Starting phenix.real_space_refine on Sat Jul 4 06:57:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oe8_70390/07_2026/9oe8_70390_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oe8_70390/07_2026/9oe8_70390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oe8_70390/07_2026/9oe8_70390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oe8_70390/07_2026/9oe8_70390.map" model { file = "/net/cci-nas-00/data/ceres_data/9oe8_70390/07_2026/9oe8_70390_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oe8_70390/07_2026/9oe8_70390_trim.cif" } resolution = 3.7 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= 0.004 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 49 5.16 5 C 5765 2.51 5 N 1533 2.21 5 O 1679 1.98 5 H 9142 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 18176 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1157, 18110 Classifications: {'peptide': 1157} Link IDs: {'PTRANS': 27, 'TRANS': 1129} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4, 'water': 2} Link IDs: {None: 5} Time building chain proxies: 2.69, per 1000 atoms: 0.15 Number of scatterers: 18176 At special positions: 0 Unit cell: (70.55, 117.03, 136.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 49 16.00 P 6 15.00 Mg 2 11.99 O 1679 8.00 N 1533 7.00 C 5765 6.00 H 9142 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 619.7 milliseconds 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 7 sheets defined 69.3% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 removed outlier: 3.708A pdb=" N LEU A 44 " --> pdb=" O PRO A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 81 Proline residue: A 71 - end of helix removed outlier: 4.416A pdb=" N VAL A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 163 removed outlier: 3.704A pdb=" N TYR A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 171 removed outlier: 3.505A pdb=" N PHE A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 182 Processing helix chain 'A' and resid 182 through 191 Processing helix chain 'A' and resid 192 through 216 removed outlier: 3.724A pdb=" N GLY A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 236 Proline residue: A 228 - end of helix removed outlier: 3.791A pdb=" N GLY A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.725A pdb=" N TYR A 252 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 265 removed outlier: 3.612A pdb=" N SER A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 273 Processing helix chain 'A' and resid 274 through 326 Processing helix chain 'A' and resid 332 through 352 Processing helix chain 'A' and resid 352 through 376 removed outlier: 4.771A pdb=" N ASN A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 removed outlier: 3.775A pdb=" N VAL A 412 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 413 " --> pdb=" O ASP A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 409 through 413' Processing helix chain 'A' and resid 438 through 446 removed outlier: 4.135A pdb=" N ILE A 442 " --> pdb=" O LYS A 438 " (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 493 Processing helix chain 'A' and resid 501 through 512 removed outlier: 3.693A pdb=" N ARG A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 538 through 552 removed outlier: 3.817A pdb=" N ARG A 552 " --> pdb=" O ARG A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 583 removed outlier: 4.163A pdb=" N ALA A 576 " --> pdb=" O THR A 572 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A 583 " --> pdb=" O ASP A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 599 removed outlier: 3.623A pdb=" N ILE A 597 " --> pdb=" O ARG A 593 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASN A 599 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 624 Processing helix chain 'A' and resid 625 through 638 Processing helix chain 'A' and resid 695 through 703 removed outlier: 3.829A pdb=" N ASN A 703 " --> pdb=" O VAL A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 737 Proline residue: A 725 - end of helix 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 742 through 794 removed outlier: 3.610A pdb=" N ALA A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 779 " --> pdb=" O PHE A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 803 removed outlier: 3.531A pdb=" N TYR A 802 " --> pdb=" O ASP A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 807 Processing helix chain 'A' and resid 808 through 818 Processing helix chain 'A' and resid 818 through 823 removed outlier: 3.848A pdb=" N VAL A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 828 removed outlier: 3.513A pdb=" N THR A 827 " --> pdb=" O VAL A 823 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 828 " --> pdb=" O GLN A 824 