Starting phenix.real_space_refine on Sat Jul 4 06:21:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oe0_70382/07_2026/9oe0_70382_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oe0_70382/07_2026/9oe0_70382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oe0_70382/07_2026/9oe0_70382_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oe0_70382/07_2026/9oe0_70382_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oe0_70382/07_2026/9oe0_70382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oe0_70382/07_2026/9oe0_70382.map" } resolution = 3.39 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 48 5.16 5 C 5753 2.51 5 N 1531 2.21 5 O 1669 1.98 5 H 9126 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 18135 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1154, 18071 Classifications: {'peptide': 1154} Link IDs: {'PTRANS': 27, 'TRANS': 1126} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.81, per 1000 atoms: 0.15 Number of scatterers: 18135 At special positions: 0 Unit cell: (72.21, 123.67, 137.78, 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 48 16.00 P 6 15.00 Mg 2 11.99 O 1669 8.00 N 1531 7.00 C 5753 6.00 H 9126 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: 1.74 Conformation dependent library (CDL) restraints added in 610.1 milliseconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 5 sheets defined 66.6% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 49 through 68 Processing helix chain 'A' and resid 68 through 79 removed outlier: 4.227A pdb=" N VAL A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE A 75 " --> pdb=" O PRO A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 158 removed outlier: 3.866A pdb=" N HIS A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 171 removed outlier: 3.566A pdb=" N PHE A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 191 removed outlier: 3.729A pdb=" N ASN A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 191 " --> pdb=" O ILE A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 216 removed outlier: 3.897A pdb=" N GLY A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 233 removed outlier: 3.575A pdb=" N THR A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Proline residue: A 228 - end of helix removed outlier: 3.792A pdb=" N SER A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 245 removed outlier: 3.697A pdb=" N VAL A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.730A pdb=" N VAL A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 273 removed outlier: 3.793A pdb=" N PHE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 322 removed outlier: 3.628A pdb=" N GLU A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 315 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 351 Processing helix chain 'A' and resid 352 through 376 removed outlier: 4.610A pdb=" N ASN A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 444 removed outlier: 3.763A pdb=" N LEU A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 466 Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 488 through 495 removed outlier: 3.509A pdb=" N ILE A 493 " --> pdb=" O ILE A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 512 removed outlier: 4.084A pdb=" N GLU A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 537 through 552 removed outlier: 3.931A pdb=" N ARG A 552 " --> pdb=" O ARG A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 582 Processing helix chain 'A' and resid 616 through 623 removed outlier: 3.699A pdb=" N ARG A 623 " --> pdb=" O GLU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 638 Processing helix chain 'A' and resid 695 through 702 Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 706 through 737 removed outlier: 3.613A pdb=" N GLN A 724 " --> pdb=" O ASN A 720 " (cutoff:3.500A) Proline residue: A 725 - end of helix Processing helix chain 'A' and resid 742 through 784 removed outlier: 3.713A pdb=" N GLN A 771 " --> pdb=" O THR A 767 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA A 778 " --> pdb=" O CYS A 774 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 782 " --> pdb=" O ALA A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 792 removed outlier: 3.567A pdb=" N PHE A 788 " --> pdb=" O MET A 784 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 790 " --> pdb=" O LEU A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 804 removed outlier: 3.703A pdb=" N TYR A 802 " --> pdb=" O ASP A 798 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 818 Processing helix chain 'A' and resid 818 through 823 Processing helix chain 'A' and resid 823 through 828 removed outlier: 4.072A pdb=" N THR A 827 " --> pdb=" O VAL A 823 " (cutoff:3.500A) removed outlier: 3.644A 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 851 Processing helix chain 'A' and