.18e-01 1.26e+03 pdb=" C31 R1H A1305 " 0.121 2.00e-02 2.50e+03 pdb=" C33 R1H A1305 " -0.120 2.00e-02 2.50e+03 pdb=" N30 R1H A1305 " 0.550 2.00e-02 2.50e+03 pdb=" O32 R1H A1305 " -0.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 R1H A1305 " -0.259 2.00e-02 2.50e+03 2.16e-01 5.83e+02 pdb=" C22 R1H A1305 " 0.056 2.00e-02 2.50e+03 pdb=" C24 R1H A1305 " -0.160 2.00e-02 2.50e+03 pdb=" N21 R1H A1305 " 0.371 2.00e-02 2.50e+03 pdb=" O23 R1H A1305 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 863 " -0.061 5.00e-02 4.00e+02 9.21e-02 1.36e+01 pdb=" N PRO A 864 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 864 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 864 " -0.051 5.00e-02 4.00e+02 ... (remaining 1599 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 59 2.58 - 3.16: 7907 3.16 - 3.74: 14580 3.74 - 4.32: 19885 4.32 - 4.90: 33560 Nonbonded interactions: 75991 Sorted by model distance: nonbonded pdb=" OG SER A1075 " pdb="MG MG A1301 " model vdw 2.004 2.170 nonbonded pdb="MG MG A1302 " pdb=" S1G AGS A1303 " model vdw 2.070 2.530 nonbonded pdb=" OE1 GLN A1110 " pdb=" O HOH A1401 " model vdw 2.236 3.040 nonbonded pdb=" O TYR A1085 " pdb=" O HOH A1402 " model vdw 2.238 3.040 nonbonded pdb=" O SER A1220 " pdb=" OG SER A1220 " model vdw 2.268 3.040 ... (remaining 75986 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 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: 3.630 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.710 Find NCS groups from input model: 0.040 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 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 : 0.004 0.085 9451 Z= 0.210 Angle : 0.681 11.912 12800 Z= 0.327 Chirality : 0.041 0.251 1478 Planarity : 0.011 0.318 1602 Dihedral : 20.602 175.958 3624 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.59 % Favored : 96.15 % Rotamer: Outliers : 3.08 % Allowed : 17.33 % Favored : 79.59 % 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: -0.17 (0.24), residues: 1170 helix: 1.09 (0.19), residues: 782 sheet: -2.93 (0.52), residues: 64 loop : -2.50 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 582 TYR 0.010 0.001 TYR A 252 PHE 0.015 0.001 PHE A 244 TRP 0.009 0.001 TRP A 141 HIS 0.004 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.21 ( 9451) covalent geometry : angle 0.68127 / 0.33 (12800) hydrogen bonds : bond 0.13395 / 9.27 ( 604) hydrogen bonds : angle 5.72055 / 4.27 ( 1782) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 265 SER cc_start: 0.9279 (OUTLIER) cc_final: 0.8893 (p) REVERT: A 423 MET cc_start: 0.9006 (mmm) cc_final: 0.8684 (mmp) REVERT: A 524 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7971 (mppt) REVERT: A 900 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8756 (mt-10) outliers start: 30 outliers final: 15 residues processed: 108 average time/residue: 0.1016 time to fit residues: 15.5472 Evaluate side-chains 78 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1243 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.0970 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 301 ASN A 634 GLN A1103 ASN ** A1128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.073590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.053657 restraints weight = 26643.557| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.48 r_work: 0.2746 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9451 Z= 0.175 Angle : 0.611 14.946 12800 Z= 0.303 Chirality : 0.040 0.153 1478 Planarity : 0.004 0.070 1602 Dihedral : 16.798 173.813 1517 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.68 % Favored : 96.07 % Rotamer: Outliers : 3.38 % Allowed : 17.64 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.59 (0.25), residues: 1170 helix: 1.64 (0.19), residues: 790 sheet: -2.53 (0.53), residues: 64 loop : -2.24 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 623 TYR 0.015 0.001 TYR A1163 PHE 0.014 0.001 PHE A 244 TRP 0.009 0.001 TRP A 853 HIS 0.005 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 ( 9451) covalent geometry : angle 0.61123 / 0.30 (12800) hydrogen bonds : bond 0.04861 / 3.16 ( 604) hydrogen bonds : angle 4.27861 / 3.09 ( 1782) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 65 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.8751 (mmm) cc_final: 0.8345 (mmm) REVERT: A 189 GLU cc_start: 0.8957 (tp30) cc_final: 0.8654 (mm-30) REVERT: A 260 GLU cc_start: 0.9068 (pp20) cc_final: 0.8827 (pp20) REVERT: A 423 MET cc_start: 0.8886 (mmm) cc_final: 0.8514 (mmp) REVERT: A 515 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.7936 (t80) REVERT: A 524 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7965 (mppt) REVERT: