Starting phenix.real_space_refine on Sat Jul 4 06:28:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oe3_70385/07_2026/9oe3_70385.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oe3_70385/07_2026/9oe3_70385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oe3_70385/07_2026/9oe3_70385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oe3_70385/07_2026/9oe3_70385.map" model { file = "/net/cci-nas-00/data/ceres_data/9oe3_70385/07_2026/9oe3_70385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oe3_70385/07_2026/9oe3_70385.cif" } resolution = 3.54 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= 0.010 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 5744 2.51 5 N 1526 2.21 5 O 1669 1.98 5 H 9044 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 18040 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 17976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1153, 17976 Classifications: {'peptide': 1153} Link IDs: {'PTRANS': 27, 'TRANS': 1125} 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: 2.90, per 1000 atoms: 0.16 Number of scatterers: 18040 At special positions: 0 Unit cell: (69.72, 122.84, 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 49 16.00 P 6 15.00 Mg 2 11.99 O 1669 8.00 N 1526 7.00 C 5744 6.00 H 9044 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: 1.29 Conformation dependent library (CDL) restraints added in 610.6 milliseconds 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 7 sheets defined 69.8% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 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 70 through 81 removed outlier: 3.815A pdb=" N ILE A 75 " --> pdb=" O PRO A 71 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 161 Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 172 through 191 Processing helix chain 'A' and resid 192 through 216 removed outlier: 3.784A pdb=" N GLY A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 removed outlier: 3.578A pdb=" N THR A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 239 through 244 Processing helix chain 'A' and resid 246 through 264 removed outlier: 4.129A pdb=" N THR A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 273 Processing helix chain 'A' and resid 275 through 326 Processing helix chain 'A' and resid 332 through 352 Processing helix chain 'A' and resid 353 through 376 Processing helix chain 'A' and resid 437 through 446 removed outlier: 3.825A pdb=" N THR A 441 " --> pdb=" O GLY A 437 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 474 removed outlier: 3.711A pdb=" N LEU A 474 " --> pdb=" O GLY A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 501 through 512 Processing helix chain 'A' and resid 513 through 520 removed outlier: 4.395A pdb=" N PHE A 517 " --> pdb=" O ASN A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 552 removed outlier: 3.943A pdb=" N ARG A 552 " --> pdb=" O ARG A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 582 Processing helix chain 'A' and resid 593 through 598 removed outlier: 4.054A pdb=" N ILE A 597 " --> pdb=" O ARG A 593 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 593 through 598' 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 704 removed outlier: 3.675A pdb=" N VAL A 699 " --> pdb=" O SER A 695 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN A 703 " --> pdb=" O VAL A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 738 removed outlier: 3.569A pdb=" N MET A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) removed outlier: 3.611A 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 797 Processing helix chain 'A' and resid 798 through 804 removed outlier: 3.890A pdb=" N TYR A 802 " --> pdb=" O ASP A 798 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 808 through 822 removed outlier: 3.571A pdb=" N ASP A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 821 " --> pdb=" O ALA A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 851 removed outlier: 3.837A pdb=" N THR A 827 " --> pdb=" O VAL A 823 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 828 " --> pdb=" O GLN A 824 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 829 " --> pdb=" O GLY A 825 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG A 830 " --> pdb=" O ALA A 826 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 901 Proline residue: A 864 - end of helix removed outlier: 3.746A pdb=" N GLU A 887 " --> pdb=" O LYS A 883 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN A 890 " --> pdb=" O LYS A 886 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN A 901 " --> pdb=" O GLU A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 908 Processing helix chain 'A' and resid 910 through 964 removed outlier: 3.816A pdb=" N GLU A 919 " --> pdb=" O GLU A 915 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU A 920 " --> pdb=" O SER A 916 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN A 921 " --> pdb=" O LEU A 917 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 922 " --> pdb=" O TYR A 918 " (cutoff:3.500A) Proline residue: A 925 - end of helix Processing helix chain 'A' and resid 968 through 992 Processing helix chain 'A' and resid 995 through 1012 removed outlier: 3.534A pdb=" N ALA A 999 " --> pdb=" O ASN A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1082 removed outlier: 3.692A pdb=" N THR A1077 " --> pdb=" O GLY A1073 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A1082 " --> pdb=" O ILE A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1102 No H-bonds generated for 'chain 'A' and resid 1100 through 1102' Processing helix chain 'A' and resid 1103 through 1110 Processing helix chain 'A' and resid 1124 through 1131 Processing helix chain 'A' and resid 1139 through 1150 Processing helix chain 'A' and resid 1152 through 1158 removed outlier: 3.663A pdb=" N ASN A1158 " --> pdb=" O SER A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1190 removed outlier: 3.783A pdb=" N GLN A1180 " --> pdb=" O GLY A1176 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG A1181 " --> pdb=" O GLY A1177 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG A1190 " --> pdb=" O ARG A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1221 removed outlier: 3.564A pdb=" N GLU A1209 " --> pdb=" O ASP A1205 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A1210 " --> pdb=" O THR A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1237 removed outlier: 3.735A pdb=" N ILE A1235 " --> pdb=" O ARG A1231 " (cutoff:3.500A) removed outlier: 4.118A 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 1274 removed outlier: 3.578A pdb=" N TYR A1266 " --> pdb=" O GLN A1262 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A1274 " --> pdb=" O THR A1270 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 429 removed outlier: 5.940A pdb=" N ALA A 429 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE A 606 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE A 603 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU A 614 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY A 605 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU A 610 " --> pdb=" O GLN A 607 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 458 Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 478 Processing sheet with id=AA4, first strand: chain 'A' and resid 1033 through 1035 Processing sheet with id=AA5, first strand: chain 'A' and resid 1039 through 1040 Processing sheet with id=AA6, first strand: chain 'A' and resid 1111 through 1114 removed outlier: 6.635A pdb=" N GLY A1112 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU A1064 " --> pdb=" O ILE A1227 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS A1240 " --> pdb=" O THR A1063 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A1065 " --> pdb=" O CYS A1240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 6.816A pdb=" N VAL A1243 " --> pdb=" O VAL A1250 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1713 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: 4.04 Time building geometry restraints manager: 1.90 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: 9035 1.06 - 1.28: 1486 1.28 - 1.50: 3775 1.50 - 1.73: 3813 1.73 - 1.95: 87 Bond restraints: 18196 Sorted by residual: bond pdb=" O3B AGS A1301 " pdb=" PB AGS A1301 " ideal model delta sigma weight residual 1.673 1.580 0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" O3B AGS A1303 " pdb=" PB AGS A1303 " ideal model delta sigma weight residual 1.673 1.582 0.091 2.00e-02 2.50e+03 2.09e+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 A1301 " pdb=" PA AGS A1301 " ideal model delta sigma weight residual 1.664 1.580 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" O5' AGS A1303 " pdb=" PA AGS A1303 " ideal model delta sigma weight residual 1.634 1.573 0.061 2.00e-02 2.50e+03 9.17e+00 ... (remaining 18191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.94: 32852 5.94 - 11.88: 26 11.88 - 17.82: 0 17.82 - 23.76: 4 23.76 - 29.70: 8 