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 823 through 828' Processing helix chain 'A' and resid 828 through 852 Processing helix chain 'A' and resid 853 through 901 Proline residue: A 864 - end of helix removed outlier: 4.071A pdb=" N ALA A 891 " --> pdb=" O GLU A 887 " (cutoff:3.500A) removed outlier: 3.746A 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 964 Proline residue: A 925 - end of helix removed outlier: 4.551A pdb=" N ASN A 928 " --> pdb=" O VAL A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 993 Processing helix chain 'A' and resid 995 through 1011 removed outlier: 3.641A pdb=" N ALA A 999 " --> pdb=" O ASN A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1080 Processing helix chain 'A' and resid 1103 through 1108 Processing helix chain 'A' and resid 1109 through 1111 No H-bonds generated for 'chain 'A' and resid 1109 through 1111' Processing helix chain 'A' and resid 1124 through 1131 Processing helix chain 'A' and resid 1139 through 1150 removed outlier: 3.688A pdb=" N ALA A1149 " --> pdb=" O GLU A1145 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A1150 " --> pdb=" O ALA A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1191 Processing helix chain 'A' and resid 1206 through 1220 Processing helix chain 'A' and resid 1231 through 1237 removed outlier: 4.083A pdb=" N ILE A1235 " --> pdb=" O ARG A1231 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN A1237 " --> pdb=" O SER A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1261 Processing helix chain 'A' and resid 1262 through 1275 removed outlier: 3.792A pdb=" N TYR A1266 " --> pdb=" O GLN A1262 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AA2, first strand: chain 'A' and resid 429 through 432 removed outlier: 6.619A pdb=" N ALA A 429 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N PHE A 606 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 431 " --> pdb=" O PHE A 606 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 613 " --> pdb=" O GLY A 605 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLN A 607 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE A 611 " --> pdb=" O GLN A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 458 Processing sheet with id=AA4, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.878A pdb=" N GLY A 476 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ASP A 560 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A 478 " --> pdb=" O ASP A 560 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N VAL A 590 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU A 559 " --> pdb=" O VAL A 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1054 through 1055 removed outlier: 5.540A pdb=" N LEU A1054 " --> pdb=" O HIS A1037 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1065 through 1068 removed outlier: 6.167A pdb=" N ALA A1065 " --> pdb=" O ALA A1242 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL A1244 " --> pdb=" O ALA A1065 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A1067 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU A1251 " --> pdb=" O VAL A1243 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1194 through 1196 removed outlier: 4.049A pdb=" N ILE A1226 " --> pdb=" O LEU A1195 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1662 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: 3.85 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 9133 1.06 - 1.28: 1494 1.28 - 1.50: 3787 1.50 - 1.73: 3830 1.73 - 1.95: 87 Bond restraints: 18331 Sorted by residual: bond pdb=" O3B AGS A1303 " pdb=" PB AGS A1303 " ideal model delta sigma weight residual 1.673 1.580 0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" O3B AGS A1304 " pdb=" PB AGS A1304 " ideal model delta sigma weight residual 1.673 1.584 0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" O3A AGS A1303 " pdb=" PA AGS A1303 " ideal model delta sigma weight residual 1.664 1.580 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" O3A AGS A1304 " pdb=" PA AGS A1304 " ideal model delta sigma weight residual 1.664 1.581 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" CA THR A1077 " pdb=" C THR A1077 " ideal model delta sigma weight residual 1.523 1.479 0.044 1.37e-02 5.33e+03 1.01e+01 ... (remaining 18326 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 32767 2.18 - 4.35: 335 4.35 - 6.53: 34 6.53 - 8.70: 16 8.70 - 10.88: 7 Bond angle restraints: 33159 Sorted by residual: angle pdb=" N THR A1077 " pdb=" CA THR A1077 " pdb=" CB THR A1077 " ideal model delta sigma weight residual 110.30 116.83 -6.53 1.54e+00 4.22e-01 1.80e+01 angle pdb=" CA THR A1077 " pdb=" C THR A1077 " pdb=" O THR A1077 " ideal model delta sigma weight residual 119.79 115.25 4.54 1.18e+00 7.18e-01 1.48e+01 