resid 852 through 899 removed outlier: 3.528A pdb=" N LEU A 857 " --> pdb=" O TRP A 853 " (cutoff:3.500A) Proline residue: A 864 - end of helix removed outlier: 3.569A pdb=" N GLN A 890 " --> pdb=" O LYS A 886 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A 891 " --> pdb=" O GLU A 887 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE A 894 " --> pdb=" O GLN A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 909 removed outlier: 3.541A pdb=" N VAL A 906 " --> pdb=" O VAL A 902 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 907 " --> pdb=" O ARG A 903 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 908 " --> pdb=" O THR A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 924 removed outlier: 4.017A pdb=" N VAL A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 964 Processing helix chain 'A' and resid 968 through 990 Processing helix chain 'A' and resid 995 through 1011 removed outlier: 3.660A pdb=" N ALA A1003 " --> pdb=" O ALA A 999 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN A1011 " --> pdb=" O LEU A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1080 Processing helix chain 'A' and resid 1081 through 1083 No H-bonds generated for 'chain 'A' and resid 1081 through 1083' Processing helix chain 'A' and resid 1103 through 1108 Processing helix chain 'A' and resid 1124 through 1131 Processing helix chain 'A' and resid 1139 through 1149 removed outlier: 3.535A pdb=" N ILE A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1157 Processing helix chain 'A' and resid 1175 through 1191 removed outlier: 4.070A pdb=" N ARG A1181 " --> pdb=" O GLY A1177 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A1190 " --> pdb=" O ARG A1186 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1221 removed outlier: 3.859A pdb=" N LYS A1210 " --> pdb=" O THR A1206 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE A1211 " --> pdb=" O GLU A1207 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1262 Processing helix chain 'A' and resid 1262 through 1275 Processing sheet with id=AA1, first strand: chain 'A' and resid 415 through 421 removed outlier: 6.886A pdb=" N ASN A 416 " --> pdb=" O HIS A 403 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N HIS A 403 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N MET A 418 " --> pdb=" O ASN A 401 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE A 399 " --> pdb=" O LEU A 420 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 431 through 432 removed outlier: 6.535A pdb=" N VAL A 431 " --> pdb=" O PHE A 606 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU A 613 " --> pdb=" O GLY A 605 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.650A pdb=" N GLY A 476 " --> pdb=" O LEU A 558 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1038 through 1039 Processing sheet with id=AA5, first strand: chain 'A' and resid 1111 through 1114 removed outlier: 6.866A pdb=" N GLY A1112 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A1197 " --> pdb=" O ILE A1226 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A1064 " --> pdb=" O ILE A1227 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A1251 " --> pdb=" O VAL A1243 " (cutoff:3.500A) 533 hydrogen bonds defined for protein. 1575 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: 4.27 Time building geometry restraints manager: 2.35 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: 9117 1.06 - 1.28: 1487 1.28 - 1.50: 3789 1.50 - 1.73: 3814 1.73 - 1.95: 85 Bond restraints: 18292 Sorted by residual: bond pdb=" O3B AGS A1303 " pdb=" PB AGS A1303 " ideal model delta sigma weight residual 1.673 1.581 0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" O3B AGS A1304 " pdb=" PB AGS A1304 " ideal model delta sigma weight residual 1.673 1.582 0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" O3A AGS A1303 " pdb=" PA AGS A1303 " ideal model delta sigma weight residual 1.664 1.579 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" O3A AGS A1304 " pdb=" PA AGS A1304 " ideal model delta sigma weight residual 1.664 1.582 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" O3B AGS A1303 " pdb=" PG AGS A1303 " ideal model delta sigma weight residual 1.614 1.555 0.059 2.00e-02 2.50e+03 8.68e+00 ... (remaining 18287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 32810 1.91 - 3.82: 237 3.82 - 5.74: 23 5.74 - 7.65: 10 7.65 - 9.56: 11 Bond angle restraints: 33091 Sorted by residual: angle pdb=" N TYR A 802 " pdb=" CA TYR A 802 " pdb=" C TYR A 802 " ideal model delta sigma weight residual 112.90 107.03 5.87 1.31e+00 5.83e-01 2.01e+01 angle pdb=" N TYR A 802 " pdb=" CA TYR A 802 " pdb=" CB TYR A 802 " ideal model delta sigma weight residual 110.33 116.47 -6.14 1.50e+00 4.44e-01 1.67e+01 angle pdb=" N ARG A 796 " pdb=" CA ARG A 796 " pdb=" C ARG A 796 " ideal model delta sigma weight residual 113.18 108.13 5.05 1.33e+00 5.65e-01 1.44e+01 angle pdb=" N GLU A 900 " pdb=" CA GLU A 900 " pdb=" C GLU A 900 " ideal model delta sigma weight residual 113.43 109.27 4.16 1.26e+00 6.30e-01 1.09e+01 angle pdb=" PB AGS A1304 " pdb=" O3B AGS A1304 " pdb=" PG AGS A1304 " ideal model delta sigma weight residual 129.21 119.65 9.56 3.00e+00 1.11e-01 1.02e+01 ... (remaining 33086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.88: 8030 28.88 - 57.77: 472 57.77 - 86.65: 61 86.65 - 115.54: 3 115.54 - 144.42: 2 Dihedral angle restraints: 8568 sinusoidal: 4710 harmonic: 3858 Sorted by residual: 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 -5.87 144.42 1 3.00e+01 1.11e-03 1.93e+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 -79.04 -142.41 1 3.00e+01 1.11e-03 1.91e+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 7.37 116.53 -109.16 1 3.00e+01 1.11e-03 1.42e+01 ... (remaining 8565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1216 0.054 - 0.108: 191 0.108 - 0.161: 22 0.161 - 0.215: 0 0.215 - 0.269: 2 Chirality restraints: 1431 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 -2.64 0.27 2.00e-01 2.50e+01 1.81e+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 -2.63 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ILE A 556 " pdb=" N ILE A 556 " pdb=" C ILE A 556 " pdb=" CB ILE A 556 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 1428 not shown) Planarity restraints: 2689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 180 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" C LEU A 180 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU A 180 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 181 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 801 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C TRP A 801 " 0.039 2.00e-02 2.50e+03 pdb=" O TRP A 801 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR A 802 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 924 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO A 925 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 925 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 925 " 0.026 5.00e-02 4.00e+02 ... (remaining 2686 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 527 2.13 - 2.75: 34094 2.75 - 3.37: 51919 3.37 - 3.98: 63897 3.98 - 4.60: 102029 Nonbonded interactions: 252466 Sorted by model distance: nonbonded pdb=" OE1 GLU A1117 " pdb=" H GLU A1117 " model vdw 1.515 2.450 nonbonded pdb=" HE ARG A 179 " pdb=" OD2 ASP A 183 " model vdw 1.617 2.450 nonbonded pdb=" O ALA A 235 " pdb=" HZ3 LYS A 239 " model vdw 1.629 2.450 nonbonded pdb=" O ALA A 844 " pdb=" HG SER A 848 " model vdw 1.630 2.450 nonbonded pdb=" OE2 GLU A 613 " pdb=" H ILE A 626 " model vdw 1.644 2.450 ... (remaining 252461 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: 3.050 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: 0.120 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 17.330 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 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 0.092 9166 Z= 0.201 Angle : 0.646 9.561 12399 Z= 0.330 Chirality : 0.039 0.269 1431 Planarity : 0.004 0.047 1566 Dihedral : 18.265 144.420 3400 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.71 % Favored : 90.94 % Rotamer: Outliers : 3.04 % Allowed : 19.92 % Favored : 77.04 % 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: -0.82 (0.26), residues: 1148 helix: 0.83 (0.20), residues: 728 sheet: -2.54 (0.82), residues: 33 loop : -3.15 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 405 TYR 0.014 0.001 TYR A 123 PHE 0.011 0.001 PHE A 757 TRP 0.008 0.001 TRP A 217 HIS 0.003 0.001 HIS A 617 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 ( 9166) covalent geometry : angle 0.64578 / 0.33 (12399) hydrogen bonds : bond 0.15270 / 9.82 ( 533) hydrogen bonds : angle 5.64356 / 4.15 ( 1575) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 336 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 0.493 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 outliers start: 29 outliers final: 17 residues processed: 86 average time/residue: 0.1556 time to fit residues: 21.2606 Evaluate side-chains 65 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 901 ASN Chi-restraints excluded: chain A residue 946 MET Chi-restraints excluded: chain A residue 1086 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 480 GLN A1101 GLN ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.061948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.050008 restraints weight = 112338.064| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.63 r_work: 0.3108 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9166 Z= 0.212 Angle : 0.589 6.367 12399 Z= 0.321 Chirality : 0.038 0.137 