Bond angle restraints: 32890 Sorted by residual: angle pdb=" HZ1 LYS A1100 " pdb=" NZ LYS A1100 " pdb=" HZ2 LYS A1100 " ideal model delta sigma weight residual 109.00 79.30 29.70 3.00e+00 1.11e-01 9.80e+01 angle pdb="HD22 LEU A 702 " pdb=" CD2 LEU A 702 " pdb="HD23 LEU A 702 " ideal model delta sigma weight residual 110.00 80.32 29.68 3.00e+00 1.11e-01 9.79e+01 angle pdb=" HZ1 LYS A1100 " pdb=" NZ LYS A1100 " pdb=" HZ3 LYS A1100 " ideal model delta sigma weight residual 109.00 79.37 29.63 3.00e+00 1.11e-01 9.75e+01 angle pdb="HD21 LEU A 702 " pdb=" CD2 LEU A 702 " pdb="HD22 LEU A 702 " ideal model delta sigma weight residual 110.00 80.73 29.27 3.00e+00 1.11e-01 9.52e+01 angle pdb=" CG LEU A 702 " pdb=" CD2 LEU A 702 " pdb="HD23 LEU A 702 " ideal model delta sigma weight residual 109.00 79.80 29.20 3.00e+00 1.11e-01 9.47e+01 ... (remaining 32885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.33: 8077 31.33 - 62.65: 415 62.65 - 93.98: 20 93.98 - 125.31: 2 125.31 - 156.63: 6 Dihedral angle restraints: 8520 sinusoidal: 4691 harmonic: 3829 Sorted by residual: dihedral pdb=" O2B AGS A1303 " pdb=" O3B AGS A1303 " pdb=" PB AGS A1303 " pdb=" PG AGS A1303 " ideal model delta sinusoidal sigma weight residual 7.37 164.00 -156.63 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" O2A AGS A1301 " pdb=" O3A AGS A1301 " pdb=" PA AGS A1301 " pdb=" PB AGS A1301 " ideal model delta sinusoidal sigma weight residual -52.28 89.00 -141.28 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" O1A AGS A1303 " pdb=" O3A AGS A1303 " pdb=" PA AGS A1303 " pdb=" PB AGS A1303 " ideal model delta sinusoidal sigma weight residual 82.37 -50.17 132.54 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 8517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1227 0.054 - 0.108: 174 0.108 - 0.162: 28 0.162 - 0.216: 0 0.216 - 0.269: 2 Chirality restraints: 1431 Sorted by residual: chirality pdb=" C3' AGS A1303 " pdb=" C2' AGS A1303 " pdb=" C4' AGS A1303 " pdb=" O3' AGS A1303 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C3' AGS A1301 " pdb=" C2' AGS A1301 " pdb=" C4' AGS A1301 " pdb=" O3' AGS A1301 " both_signs ideal model delta sigma weight residual False -2.37 -2.61 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA PRO A1160 " pdb=" N PRO A1160 " pdb=" C PRO A1160 " pdb=" CB PRO A1160 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 1428 not shown) Planarity restraints: 2680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1159 " -0.045 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO A1160 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A1160 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1160 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 704 " 0.031 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 705 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 705 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 705 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 724 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.26e+00 pdb=" N PRO A 725 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 725 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 725 " -0.025 5.00e-02 4.00e+02 ... (remaining 2677 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 2726 2.27 - 2.86: 41294 2.86 - 3.44: 47527 3.44 - 4.02: 61638 4.02 - 4.60: 96528 Nonbonded interactions: 249713 Sorted by model distance: nonbonded pdb=" H THR A1076 " pdb=" O2A AGS A1303 " model vdw 1.693 2.450 nonbonded pdb=" H GLU A1030 " pdb=" OD2 ASP A1095 " model vdw 1.700 2.450 nonbonded pdb=" O TRP A 167 " pdb="HD22 ASN A 171 " model vdw 1.702 2.450 nonbonded pdb=" HZ3 LYS A1074 " pdb=" O2B AGS A1303 " model vdw 1.715 2.450 nonbonded pdb="HE22 GLN A 797 " pdb=" O ARG A1012 " model vdw 1.717 2.450 ... (remaining 249708 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: 5.