angle pdb=" CA SER A 629 " pdb=" C SER A 629 " pdb=" O SER A 629 " ideal model delta sigma weight residual 120.90 117.09 3.81 1.03e+00 9.43e-01 1.37e+01 angle pdb=" CB MET A1093 " pdb=" CG MET A1093 " pdb=" SD MET A1093 " ideal model delta sigma weight residual 112.70 123.58 -10.88 3.00e+00 1.11e-01 1.32e+01 angle pdb=" CA MET A1008 " pdb=" CB MET A1008 " pdb=" CG MET A1008 " ideal model delta sigma weight residual 114.10 121.08 -6.98 2.00e+00 2.50e-01 1.22e+01 ... (remaining 33154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 8232 35.92 - 71.85: 337 71.85 - 107.77: 11 107.77 - 143.69: 6 143.69 - 179.61: 4 Dihedral angle restraints: 8590 sinusoidal: 4720 harmonic: 3870 Sorted by residual: dihedral pdb=" O3A AGS A1304 " pdb=" O3B AGS A1304 " pdb=" PB AGS A1304 " pdb=" PG AGS A1304 " ideal model delta sinusoidal sigma weight residual 252.61 73.00 179.61 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2B AGS A1304 " pdb=" O3B AGS A1304 " pdb=" PB AGS A1304 " pdb=" PG AGS A1304 " ideal model delta sinusoidal sigma weight residual 7.37 -173.18 -179.45 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B AGS A1304 " pdb=" O3B AGS A1304 " pdb=" PB AGS A1304 " pdb=" PG AGS A1304 " ideal model delta sinusoidal sigma weight residual 138.55 -49.00 -172.45 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 8587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1239 0.056 - 0.112: 176 0.112 - 0.167: 17 0.167 - 0.223: 1 0.223 - 0.279: 2 Chirality restraints: 1435 Sorted by residual: 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 -2.65 0.28 2.00e-01 2.50e+01 1.94e+00 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 1.58e+00 chirality pdb=" CB ILE A 976 " pdb=" CA ILE A 976 " pdb=" CG1 ILE A 976 " pdb=" CG2 ILE A 976 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1432 not shown) Planarity restraints: 2698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A1077 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.54e+00 pdb=" C THR A1077 " 0.053 2.00e-02 2.50e+03 pdb=" O THR A1077 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE A1078 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1077 " -0.015 2.00e-02 2.50e+03 2.90e-02 8.44e+00 pdb=" N ILE A1078 " 0.050 2.00e-02 2.50e+03 pdb=" CA ILE A1078 " -0.013 2.00e-02 2.50e+03 pdb=" H ILE A1078 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 70 " -0.038 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO A 71 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 71 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 71 " -0.032 5.00e-02 4.00e+02 ... (remaining 2695 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 2918 2.27 - 2.86: 41666 2.86 - 3.44: 47657 3.44 - 4.02: 61885 4.02 - 4.60: 95872 Nonbonded interactions: 249998 Sorted by model distance: nonbonded pdb=" OE1 GLU A 613 " pdb=" H TYR A 627 " model vdw 1.694 2.450 nonbonded pdb=" O PHE A 77 " pdb=" HG1 THR A 81 " model vdw 1.702 2.450 nonbonded pdb=" OE2 GLU A 261 " pdb=" H ASP A1122 " model vdw 1.703 2.450 nonbonded pdb=" H ALA A 486 " pdb=" OE2 GLU A 897 " model vdw 1.705 2.450 nonbonded pdb=" OD1 ASP A1139 " pdb=" H GLU A1142 " model vdw 1.709 2.450 ... (remaining 249993 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 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: 4.200 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: 0.130 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.090 Find NCS groups from input model: 0.050 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 0.093 9189 Z= 0.211 Angle : 0.745 10.880 12431 Z= 0.373 Chirality : 0.039 0.279 1435 Planarity : 0.004 0.058 1571 Dihedral : 18.545 179.613 3408 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.30 % Favored : 94.61 % Rotamer: Outliers : 1.25 % Allowed : 17.97 % Favored : 80.77 % 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: 0.97 (0.26), residues: 1151 helix: 2.03 (0.19), residues: 730 sheet: -2.60 (0.66), residues: 53 loop : -1.79 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1190 TYR 0.015 0.001 TYR A 981 PHE 0.008 0.001 PHE A 340 TRP 0.012 0.001 TRP A 707 HIS 0.005 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.21 ( 9189) covalent geometry : angle 0.74546 / 0.37 (12431) hydrogen bonds : bond 0.12759 / 8.61 ( 560) hydrogen bonds : angle 5.33804 / 3.89 ( 1662) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 237 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 SER cc_start: 0.8275 (OUTLIER) cc_final: 0.7933 (m) REVERT: A 866 MET cc_start: 0.8552 (tmm) cc_final: 0.8319 (tmm) REVERT: A 1195 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8725 (tt) outliers start: 12 outliers final: 10 residues processed: 67 average time/residue: 0.1809 time to fit residues: 18.7145 Evaluate side-chains 71 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1236 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 513 ASN A1103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.050507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.038915 restraints weight = 146974.