A 900 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8882 (mt-10) REVERT: A 1078 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8913 (mp) outliers start: 33 outliers final: 17 residues processed: 94 average time/residue: 0.0780 time to fit residues: 11.2433 Evaluate side-chains 83 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1243 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.0770 chunk 31 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.074384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.054601 restraints weight = 26576.883| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.46 r_work: 0.2773 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9451 Z= 0.121 Angle : 0.547 12.383 12800 Z= 0.271 Chirality : 0.038 0.143 1478 Planarity : 0.004 0.061 1602 Dihedral : 15.566 170.567 1505 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.68 % Favored : 96.15 % Rotamer: Outliers : 2.77 % Allowed : 18.46 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.88 (0.25), residues: 1170 helix: 1.83 (0.19), residues: 800 sheet: -2.20 (0.55), residues: 64 loop : -2.23 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1091 TYR 0.014 0.001 TYR A 515 PHE 0.013 0.001 PHE A 244 TRP 0.008 0.001 TRP A 217 HIS 0.006 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 9451) covalent geometry : angle 0.54725 / 0.27 (12800) hydrogen bonds : bond 0.04390 / 2.86 ( 604) hydrogen bonds : angle 3.98807 / 2.89 ( 1782) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.393 Fit side-chains REVERT: A 116 MET cc_start: 0.8693 (mmm) cc_final: 0.8294 (mmm) REVERT: A 189 GLU cc_start: 0.8889 (tp30) cc_final: 0.8599 (mm-30) REVERT: A 260 GLU cc_start: 0.9100 (pp20) cc_final: 0.8859 (pp20) REVERT: A 423 MET cc_start: 0.8878 (mmm) cc_final: 0.8503 (mmp) REVERT: A 524 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8004 (mppt) REVERT: A 900 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8866 (mt-10) REVERT: A 1093 MET cc_start: 0.8461 (mtm) cc_final: 0.7941 (mmm) outliers start: 27 outliers final: 15 residues processed: 89 average time/residue: 0.0701 time to fit residues: 9.9908 Evaluate side-chains 76 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 1016 ILE Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1243 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 93 optimal weight: 0.0030 chunk 116 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 34 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 634 GLN A 944 GLN A1161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.073997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.054153 restraints weight = 26894.365| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.49 r_work: 0.2764 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9451 Z= 0.137 Angle : 0.545 11.573 12800 Z= 0.271 Chirality : 0.038 0.140 1478 Planarity : 0.004 0.055 1602 Dihedral : 15.072 169.310 1505 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.76 % Favored : 96.07 % Rotamer: Outliers : 3.18 % Allowed : 18.87 % Favored : 77.95 % 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: 1.11 (0.25), residues: 1170 helix: 2.02 (0.19), residues: 795 sheet: -2.06 (0.54), residues: 64 loop : -2.15 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 747 TYR 0.013 0.001 TYR A 515 PHE 0.012 0.001 PHE A 244 TRP 0.008 0.001 TRP A 217 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 9451) covalent geometry : angle 0.54453 / 0.27 (12800) hydrogen bonds : bond 0.04240 / 2.75 ( 604) hydrogen bonds : angle 3.85175 / 2.79 ( 1782) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 60 time to evaluate : 0.369 Fit side-chains REVERT: A 189 GLU cc_start: 0.8877 (tp30) cc_final: 0.8618 (mm-30) REVERT: A 260 GLU cc_start: 0.9150 (pp20) cc_final: 0.8910 (pp20) REVERT: A 423 MET cc_start: 0.8925 (mmm) cc_final: 0.8641 (mmp) REVERT: A 515 TYR cc_start: 0.8411 (OUTLIER) cc_final: 0.7954 (t80) REVERT: A 516 ASN cc_start: 0.9005 (OUTLIER) cc_final: 0.8670 (m-40) REVERT: A 524 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8072 (mppt) REVERT: A 900 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8857 (mt-10) REVERT: A 1093 MET cc_start: 0.8478 (mtm) cc_final: 0.8064 (mmm) outliers start: 31 outliers final: 17 residues processed: 84 average time/residue: 0.0671 time to fit residues: 9.1925 Evaluate side-chains 78 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1243 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 7 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 67 optimal weight: 0.1980 chunk 22 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 101 optimal weight: 0.0040 chunk 99 