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.360 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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 9152 Z= 0.199 Angle : 0.720 10.876 12382 Z= 0.339 Chirality : 0.039 0.269 1431 Planarity : 0.004 0.068 1564 Dihedral : 17.419 156.633 3393 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.68 % Allowed : 14.69 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.26), residues: 1147 helix: 2.13 (0.19), residues: 734 sheet: -4.25 (0.50), residues: 58 loop : -1.87 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 364 TYR 0.008 0.001 TYR A 252 PHE 0.014 0.001 PHE A 731 TRP 0.006 0.001 TRP A 707 HIS 0.004 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 ( 9152) covalent geometry : angle 0.72026 / 0.34 (12382) hydrogen bonds : bond 0.12324 / 8.01 ( 578) hydrogen bonds : angle 5.23717 / 3.90 ( 1713) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 237 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.351 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 946 MET cc_start: 0.9281 (tmm) cc_final: 0.8999 (tmm) REVERT: A 984 MET cc_start: 0.8417 (tpt) cc_final: 0.7812 (tpp) REVERT: A 1008 MET cc_start: 0.9025 (ptm) cc_final: 0.8773 (ppp) REVERT: A 1093 MET cc_start: 0.8467 (ttm) cc_final: 0.7703 (tpp) outliers start: 16 outliers final: 12 residues processed: 79 average time/residue: 0.1676 time to fit residues: 19.7412 Evaluate side-chains 76 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1223 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 ASN ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 HIS ** 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 = 0.3277 r_free = 0.3277 target = 0.050204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.038882 restraints weight = 151711.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.040841 restraints weight = 63157.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.042155 restraints weight = 38028.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.042965 restraints weight = 27532.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.043558 restraints weight = 22444.602| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9152 Z= 0.308 Angle : 0.595 5.522 12382 Z= 0.330 Chirality : 0.037 0.136 1431 Planarity : 0.004 0.051 1564 Dihedral : 13.320 170.152 1334 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.31 % Allowed : 14.59 % Favored : 83.11 % 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: 0.57 (0.25), residues: 1147 helix: 1.89 (0.19), residues: 744 sheet: -3.59 (0.59), residues: 53 loop : -2.44 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 510 TYR 0.009 0.001 TYR A 312 PHE 0.014 0.001 PHE A 319 TRP 0.011 0.002 TRP A 801 HIS 0.005 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.31 ( 9152) covalent geometry : angle 0.59459 / 0.33 (12382) hydrogen bonds : bond 0.04852 / 3.19 ( 578) hydrogen bonds : angle 4.75074 / 3.51 ( 1713) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 237 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.487 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: symmetry clash revert: symmetry clash REVERT: A 946 MET cc_start: 0.9293 (tmm) cc_final: 0.9073 (tmm) REVERT: A 984 MET cc_start: 0.8395 (tpt) cc_final: 0.7757 (tpp) REVERT: A 1008 MET cc_start: 0.8997 (ptm) cc_final: 0.8789 (ppp) outliers start: 22 outliers final: 17 residues processed: 78 average time/residue: 0.1687 time to fit residues: 19.6015 Evaluate side-chains 73 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1075 SER Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1223 ARG Chi-restraints excluded: chain A residue 1266 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 17 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 HIS ** 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 = 0.3287 r_free = 0.3287 target = 0.050668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.039303 restraints weight = 153316.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.041311 restraints weight = 64085.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.042647 restraints weight = 38625.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.043510 restraints weight = 27922.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.044082 restraints weight = 22514.431| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9152 Z= 0.192 Angle : 0.513 6.684 12382 Z= 0.278 Chirality : 0.036 0.139 1431 Planarity : 0.003 0.048 1564 Dihedral : 12.486 175.345 1325 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.41 % Favored : 94.51 % Rotamer: Outliers : 2.31 % Allowed : 14.69 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.26), residues: 1147 helix: 2.10 (0.19), residues: 739 sheet: -3.73 (0.54), residues: 63 loop : -2.35 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1223 TYR 0.009 0.001 TYR A1265 PHE 0.012 0.001 PHE A 319 TRP 0.004 0.001 TRP A1106 HIS 0.004 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.19 ( 9152) covalent geometry : angle 0.51307 / 0.28 (12382) hydrogen bonds : bond 0.04573 / 3.02 ( 578) hydrogen bonds : angle 4.40260 / 3.26 ( 