1431 Planarity : 0.004 0.049 1566 Dihedral : 12.168 155.428 1341 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.49 % Favored : 90.24 % Rotamer: Outliers : 2.83 % Allowed : 21.59 % Favored : 75.58 % 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: 1148 helix: 0.94 (0.20), residues: 729 sheet: -3.45 (0.66), residues: 41 loop : -3.07 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 598 TYR 0.009 0.001 TYR A1163 PHE 0.013 0.001 PHE A 308 TRP 0.007 0.001 TRP A 217 HIS 0.006 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 ( 9166) covalent geometry : angle 0.58923 / 0.32 (12399) hydrogen bonds : bond 0.04672 / 3.05 ( 533) hydrogen bonds : angle 4.86161 / 3.54 ( 1575) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 336 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 49 time to evaluate : 0.424 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 988 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8162 (mm-30) REVERT: A 992 PHE cc_start: 0.8551 (m-80) cc_final: 0.7877 (m-80) REVERT: A 1181 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.8796 (ttm110) outliers start: 27 outliers final: 16 residues processed: 74 average time/residue: 0.1561 time to fit residues: 18.3935 Evaluate side-chains 65 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 946 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1181 ARG Chi-restraints excluded: chain A residue 1225 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 19 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 ASN ** A1140 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 = 0.3627 r_free = 0.3627 target = 0.064538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.052301 restraints weight = 113499.396| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.70 r_work: 0.3118 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9166 Z= 0.163 Angle : 0.527 6.167 12399 Z= 0.286 Chirality : 0.037 0.140 1431 Planarity : 0.003 0.048 1566 Dihedral : 10.727 153.247 1329 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.19 % Favored : 91.55 % Rotamer: Outliers : 2.73 % Allowed : 22.33 % Favored : 74.95 % 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: -0.43 (0.26), residues: 1148 helix: 1.14 (0.20), residues: 731 sheet: -3.00 (0.69), residues: 41 loop : -2.95 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 405 TYR 0.011 0.001 TYR A 406 PHE 0.012 0.001 PHE A 308 TRP 0.007 0.001 TRP A 217 HIS 0.003 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 ( 9166) covalent geometry : angle 0.52741 / 0.29 (12399) hydrogen bonds : bond 0.04169 / 2.73 ( 533) hydrogen bonds : angle 4.55390 / 3.32 ( 1575) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 336 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 46 time to evaluate : 0.435 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 946 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8355 (tmm) REVERT: A 988 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8174 (mm-30) REVERT: A 992 PHE cc_start: 0.8526 (m-80) cc_final: 0.7813 (m-80) REVERT: A 1181 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8834 (ttm110) outliers start: 26 outliers final: 17 residues processed: 67 average time/residue: 0.1530 time to fit residues: 15.6274 Evaluate side-chains 66 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 901 ASN Chi-restraints excluded: chain A residue 946 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1181 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 54 optimal weight: 0.0570 chunk 44 optimal weight: 4.9990 chunk 57 optimal weight: 0.1980 chunk 112 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 743 GLN ** A1140 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 = 0.3660 r_free = 0.3660 target = 0.065503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.053127 restraints weight = 113960.084| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.82 r_work: 0.3175 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9166 Z= 0.122 Angle : 0.500 6.228 12399 Z= 0.267 Chirality : 0.036 0.137 1431 Planarity : 0.003 0.049 1566 Dihedral : 10.121 152.753 1324 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.10 % Favored : 91.64 % Rotamer: Outliers : 2.20 % Allowed : 22.12 % Favored : 75.68 % 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: -0.13 (0.26), residues: 1148 helix: 1.37 (0.20), residues: 733 sheet: -2.93 (0.69), residues: 41 loop : -2.84 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 267 TYR 0.007 0.001 TYR A 627 PHE 0.011 0.001 PHE A 308 TRP 0.006 0.001 TRP A 217 HIS 0.002 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 9166) covalent geometry : angle 0.49952 / 0.27 (12399) hydrogen bonds : bond 0.03802 / 2.48 ( 533) hydrogen bonds : angle 4.32927 / 3.16 ( 1575) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 