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.3382 r_free = 0.3382 target = 0.074748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.054980 restraints weight = 26512.735| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.48 r_work: 0.2788 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9451 Z= 0.112 Angle : 0.525 11.073 12800 Z= 0.260 Chirality : 0.038 0.198 1478 Planarity : 0.003 0.052 1602 Dihedral : 14.740 173.549 1504 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.42 % Favored : 96.41 % Rotamer: Outliers : 3.28 % Allowed : 19.38 % Favored : 77.33 % 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: 1.14 (0.25), residues: 1170 helix: 2.09 (0.19), residues: 800 sheet: -2.57 (0.49), residues: 81 loop : -2.14 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 747 TYR 0.029 0.001 TYR A1266 PHE 0.011 0.001 PHE A 244 TRP 0.008 0.001 TRP A 217 HIS 0.006 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 9451) covalent geometry : angle 0.52540 / 0.26 (12800) hydrogen bonds : bond 0.03998 / 2.59 ( 604) hydrogen bonds : angle 3.73522 / 2.72 ( 1782) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 59 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 189 GLU cc_start: 0.8841 (tp30) cc_final: 0.8592 (mm-30) REVERT: A 260 GLU cc_start: 0.9163 (pp20) cc_final: 0.8918 (pp20) REVERT: A 423 MET cc_start: 0.8914 (mmm) cc_final: 0.8607 (mmp) REVERT: A 515 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.8152 (t80) REVERT: A 516 ASN cc_start: 0.9022 (OUTLIER) cc_final: 0.8735 (m-40) REVERT: A 900 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8839 (mt-10) REVERT: A 1078 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8852 (mp) REVERT: A 1093 MET cc_start: 0.8471 (mtm) cc_final: 0.7632 (mmm) outliers start: 32 outliers final: 19 residues processed: 85 average time/residue: 0.0646 time to fit residues: 9.0044 Evaluate side-chains 81 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1243 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 46 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1128 ASN ** A1178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.074274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.054407 restraints weight = 26708.315| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.49 r_work: 0.2779 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9451 Z= 0.134 Angle : 0.521 10.337 12800 Z= 0.261 Chirality : 0.038 0.139 1478 Planarity : 0.003 0.049 1602 Dihedral : 14.491 176.265 1500 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.93 % Favored : 95.90 % Rotamer: Outliers : 3.28 % Allowed : 19.79 % Favored : 76.92 % 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: 1.36 (0.25), residues: 1170 helix: 2.18 (0.19), residues: 794 sheet: -1.70 (0.54), residues: 69 loop : -2.04 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 747 TYR 0.016 0.001 TYR A1266 PHE 0.024 0.001 PHE A1155 TRP 0.007 0.001 TRP A 217 HIS 0.005 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 9451) covalent geometry : angle 0.52106 / 0.26 (12800) hydrogen bonds : bond 0.04058 / 2.62 ( 604) hydrogen bonds : angle 3.74506 / 2.72 ( 1782) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 60 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 116 MET cc_start: 0.8728 (mmm) cc_final: 0.8254 (mmm) REVERT: A 189 GLU cc_start: 0.8841 (tp30) cc_final: 0.8614 (mm-30) REVERT: A 260 GLU cc_start: 0.9167 (pp20) cc_final: 0.8929 (pp20) REVERT: A 423 MET cc_start: 0.8929 (mmm) cc_final: 0.8685 (mmp) REVERT: A 515 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.8108 (t80) REVERT: A 516 ASN cc_start: 0.9018 (OUTLIER) cc_final: 0.8722 (m-40) REVERT: A 524 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8047 (mppt) REVERT: A 900 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8803 (mt-10) REVERT: A 1078 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8851 (mp) REVERT: A 1093 MET cc_start: 0.8480 (mtm) cc_final: 0.8184 (mmm) REVERT: A 1157 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8534 (mm-30) outliers start: 32 outliers final: 20 residues processed: 83 average time/residue: 0.0635 time to fit residues: 8.4467 Evaluate side-chains 84 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1157 GLU Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1266 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 102 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.074142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.054289 restraints weight = 26814.221| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.49 r_work: 0.2764 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9451 Z= 0.128 Angle : 0.504 9.700 