1713) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 237 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.375 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: symmetry clash revert: symmetry clash REVERT: A 946 MET cc_start: 0.9301 (tmm) cc_final: 0.9062 (tmm) REVERT: A 984 MET cc_start: 0.8370 (tpt) cc_final: 0.7728 (tpp) REVERT: A 1008 MET cc_start: 0.9021 (ptm) cc_final: 0.8765 (ppp) outliers start: 22 outliers final: 20 residues processed: 81 average time/residue: 0.1591 time to fit residues: 19.4459 Evaluate side-chains 78 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1075 SER Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1223 ARG Chi-restraints excluded: chain A residue 1266 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 70 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.050341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.039032 restraints weight = 150627.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.040990 restraints weight = 62268.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.042315 restraints weight = 37486.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.043143 restraints weight = 27116.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.043747 restraints weight = 22047.046| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9152 Z= 0.202 Angle : 0.514 7.055 12382 Z= 0.280 Chirality : 0.036 0.132 1431 Planarity : 0.003 0.044 1564 Dihedral : 12.185 174.153 1324 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.28 % Favored : 93.64 % Rotamer: Outliers : 2.52 % Allowed : 15.32 % Favored : 82.16 % 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: 0.81 (0.26), residues: 1147 helix: 2.15 (0.19), residues: 740 sheet: -3.67 (0.59), residues: 57 loop : -2.40 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1223 TYR 0.008 0.001 TYR A1265 PHE 0.012 0.001 PHE A 731 TRP 0.005 0.001 TRP A 141 HIS 0.004 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.20 ( 9152) covalent geometry : angle 0.51403 / 0.28 (12382) hydrogen bonds : bond 0.04410 / 2.91 ( 578) hydrogen bonds : angle 4.33649 / 3.22 ( 1713) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 237 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.368 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 946 MET cc_start: 0.9287 (tmm) cc_final: 0.9054 (tmm) REVERT: A 984 MET cc_start: 0.8347 (tpt) cc_final: 0.7706 (tpp) REVERT: A 1008 MET cc_start: 0.9057 (ptm) cc_final: 0.8834 (ppp) outliers start: 24 outliers final: 22 residues processed: 82 average time/residue: 0.1616 time to fit residues: 19.7093 Evaluate side-chains 80 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1075 SER Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1223 ARG Chi-restraints excluded: chain A residue 1266 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 76 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 0.0470 chunk 105 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- 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 = 0.3301 r_free = 0.3301 target = 0.051070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.039719 restraints weight = 151133.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.041748 restraints weight = 62905.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.043078 restraints weight = 37754.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.043970 restraints weight = 27317.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.044553 restraints weight = 21926.768| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9152 Z= 0.126 Angle : 0.475 7.143 12382 Z= 0.252 Chirality : 0.036 0.145 1431 Planarity : 0.003 0.046 1564 Dihedral : 12.083 176.061 1324 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.06 % Favored : 94.86 % Rotamer: Outliers : 2.31 % Allowed : 16.37 % Favored : 81.32 % 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: 1.13 (0.26), residues: 1147 helix: 2.40 (0.19), residues: 741 sheet: -3.34 (0.64), residues: 52 loop : -2.38 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 364 TYR 0.009 0.001 TYR A1265 PHE 0.010 0.001 PHE A 731 TRP 0.004 0.001 TRP A 707 HIS 0.003 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 ( 9152) covalent geometry : angle 0.47469 / 0.25 (12382) hydrogen bonds : bond 0.04257 / 2.79 ( 578) hydrogen bonds : angle 4.07230 / 3.02 ( 1713) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 237 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.328 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.8179 (ptp) cc_final: 0.7682 (tmm) REVERT: A 946 MET cc_start: 0.9291 (tmm) cc_final: 0.9044 (tmm) REVERT: A 984 MET cc_start: 0.8355 (tpt) cc_final: 0.7713 (tpp) REVERT: A 1008 MET cc_start: 0.9060 (ptm) cc_final: 0.8808 (ppp) outliers start: 22 outliers final: 19 residues processed: 80 average time/residue: 0.1639 time to fit residues: 19.1783 Evaluate side-chains 77 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1075 SER Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1223 ARG Chi-restraints excluded: chain A residue 1266 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 71 optimal weight: 4.9990 chunk 92 optimal weight: 0.0670 chunk 22 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 overall best weight: 1.4922 ------------------------------------------------------------------------------- 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 = 0.3297 r_free = 0.3297 target = 0.050978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.039610 restraints weight = 150170.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.041638 restraints weight = 63363.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.042969 restraints weight = 38131.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.043797 restraints weight = 27624.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.044401 restraints weight = 22520.905| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9152 Z= 0.149 Angle : 0.477 7.334 12382 Z= 0.255 Chirality : 0.036 0.132 1431 Planarity : 0.003 0.043 1564 Dihedral : 11.971 176.173 1321 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.67 % Favored : 94.25 % Rotamer: Outliers : 2.41 % Allowed : 16.16 % Favored : 81.43 % 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: 1.19 (0.26), residues: 1147 helix: 2.45 (0.19), residues: 741 sheet: -3.31 (0.64), residues: 52 loop : -2.36 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 364 TYR 0.007 0.001 TYR A1265 PHE 0.010 0.001 PHE A 319 TRP 0.004 0.001 TRP A1106 HIS 0.003 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 ( 9152) covalent geometry : angle 0.47696 / 0.26 (12382) hydrogen bonds : bond 0.04202 / 2.76 ( 578) hydrogen bonds : angle 4.07281 / 3.02 ( 1713) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 237 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 0.318 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.8183 (ptp) cc_final: 0.7706 (tmm) REVERT: A 946 MET cc_start: 0.9295 (tmm) cc_final: 0.9056 (tmm) REVERT: A 984 MET cc_start: 0.8356 (tpt) cc_final: 0.7714 (tpp) REVERT: A 1008 MET cc_start: 0.9074 (ptm) cc_final: 0.8845 (ppp) REVERT: A 1093 MET cc_start: 0.8703 (ttm) cc_final: 0.7813 (tpp) outliers start: 23 outliers final: 22 residues processed: 79 average time/residue: 0.1486 time to fit residues: 17.5444 Evaluate side-chains 80 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1075 SER Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1223 ARG Chi-restraints excluded: chain A residue 1266 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 90 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 HIS ** 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 = 0.3270 r_free = 0.3270 target = 0.050090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.038680 restraints weight = 153657.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.040646 restraints weight = 64526.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.041969 restraints weight = 39050.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.042779 restraints weight = 28399.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.043349 restraints weight = 23220.753| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9152 Z= 0.252 Angle : 0.542 7.593 12382 Z= 0.299 Chirality : 0.036 0.135 1431 Planarity : 0.003 0.042 1564 Dihedral : 12.007 176.577 1321 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.71 % Favored : 93.20 % Rotamer: Outliers : 2.94 % Allowed : 15.63 % Favored : 81.43 % 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: 0.80 (0.25), residues: 1147 helix: 2.12 (0.19), residues: 745 sheet: -3.35 (0.64), residues: 52 loop : -2.53 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 364 TYR 0.008 0.001 TYR A 312 PHE 0.014 0.001 PHE A 319 TRP 0.006 0.001 TRP A 801 HIS 0.005 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.25 ( 9152) covalent geometry : angle 0.54227 / 0.30 (12382) hydrogen bonds : bond 0.04391 / 2.90 ( 578) hydrogen bonds : angle 4.38564 / 3.26 ( 