336 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 0.345 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 126 MET cc_start: 0.9043 (mmp) cc_final: 0.8824 (mmp) REVERT: A 946 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8330 (tmm) REVERT: A 988 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8153 (mm-30) REVERT: A 992 PHE cc_start: 0.8525 (m-80) cc_final: 0.7829 (m-80) REVERT: A 1181 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8314 (ttm110) outliers start: 21 outliers final: 11 residues processed: 63 average time/residue: 0.1469 time to fit residues: 14.8758 Evaluate side-chains 59 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 946 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1181 ARG Chi-restraints excluded: chain A residue 1225 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 45 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1140 GLN ** 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 = 0.3624 r_free = 0.3624 target = 0.064127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.051295 restraints weight = 116127.473| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.96 r_work: 0.3138 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9166 Z= 0.213 Angle : 0.540 7.295 12399 Z= 0.293 Chirality : 0.037 0.139 1431 Planarity : 0.003 0.048 1566 Dihedral : 9.997 154.489 1318 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.06 % Favored : 90.68 % Rotamer: Outliers : 2.41 % Allowed : 23.27 % Favored : 74.32 % 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: -0.18 (0.26), residues: 1148 helix: 1.32 (0.20), residues: 733 sheet: -2.88 (0.69), residues: 41 loop : -2.85 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1181 TYR 0.008 0.001 TYR A 406 PHE 0.018 0.001 PHE A 308 TRP 0.008 0.001 TRP A 217 HIS 0.003 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.21 ( 9166) covalent geometry : angle 0.53964 / 0.29 (12399) hydrogen bonds : bond 0.03876 / 2.53 ( 533) hydrogen bonds : angle 4.49692 / 3.28 ( 1575) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 336 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 0.382 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 423 MET cc_start: 0.9121 (tpp) cc_final: 0.8898 (tpp) REVERT: A 946 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8398 (tmm) REVERT: A 988 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8155 (mm-30) REVERT: A 992 PHE cc_start: 0.8516 (m-80) cc_final: 0.7800 (m-80) REVERT: A 1181 ARG cc_start: 0.9215 (OUTLIER) cc_final: 0.8284 (ttm110) outliers start: 23 outliers final: 12 residues processed: 63 average time/residue: 0.1357 time to fit residues: 13.4377 Evaluate side-chains 60 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 901 ASN Chi-restraints excluded: chain A residue 946 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1181 ARG Chi-restraints excluded: chain A residue 1225 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 3 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1140 GLN ** 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 = 0.3688 r_free = 0.3688 target = 0.066346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.053786 restraints weight = 112449.089| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.79 r_work: 0.3179 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9166 Z= 0.142 Angle : 0.500 6.283 12399 Z= 0.267 Chirality : 0.036 0.144 1431 Planarity : 0.003 0.049 1566 Dihedral : 9.938 161.029 1316 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.84 % Favored : 91.90 % Rotamer: Outliers : 1.78 % Allowed : 23.79 % Favored : 74.42 % 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: 0.09 (0.26), residues: 1148 helix: 1.53 (0.20), residues: 736 sheet: -2.78 (0.68), residues: 41 loop : -2.76 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.007 0.001 TYR A 123 PHE 0.015 0.001 PHE A 308 TRP 0.007 0.001 TRP A 217 HIS 0.002 0.001 HIS A1255 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 9166) covalent geometry : angle 0.50039 / 0.27 (12399) hydrogen bonds : bond 0.03695 / 2.42 ( 533) hydrogen bonds : angle 4.26967 / 3.12 ( 1575) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 336 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.485 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 126 MET cc_start: 0.9078 (mmp) cc_final: 0.8872 (mmm) REVERT: A 946 MET cc_start: 0.8808 (ttm) cc_final: 0.8350 (tmm) REVERT: A 988 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8147 (mm-30) REVERT: A 992 PHE cc_start: 0.8520 (m-80) cc_final: 0.7791 (m-80) REVERT: A 1123 CYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8382 (t) outliers start: 17 outliers final: 13 residues processed: 61 average time/residue: 0.1347 time to fit residues: 13.0247 Evaluate side-chains 60 