12800 Z= 0.256 Chirality : 0.038 0.157 1478 Planarity : 0.003 0.048 1602 Dihedral : 14.144 176.648 1500 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.68 % Favored : 96.15 % Rotamer: Outliers : 3.28 % Allowed : 20.10 % Favored : 76.62 % 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 are not related in a simple way. whole: 1.39 (0.25), residues: 1170 helix: 2.23 (0.19), residues: 794 sheet: -2.26 (0.52), residues: 79 loop : -1.88 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 747 TYR 0.014 0.001 TYR A1266 PHE 0.011 0.001 PHE A 244 TRP 0.008 0.001 TRP A 217 HIS 0.005 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 9451) covalent geometry : angle 0.50437 / 0.26 (12800) hydrogen bonds : bond 0.03995 / 2.59 ( 604) hydrogen bonds : angle 3.73303 / 2.72 ( 1782) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 62 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 189 GLU cc_start: 0.8849 (tp30) cc_final: 0.8622 (mm-30) REVERT: A 260 GLU cc_start: 0.9188 (pp20) cc_final: 0.8952 (pp20) REVERT: A 423 MET cc_start: 0.8927 (mmm) cc_final: 0.8686 (mmp) REVERT: A 515 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.8133 (t80) REVERT: A 516 ASN cc_start: 0.9011 (OUTLIER) cc_final: 0.8728 (m-40) REVERT: A 524 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8005 (mppt) REVERT: A 1078 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8830 (mp) REVERT: A 1093 MET cc_start: 0.8503 (mtm) cc_final: 0.8231 (mtp) outliers start: 32 outliers final: 21 residues processed: 87 average time/residue: 0.0692 time to fit residues: 9.2644 Evaluate side-chains 83 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1266 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 103 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 70 optimal weight: 0.0050 chunk 54 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.074406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.054622 restraints weight = 26730.915| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.49 r_work: 0.2779 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9451 Z= 0.123 Angle : 0.518 11.537 12800 Z= 0.263 Chirality : 0.038 0.149 1478 Planarity : 0.004 0.058 1602 Dihedral : 14.087 177.161 1499 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.68 % Favored : 96.15 % Rotamer: Outliers : 2.77 % Allowed : 20.92 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.46 (0.25), residues: 1170 helix: 2.26 (0.19), residues: 794 sheet: -2.06 (0.58), residues: 65 loop : -1.89 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1083 TYR 0.013 0.001 TYR A1266 PHE 0.010 0.001 PHE A 244 TRP 0.008 0.001 TRP A 217 HIS 0.006 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 9451) covalent geometry : angle 0.51788 / 0.26 (12800) hydrogen bonds : bond 0.03952 / 2.55 ( 604) hydrogen bonds : angle 3.71665 / 2.71 ( 1782) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 189 GLU cc_start: 0.8833 (tp30) cc_final: 0.8615 (mm-30) REVERT: A 260 GLU cc_start: 0.9193 (pp20) cc_final: 0.8951 (pp20) REVERT: A 423 MET cc_start: 0.8924 (mmm) cc_final: 0.8682 (mmp) REVERT: A 515 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.8127 (t80) REVERT: A 516 ASN cc_start: 0.9002 (OUTLIER) cc_final: 0.8729 (m-40) REVERT: A 524 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7986 (mppt) REVERT: A 900 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8643 (mt-10) REVERT: A 1078 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8797 (mp) REVERT: A 1093 MET cc_start: 0.8487 (mtm) cc_final: 0.8204 (mtp) REVERT: A 1156 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8007 (tp) outliers start: 27 outliers final: 21 residues processed: 84 average time/residue: 0.0594 time to fit residues: 8.0623 Evaluate side-chains 85 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1156 ILE Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1266 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.074521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.054735 restraints weight = 26614.171| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.48 r_work: 0.2776 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9451 Z= 0.120 Angle : 0.507 9.821 12800 Z= 0.259 Chirality : 0.038 0.146 1478 Planarity : 0.003 0.046 1602 Dihedral : 13.999 179.125 1499 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.76 % Favored : 96.07 % Rotamer: Outliers : 2.97 % Allowed : 20.72 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.48 (0.25), residues: 1170 helix: 2.28 (0.19), residues: 792 sheet: -2.01 (0.56), residues: 70 loop : -1.85 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1083 TYR 0.012 0.001 TYR A1266 PHE 0.010 