1713) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 237 is missing expected H atoms. Skipping. Evaluate side-chains 85 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 57 time to evaluate : 0.457 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.8217 (ptp) cc_final: 0.7753 (tmm) REVERT: A 946 MET cc_start: 0.9283 (tmm) cc_final: 0.9062 (tmm) REVERT: A 984 MET cc_start: 0.8351 (tpt) cc_final: 0.7714 (tpp) outliers start: 28 outliers final: 23 residues processed: 82 average time/residue: 0.1512 time to fit residues: 18.5248 Evaluate side-chains 80 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1075 SER Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1223 ARG Chi-restraints excluded: chain A residue 1266 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.050464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.039065 restraints weight = 151283.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.041077 restraints weight = 63231.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.042400 restraints weight = 38125.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.043253 restraints weight = 27584.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.043797 restraints weight = 22331.735| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9152 Z= 0.176 Angle : 0.502 6.255 12382 Z= 0.270 Chirality : 0.036 0.133 1431 Planarity : 0.003 0.043 1564 Dihedral : 11.946 177.333 1321 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.45 % Favored : 93.46 % Rotamer: Outliers : 3.04 % Allowed : 15.53 % Favored : 81.43 % 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: 0.93 (0.26), residues: 1147 helix: 2.23 (0.19), residues: 746 sheet: -3.64 (0.55), residues: 63 loop : -2.38 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 364 TYR 0.009 0.001 TYR A1265 PHE 0.012 0.001 PHE A 319 TRP 0.004 0.001 TRP A 141 HIS 0.004 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.18 ( 9152) covalent geometry : angle 0.50229 / 0.27 (12382) hydrogen bonds : bond 0.04343 / 2.87 ( 578) hydrogen bonds : angle 4.19714 / 3.12 ( 1713) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 237 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 0.370 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.8238 (ptp) cc_final: 0.7594 (tmm) REVERT: A 946 MET cc_start: 0.9285 (tmm) cc_final: 0.9072 (tmm) REVERT: A 984 MET cc_start: 0.8338 (tpt) cc_final: 0.7692 (tpp) REVERT: A 1008 MET cc_start: 0.9109 (ptm) cc_final: 0.8702 (ppp) REVERT: A 1093 MET cc_start: 0.8717 (ttm) cc_final: 0.7863 (tpp) outliers start: 29 outliers final: 25 residues processed: 84 average time/residue: 0.1660 time to fit residues: 21.1381 Evaluate side-chains 82 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 57 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1075 SER Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1223 ARG Chi-restraints excluded: chain A residue 1266 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.050446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.038969 restraints weight = 152389.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.040950 restraints weight = 64228.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.042270 restraints weight = 39055.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.043130 restraints weight = 28506.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.043672 restraints weight = 23069.607| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9152 Z= 0.200 Angle : 0.517 8.205 12382 Z= 0.279 Chirality : 0.036 0.133 1431 Planarity : 0.003 0.042 1564 Dihedral : 11.894 176.895 1321 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.10 % Favored : 93.81 % Rotamer: Outliers : 2.83 % Allowed : 16.47 % Favored : 80.69 % 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: 0.87 (0.26), residues: 1147 helix: 2.19 (0.19), residues: 746 sheet: -3.64 (0.55), residues: 63 loop : -2.41 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 364 TYR 0.008 0.001 TYR A1265 PHE 0.012 0.001 PHE A 319 TRP 0.004 0.001 TRP A 141 HIS 0.004 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.20 ( 9152) covalent geometry : angle 0.51711 / 0.28 (12382) hydrogen bonds : bond 0.04355 / 2.88 ( 578) hydrogen bonds : angle 4.25053 / 3.16 ( 1713) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 237 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.320 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.8256 (ptp) cc_final: 0.7604 (tmm) REVERT: A 984 MET cc_start: 