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1181 ARG Chi-restraints excluded: chain A residue 1225 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 54 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 84 optimal weight: 0.0870 chunk 80 optimal weight: 0.0770 chunk 103 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.6322 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.059858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.047661 restraints weight = 115239.752| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.90 r_work: 0.2995 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9166 Z= 0.099 Angle : 0.477 6.080 12399 Z= 0.250 Chirality : 0.036 0.142 1431 Planarity : 0.003 0.049 1566 Dihedral : 9.730 167.369 1313 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.97 % Favored : 92.77 % Rotamer: Outliers : 1.89 % Allowed : 23.58 % Favored : 74.53 % 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: 0.44 (0.27), residues: 1148 helix: 1.80 (0.20), residues: 735 sheet: -2.75 (0.69), residues: 41 loop : -2.60 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 267 TYR 0.007 0.001 TYR A 123 PHE 0.013 0.001 PHE A 308 TRP 0.006 0.001 TRP A 217 HIS 0.002 0.001 HIS A 617 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 ( 9166) covalent geometry : angle 0.47697 / 0.25 (12399) hydrogen bonds : bond 0.03522 / 2.30 ( 533) hydrogen bonds : angle 4.03906 / 2.95 ( 1575) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 336 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.412 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: A 126 MET cc_start: 0.9073 (mmp) cc_final: 0.8687 (mmt) REVERT: A 946 MET cc_start: 0.8820 (ttm) cc_final: 0.8366 (tmm) REVERT: A 988 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8164 (mm-30) REVERT: A 992 PHE cc_start: 0.8480 (m-80) cc_final: 0.7756 (m-80) outliers start: 18 outliers final: 14 residues processed: 63 average time/residue: 0.1391 time to fit residues: 13.8398 Evaluate side-chains 62 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1181 ARG Chi-restraints excluded: chain A residue 1225 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 78 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1140 GLN ** 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 = 0.3459 r_free = 0.3459 target = 0.059052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.047200 restraints weight = 116414.227| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.81 r_work: 0.2979 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9166 Z= 0.153 Angle : 0.493 6.213 12399 Z= 0.264 Chirality : 0.036 0.140 1431 Planarity : 0.003 0.049 1566 Dihedral : 9.697 170.242 1313 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.67 % Favored : 92.07 % Rotamer: Outliers : 1.99 % Allowed : 23.58 % Favored : 74.42 % 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: 0.42 (0.26), residues: 1148 helix: 1.77 (0.20), residues: 736 sheet: -2.63 (0.69), residues: 41 loop : -2.61 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1181 TYR 0.007 0.001 TYR A 123 PHE 0.013 0.001 PHE A 308 TRP 0.007 0.001 TRP A 217 HIS 0.002 0.001 HIS A 880 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 ( 9166) covalent geometry : angle 0.49265 / 0.26 (12399) hydrogen bonds : bond 0.03548 / 2.32 ( 533) hydrogen bonds : angle 4.17109 / 3.05 ( 1575) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 336 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.557 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 946 MET cc_start: 0.8860 (ttm) cc_final: 0.8403 (tmm) REVERT: A 988 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8148 (mm-30) REVERT: A 992 PHE cc_start: 0.8498 (m-80) cc_final: 0.7786 (m-80) REVERT: A 1123 CYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8440 (t) outliers start: 19 outliers final: 15 residues processed: 63 average time/residue: 0.1607 time to fit residues: 16.0234 Evaluate side-chains 63 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 901 ASN Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1106 TRP Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1181 ARG Chi-restraints excluded: chain A residue 1225 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 21 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 87 optimal weight: 0.0060 chunk 45 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1140 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 = 0.3455 r_free = 0.3455 target = 0.059034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.047229 restraints weight = 116508.549| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.73 r_work: 0.2971 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9166 Z= 0.175 Angle : 0.513 6.562 12399 Z= 0.275 Chirality : 0.037 0.143 1431 Planarity : 0.003 0.049 1566 Dihedral : 9.819 