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.040881 restraints weight = 60947.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.042182 restraints weight = 36200.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.043006 restraints weight = 25917.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.043617 restraints weight = 20904.286| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9189 Z= 0.274 Angle : 0.569 6.340 12431 Z= 0.317 Chirality : 0.036 0.136 1435 Planarity : 0.004 0.054 1571 Dihedral : 14.535 177.985 1335 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.78 % Favored : 93.14 % Rotamer: Outliers : 2.30 % Allowed : 17.24 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.26), residues: 1151 helix: 1.84 (0.19), residues: 736 sheet: -3.02 (0.60), residues: 53 loop : -1.92 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 510 TYR 0.010 0.001 TYR A 981 PHE 0.017 0.001 PHE A 757 TRP 0.009 0.001 TRP A 707 HIS 0.006 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.27 ( 9189) covalent geometry : angle 0.56852 / 0.32 (12431) hydrogen bonds : bond 0.04490 / 3.02 ( 560) hydrogen bonds : angle 4.75972 / 3.47 ( 1662) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 237 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8749 (tt) REVERT: A 536 MET cc_start: 0.7656 (mmp) cc_final: 0.7451 (mmp) REVERT: A 606 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8685 (t80) outliers start: 22 outliers final: 16 residues processed: 73 average time/residue: 0.1883 time to fit residues: 20.8004 Evaluate side-chains 70 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1181 ARG Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1236 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 85 optimal weight: 0.3980 chunk 78 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 628 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.051411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.039926 restraints weight = 142914.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.041933 restraints weight = 59008.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.043264 restraints weight = 34892.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.044149 restraints weight = 24883.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.044692 restraints weight = 19797.662| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9189 Z= 0.106 Angle : 0.462 6.078 12431 Z= 0.247 Chirality : 0.035 0.135 1435 Planarity : 0.003 0.046 1571 Dihedral : 13.260 173.027 1328 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.13 % Favored : 94.79 % Rotamer: Outliers : 1.88 % Allowed : 18.50 % Favored : 79.62 % 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: 1.10 (0.26), residues: 1151 helix: 2.16 (0.19), residues: 730 sheet: -2.81 (0.62), residues: 53 loop : -1.77 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1190 TYR 0.009 0.001 TYR A 981 PHE 0.008 0.001 PHE A 319 TRP 0.009 0.001 TRP A 167 HIS 0.003 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.11 ( 9189) covalent geometry : angle 0.46152 / 0.25 (12431) hydrogen bonds : bond 0.04342 / 2.93 ( 560) hydrogen bonds : angle 4.22296 / 3.09 ( 1662) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 237 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8744 (t80) outliers start: 18 outliers final: 14 residues processed: 72 average time/residue: 0.1671 time to fit residues: 18.9755 Evaluate side-chains 69 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1181 ARG Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1236 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.3264 r_free = 0.3264 target = 0.050530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.039124 restraints weight = 145054.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.041087 restraints weight = 60233.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.042371 restraints weight = 35723.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.043227 restraints weight = 25608.