0.001 PHE A 244 TRP 0.008 0.001 TRP A 217 HIS 0.007 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 9451) covalent geometry : angle 0.50662 / 0.26 (12800) hydrogen bonds : bond 0.03901 / 2.52 ( 604) hydrogen bonds : angle 3.69519 / 2.69 ( 1782) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 189 GLU cc_start: 0.8839 (tp30) cc_final: 0.8621 (mm-30) REVERT: A 260 GLU cc_start: 0.9197 (pp20) cc_final: 0.8952 (pp20) REVERT: A 423 MET cc_start: 0.8901 (mmm) cc_final: 0.8660 (mmp) REVERT: A 515 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.8140 (t80) REVERT: A 516 ASN cc_start: 0.8993 (OUTLIER) cc_final: 0.8728 (m-40) REVERT: A 524 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8000 (mppt) REVERT: A 900 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8646 (mt-10) REVERT: A 1078 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8820 (mp) REVERT: A 1093 MET cc_start: 0.8482 (mtm) cc_final: 0.8209 (mtp) REVERT: A 1156 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7982 (tp) outliers start: 29 outliers final: 22 residues processed: 84 average time/residue: 0.0603 time to fit residues: 8.1572 Evaluate side-chains 86 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1156 ILE Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1266 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 115 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.074350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.054591 restraints weight = 26624.800| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.48 r_work: 0.2772 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9451 Z= 0.123 Angle : 0.517 9.726 12800 Z= 0.261 Chirality : 0.038 0.168 1478 Planarity : 0.003 0.046 1602 Dihedral : 13.953 179.926 1499 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.85 % Favored : 95.98 % Rotamer: Outliers : 2.97 % Allowed : 20.72 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.52 (0.25), residues: 1170 helix: 2.29 (0.19), residues: 792 sheet: -1.96 (0.57), residues: 70 loop : -1.79 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 747 TYR 0.012 0.001 TYR A1266 PHE 0.010 0.001 PHE A 244 TRP 0.008 0.001 TRP A 217 HIS 0.007 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 9451) covalent geometry : angle 0.51657 / 0.26 (12800) hydrogen bonds : bond 0.03883 / 2.51 ( 604) hydrogen bonds : angle 3.67195 / 2.67 ( 1782) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.328 Fit side-chains REVERT: A 189 GLU cc_start: 0.8850 (tp30) cc_final: 0.8629 (mm-30) REVERT: A 260 GLU cc_start: 0.9203 (pp20) cc_final: 0.8956 (pp20) REVERT: A 423 MET cc_start: 0.8952 (mmm) cc_final: 0.8719 (mmp) REVERT: A 515 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.8131 (t80) REVERT: A 516 ASN cc_start: 0.8984 (OUTLIER) cc_final: 0.8721 (m-40) REVERT: A 524 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8010 (mppt) REVERT: A 900 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8658 (mt-10) REVERT: A 1078 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8822 (mp) REVERT: A 1093 MET cc_start: 0.8509 (mtm) cc_final: 0.8228 (mtp) REVERT: A 1156 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7971 (tp) outliers start: 29 outliers final: 22 residues processed: 83 average time/residue: 0.0678 time to fit residues: 9.0754 Evaluate side-chains 86 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1156 ILE Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1273 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 11 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.074354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.054529 restraints weight = 26474.799| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.48 r_work: 0.2770 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9451 Z= 0.126 Angle : 0.518 9.244 12800 Z= 0.263 Chirality : 0.039 0.168 1478 Planarity : 0.003 0.046 1602 Dihedral : 13.905 178.809 1499 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.68 % Favored : 96.15 % Rotamer: Outliers : 2.87 % Allowed : 20.82 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.51 (0.25), residues: 1170 helix: 2.27 (0.19), residues: 792 sheet: -1.96 (0.57), residues: 70 loop : -1.77 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 747 TYR 0.028 0.001 TYR A1266 PHE 0.010 0.001 PHE A 244 TRP 0.008 0.001 TRP A 217 HIS 0.007 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 9451) covalent geometry : angle 0.51792 / 0.26 (12800) hydrogen bonds : bond 0.03914 / 2.53 ( 604) hydrogen bonds : angle 3.67015 / 2.67 ( 1782) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1839.77 seconds wall clock time: 32 minutes 21.86 seconds (1941.86 seconds total)