178.082 1313 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.93 % Favored : 91.81 % Rotamer: Outliers : 1.99 % Allowed : 23.58 % Favored : 74.42 % 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: 0.38 (0.26), residues: 1148 helix: 1.74 (0.20), residues: 734 sheet: -2.56 (0.71), residues: 41 loop : -2.59 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 405 TYR 0.008 0.001 TYR A 123 PHE 0.014 0.001 PHE A 308 TRP 0.008 0.001 TRP A 217 HIS 0.003 0.001 HIS A1255 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 ( 9166) covalent geometry : angle 0.51335 / 0.28 (12399) hydrogen bonds : bond 0.03644 / 2.37 ( 533) hydrogen bonds : angle 4.25004 / 3.10 ( 1575) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 336 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.9161 (mmp) cc_final: 0.8941 (mmp) REVERT: A 946 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8408 (tmm) REVERT: A 988 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8152 (mm-30) REVERT: A 992 PHE cc_start: 0.8493 (m-80) cc_final: 0.7766 (m-80) outliers start: 19 outliers final: 16 residues processed: 59 average time/residue: 0.1703 time to fit residues: 15.7912 Evaluate side-chains 61 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 901 ASN Chi-restraints excluded: chain A residue 946 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1106 TRP Chi-restraints excluded: chain A residue 1181 ARG Chi-restraints excluded: chain A residue 1225 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1140 GLN ** 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 = 0.3449 r_free = 0.3449 target = 0.058686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.046526 restraints weight = 116025.492| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.89 r_work: 0.2974 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9166 Z= 0.137 Angle : 0.490 7.015 12399 Z= 0.260 Chirality : 0.036 0.144 1431 Planarity : 0.003 0.049 1566 Dihedral : 9.746 177.647 1313 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.75 % Favored : 91.99 % Rotamer: Outliers : 1.68 % Allowed : 23.79 % Favored : 74.53 % 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: 0.56 (0.26), residues: 1148 helix: 1.87 (0.20), residues: 737 sheet: -2.49 (0.71), residues: 41 loop : -2.54 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 405 TYR 0.006 0.001 TYR A 135 PHE 0.013 0.001 PHE A 308 TRP 0.008 0.001 TRP A 217 HIS 0.002 0.001 HIS A 880 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 ( 9166) covalent geometry : angle 0.49001 / 0.26 (12399) hydrogen bonds : bond 0.03547 / 2.31 ( 533) hydrogen bonds : angle 4.13219 / 3.02 ( 1575) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 336 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.506 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 313 MET cc_start: 0.8648 (mtt) cc_final: 0.8231 (tmm) REVERT: A 946 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8390 (tmm) REVERT: A 988 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8362 (mm-30) REVERT: A 992 PHE cc_start: 0.8534 (m-80) cc_final: 0.8102 (m-80) outliers start: 16 outliers final: 14 residues processed: 59 average time/residue: 0.1736 time to fit residues: 16.1018 Evaluate side-chains 61 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 946 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1106 TRP Chi-restraints excluded: chain A residue 1181 ARG Chi-restraints excluded: chain A residue 1225 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 4 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1140 GLN ** 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 = 0.3454 r_free = 0.3454 target = 0.058901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.046971 restraints weight = 116933.813| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.80 r_work: 0.2970 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9166 Z= 0.174 Angle : 0.509 6.850 12399 Z= 0.272 Chirality : 0.036 0.142 1431 Planarity : 0.003 0.049 1566 Dihedral : 9.686 174.483 1313 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.93 % Favored : 91.81 % Rotamer: Outliers : 1.99 % Allowed : 23.48 % Favored : 74.53 % 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: 0.51 (0.26), residues: 1148 helix: 1.83 (0.20), residues: 735 sheet: -2.51 (0.71), residues: 41 loop : -2.54 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 405 TYR 0.007 0.001 TYR A 135 PHE 0.013 0.001 PHE A 308 TRP 0.007 0.001 TRP A 217 HIS 0.002 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 ( 9166) covalent geometry : angle 0.50889 / 0.27 (12399) hydrogen bonds : bond 0.03606 / 2.35 ( 533) hydrogen bonds : angle 4.22378 / 3.09 ( 1575) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3258.81 seconds wall clock time: 56 minutes 15.69 seconds (3375.69 seconds total)