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.043808 restraints weight = 20487.427| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9189 Z= 0.203 Angle : 0.502 6.250 12431 Z= 0.274 Chirality : 0.035 0.135 1435 Planarity : 0.003 0.048 1571 Dihedral : 12.032 168.310 1327 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.26 % Favored : 93.66 % Rotamer: Outliers : 2.09 % Allowed : 18.18 % Favored : 79.73 % 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: 0.99 (0.26), residues: 1151 helix: 2.09 (0.19), residues: 730 sheet: -2.89 (0.61), residues: 53 loop : -1.85 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1223 TYR 0.009 0.001 TYR A 312 PHE 0.011 0.001 PHE A 319 TRP 0.008 0.001 TRP A 707 HIS 0.002 0.001 HIS A 617 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.20 ( 9189) covalent geometry : angle 0.50228 / 0.27 (12431) hydrogen bonds : bond 0.04134 / 2.78 ( 560) hydrogen bonds : angle 4.39170 / 3.19 ( 1662) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 237 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9315 (tpp) cc_final: 0.8899 (tpp) REVERT: A 606 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8615 (t80) outliers start: 20 outliers final: 16 residues processed: 69 average time/residue: 0.1778 time to fit residues: 18.7343 Evaluate side-chains 69 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1181 ARG Chi-restraints excluded: chain A residue 1236 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 75 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 = 0.3259 r_free = 0.3259 target = 0.050365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.038985 restraints weight = 144060.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.040902 restraints weight = 60091.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.042183 restraints weight = 35780.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.043042 restraints weight = 25699.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.043603 restraints weight = 20554.171| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9189 Z= 0.191 Angle : 0.492 6.171 12431 Z= 0.269 Chirality : 0.035 0.135 1435 Planarity : 0.003 0.056 1571 Dihedral : 11.457 163.980 1327 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.34 % Favored : 93.57 % Rotamer: Outliers : 2.19 % Allowed : 18.70 % Favored : 79.10 % 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: 0.96 (0.26), residues: 1151 helix: 2.09 (0.19), residues: 730 sheet: -2.95 (0.60), residues: 53 loop : -1.89 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 747 TYR 0.010 0.001 TYR A 981 PHE 0.012 0.001 PHE A 319 TRP 0.008 0.001 TRP A 167 HIS 0.002 0.001 HIS A 617 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 ( 9189) covalent geometry : angle 0.49250 / 0.27 (12431) hydrogen bonds : bond 0.04123 / 2.77 ( 560) hydrogen bonds : angle 4.32496 / 3.14 ( 1662) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 237 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9312 (tpp) cc_final: 0.8900 (tpp) REVERT: A 606 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8572 (t80) outliers start: 21 outliers final: 19 residues processed: 68 average time/residue: 0.1624 time to fit residues: 17.5761 Evaluate side-chains 70 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1181 ARG Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1236 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3270 r_free = 0.3270 target = 0.050711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.039324 restraints weight = 143221.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.041313 restraints weight = 59193.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.042615 restraints weight = 34856.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.043495 restraints weight = 24908.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.044044 restraints weight = 19836.611| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9189 Z= 0.124 Angle : 0.468 7.011 12431 Z= 0.248 Chirality : 0.035 0.134 1435 Planarity : 0.003 0.053 1571 Dihedral : 11.186 158.077 1327 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.83 % Rotamer: Outliers : 2.30 % Allowed : 18.91 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.26), residues: 1151 helix: 2.25 (0.19), residues: 731 sheet: -2.89 (0.60), residues: 53 loop : -1.85 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1190 TYR 0.010 0.001 TYR A 981 PHE 0.009 0.001 PHE A 319 TRP 0.008 0.001 TRP A 167 HIS 0.002 0.001 HIS A 617 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 9189) covalent geometry : angle 0.46774 / 0.25 (12431) hydrogen bonds : bond 0.04013 / 2.70 ( 560) hydrogen bonds : angle 4.08880 / 2.98 ( 1662) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 237 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9294 (tpp) cc_final: 0.8924 (tpp) REVERT: A 606 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8540 (t80) outliers start: 22 outliers final: 19 residues processed: 69 average time/residue: 0.1576 time to fit residues: 17.3203 Evaluate side-chains 71 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1181 ARG Chi-restraints excluded: chain A residue 1184 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 112 optimal weight: 9.9990 chunk 32 optimal weight: 0.0050 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- 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 = 0.3277 r_free = 0.3277 target = 0.050918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.039531 restraints weight = 142708.