0.8351 (tpt) cc_final: 0.7713 (tpp) REVERT: A 1008 MET cc_start: 0.9117 (ptm) cc_final: 0.8762 (ppp) REVERT: A 1093 MET cc_start: 0.8683 (ttm) cc_final: 0.7815 (tpp) outliers start: 27 outliers final: 24 residues processed: 81 average time/residue: 0.1380 time to fit residues: 17.0418 Evaluate side-chains 81 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1075 SER Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1223 ARG Chi-restraints excluded: chain A residue 1266 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 105 optimal weight: 0.0270 chunk 78 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7042 ------------------------------------------------------------------------------- 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 = 0.3308 r_free = 0.3308 target = 0.051326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.039917 restraints weight = 150046.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.041957 restraints weight = 62919.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.043293 restraints weight = 37779.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.044181 restraints weight = 27364.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.044730 restraints weight = 22053.349| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9152 Z= 0.108 Angle : 0.480 7.784 12382 Z= 0.249 Chirality : 0.036 0.136 1431 Planarity : 0.003 0.044 1564 Dihedral : 11.877 179.028 1321 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.67 % Favored : 94.25 % Rotamer: Outliers : 2.20 % Allowed : 16.89 % Favored : 80.90 % 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: 1.26 (0.26), residues: 1147 helix: 2.52 (0.19), residues: 741 sheet: -3.56 (0.56), residues: 63 loop : -2.24 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1223 TYR 0.009 0.001 TYR A1265 PHE 0.010 0.001 PHE A 731 TRP 0.004 0.001 TRP A 141 HIS 0.003 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 ( 9152) covalent geometry : angle 0.48018 / 0.25 (12382) hydrogen bonds : bond 0.04225 / 2.78 ( 578) hydrogen bonds : angle 3.94198 / 2.92 ( 1713) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 237 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.403 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.8267 (ptp) cc_final: 0.7642 (tmm) REVERT: A 946 MET cc_start: 0.9269 (tmm) cc_final: 0.9045 (tmm) REVERT: A 984 MET cc_start: 0.8331 (tpt) cc_final: 0.7686 (tpp) REVERT: A 1008 MET cc_start: 0.9140 (ptm) cc_final: 0.8815 (ppp) REVERT: A 1093 MET cc_start: 0.8678 (ttm) cc_final: 0.7798 (tpp) outliers start: 21 outliers final: 21 residues processed: 77 average time/residue: 0.1646 time to fit residues: 18.8474 Evaluate side-chains 79 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1223 ARG Chi-restraints excluded: chain A residue 1266 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 61 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 114 optimal weight: 0.0770 chunk 29 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- 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 = 0.3311 r_free = 0.3311 target = 0.051465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.039975 restraints weight = 151760.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.042029 restraints weight = 63671.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.043375 restraints weight = 38332.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.044258 restraints weight = 27804.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.044786 restraints weight = 22456.773| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9152 Z= 0.117 Angle : 0.479 7.510 12382 Z= 0.250 Chirality : 0.036 0.135 1431 Planarity : 0.003 0.042 1564 Dihedral : 11.779 177.694 1321 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.49 % Favored : 94.42 % Rotamer: Outliers : 2.20 % Allowed : 17.10 % Favored : 80.69 % 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: 1147 helix: 2.59 (0.19), residues: 741 sheet: -3.16 (0.61), residues: 53 loop : -2.22 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1223 TYR 0.007 0.001 TYR A 252 PHE 0.010 0.001 PHE A 731 TRP 0.004 0.001 TRP A 141 HIS 0.003 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 ( 9152) covalent geometry : angle 0.47917 / 0.25 (12382) hydrogen bonds : bond 0.04111 / 2.70 ( 578) hydrogen bonds : angle 3.89994 / 2.89 ( 1713) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2393.84 seconds wall clock time: 41 minutes 36.83 seconds (2496.83 seconds total)