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.041515 restraints weight = 58968.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.042825 restraints weight = 34776.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.043697 restraints weight = 24766.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.044237 restraints weight = 19712.068| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9189 Z= 0.113 Angle : 0.462 7.566 12431 Z= 0.243 Chirality : 0.035 0.134 1435 Planarity : 0.003 0.052 1571 Dihedral : 10.686 151.911 1324 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.56 % Favored : 94.35 % Rotamer: Outliers : 2.61 % Allowed : 18.50 % Favored : 78.89 % 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: 1.27 (0.26), residues: 1151 helix: 2.36 (0.19), residues: 732 sheet: -2.85 (0.60), residues: 53 loop : -1.86 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1190 TYR 0.010 0.001 TYR A 981 PHE 0.007 0.001 PHE A 319 TRP 0.007 0.001 TRP A 167 HIS 0.002 0.000 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 9189) covalent geometry : angle 0.46173 / 0.24 (12431) hydrogen bonds : bond 0.03876 / 2.61 ( 560) hydrogen bonds : angle 3.97342 / 2.89 ( 1662) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 237 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9279 (tpp) cc_final: 0.8896 (tpp) REVERT: A 606 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.8490 (t80) outliers start: 25 outliers final: 17 residues processed: 73 average time/residue: 0.1611 time to fit residues: 18.4281 Evaluate side-chains 68 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1181 ARG Chi-restraints excluded: chain A residue 1208 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 11 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3275 r_free = 0.3275 target = 0.050778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.039377 restraints weight = 142269.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.041345 restraints weight = 58907.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.042654 restraints weight = 34850.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.043506 restraints weight = 24872.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.044078 restraints weight = 19913.492| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9189 Z= 0.134 Angle : 0.475 8.526 12431 Z= 0.250 Chirality : 0.035 0.134 1435 Planarity : 0.003 0.052 1571 Dihedral : 10.347 148.895 1324 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.73 % Favored : 94.18 % Rotamer: Outliers : 2.30 % Allowed : 18.50 % Favored : 79.21 % 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: 1.30 (0.26), residues: 1151 helix: 2.39 (0.19), residues: 732 sheet: -2.84 (0.60), residues: 53 loop : -1.87 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1190 TYR 0.010 0.001 TYR A 981 PHE 0.008 0.001 PHE A 319 TRP 0.007 0.001 TRP A 167 HIS 0.002 0.000 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 9189) covalent geometry : angle 0.47507 / 0.25 (12431) hydrogen bonds : bond 0.03845 / 2.60 ( 560) hydrogen bonds : angle 4.00572 / 2.92 ( 1662) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 237 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9285 (tpp) cc_final: 0.8895 (tpp) REVERT: A 606 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8550 (t80) outliers start: 22 outliers final: 19 residues processed: 67 average time/residue: 0.1634 time to fit residues: 17.4031 Evaluate side-chains 69 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1181 ARG Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1208 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 62 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3280 r_free = 0.3280 target = 0.050981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.039559 restraints weight = 142404.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.041532 restraints weight = 59189.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.042866 restraints weight = 34792.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.043733 restraints weight = 24735.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.044325 restraints weight = 19723.819| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9189 Z= 0.114 Angle : 0.474 9.201 12431 Z= 0.246 Chirality : 0.035 0.134 1435 Planarity : 0.003 0.051 1571 Dihedral : 10.034 144.225 1324 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.47 % Favored : 94.44 % Rotamer: Outliers : 2.19 % Allowed : 18.60 % Favored : 79.21 % 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: 1.40 (0.26), residues: 1151 helix: 2.47 (0.19), residues: 732 sheet: -2.78 (0.61), residues: 53 loop : -1.84 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1190 TYR 0.010 0.001 TYR A 981 PHE 0.008 0.001 PHE A 319 TRP 0.007 0.001 TRP A 167 HIS 0.003 0.000 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 9189) covalent geometry : angle 0.47448 / 0.25 (12431) hydrogen bonds : bond 0.03831 / 2.59 ( 560) hydrogen bonds : angle 3.92529 / 2.86 ( 1662) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 237 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9277 (tpp) cc_final: 0.8890 (tpp) REVERT: A 606 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8501 (t80) outliers start: 21 outliers final: 18 residues processed: 68 average time/residue: 0.1536 time to fit residues: 16.6687 Evaluate side-chains 69 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1181 ARG Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1208 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3283 r_free = 0.3283 target = 0.051059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.039615 restraints weight = 143599.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.041619 restraints weight = 59293.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.042955 restraints weight = 34868.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.043836 restraints weight = 24789.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.044399 restraints weight = 19706.537| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9189 Z= 0.113 Angle : 0.480 9.980 12431 Z= 0.248 Chirality : 0.035 0.133 1435 Planarity : 0.003 0.050 1571 Dihedral : 9.666 136.576 1323 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.65 % Favored : 94.27 % Rotamer: Outliers : 1.99 % Allowed : 18.81 % Favored : 79.21 % 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: 1.47 (0.26), residues: 1151 helix: 2.52 (0.19), residues: 732 sheet: -2.72 (0.62), residues: 53 loop : -1.81 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1190 TYR 0.010 0.001 TYR A 981 PHE 0.007 0.001 PHE A 319 TRP 0.007 0.001 TRP A 167 HIS 0.003 0.000 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 9189) covalent geometry : angle 0.47985 / 0.25 (12431) hydrogen bonds : bond 0.03759 / 2.54 ( 560) hydrogen bonds : angle 3.89258 / 2.84 ( 1662) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 237 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9271 (tpp) cc_final: 0.8898 (tpp) REVERT: A 606 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8506 (t80) outliers start: 19 outliers final: 18 residues processed: 67 average time/residue: 0.1544 time to fit residues: 16.2963 Evaluate side-chains 70 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1181 ARG Chi-restraints excluded: chain A residue 1208 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 36 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 110 optimal weight: 0.0670 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- 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 = 0.3292 r_free = 0.3292 target = 0.051400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.039934 restraints weight = 142460.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.041955 restraints weight = 59019.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.043302 restraints weight = 34714.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.044190 restraints weight = 24596.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.044762 restraints weight = 19530.429| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9189 Z= 0.098 Angle : 0.470 9.461 12431 Z= 0.242 Chirality : 0.035 0.133 1435 Planarity : 0.003 0.049 1571 Dihedral : 9.370 137.051 1323 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.13 % Favored : 94.79 % Rotamer: Outliers : 2.19 % Allowed : 18.70 % Favored : 79.10 % 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: 1.58 (0.27), residues: 1151 helix: 2.61 (0.19), residues: 731 sheet: -2.66 (0.63), residues: 53 loop : -1.76 (0.35), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1190 TYR 0.010 0.001 TYR A 981 PHE 0.006 0.001 PHE A 973 TRP 0.007 0.001 TRP A 167 HIS 0.003 0.000 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 ( 9189) covalent geometry : angle 0.46993 / 0.24 (12431) hydrogen bonds : bond 0.03713 / 2.51 ( 560) hydrogen bonds : angle 3.79905 / 2.77 ( 1662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2896.10 seconds wall clock time: 50 minutes 12.84 seconds (3012.84 seconds total)