Starting phenix.real_space_refine on Fri Feb 6 06:00:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jl2_61576/02_2026/9jl2_61576.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jl2_61576/02_2026/9jl2_61576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jl2_61576/02_2026/9jl2_61576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jl2_61576/02_2026/9jl2_61576.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jl2_61576/02_2026/9jl2_61576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jl2_61576/02_2026/9jl2_61576.map" } resolution = 3.0 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 133 5.49 5 S 18 5.16 5 C 7146 2.51 5 N 2101 2.21 5 O 2605 1.98 5 H 10804 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22807 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 885 Classifications: {'DNA': 28} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 27} Chain: "D" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 320 Classifications: {'DNA': 10} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 18511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1125, 18511 Classifications: {'peptide': 1125} Link IDs: {'PTRANS': 30, 'TRANS': 1094} Chain breaks: 2 Chain: "B" Number of atoms: 3091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 3091 Classifications: {'RNA': 96} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 51, 'rna3p_pyr': 34} Link IDs: {'rna2p': 11, 'rna3p': 84} Time building chain proxies: 4.24, per 1000 atoms: 0.19 Number of scatterers: 22807 At special positions: 0 Unit cell: (89.1, 128.7, 122.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 18 16.00 P 133 15.00 O 2605 8.00 N 2101 7.00 C 7146 6.00 H 10804 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: 1.92 Conformation dependent library (CDL) restraints added in 612.0 milliseconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 8 sheets defined 54.3% alpha, 7.6% beta 49 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 4.03 Creating SS restraints... Processing helix chain 'A' and resid 59 through 86 removed outlier: 3.586A pdb=" N PHE A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.515A pdb=" N ALA A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 removed outlier: 3.746A pdb=" N GLU A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 103 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.559A pdb=" N HIS A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 144 removed outlier: 3.822A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 180 through 194 removed outlier: 3.596A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.920A pdb=" N ALA A 214 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 236 through 246 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 270 through 282 removed outlier: 4.199A pdb=" N ASP A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 286 through 306 removed outlier: 3.733A pdb=" N ILE A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 342 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 381 removed outlier: 3.571A pdb=" N PHE A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS A 377 " --> pdb=" O TYR A 373 " (cutoff:3.500A) Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.887A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 411 through 427 removed outlier: 3.938A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.827A pdb=" N ASP A 435 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 512 through 522 removed outlier: 3.657A pdb=" N VAL A 520 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 526 Processing helix chain 'A' and resid 541 through 553 removed outlier: 3.675A pdb=" N ASP A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 568 removed outlier: 4.366A pdb=" N GLU A 566 " --> pdb=" O LYS A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.695A pdb=" N ASP A 618 " --> pdb=" O ASP A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 643 removed outlier: 5.283A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 642 " --> pdb=" O TYR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 654 removed outlier: 3.828A pdb=" N ARG A 653 " --> pdb=" O LYS A 649 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG A 654 " --> pdb=" O GLN A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 678 through 684 Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 703 through 715 Processing helix chain 'A' and resid 721 through 726 Processing helix chain 'A' and resid 734 through 749 Processing helix chain 'A' and resid 927 through 939 removed outlier: 3.918A pdb=" N GLN A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 970 removed outlier: 4.280A pdb=" N LYS A 968 " --> pdb=" O SER A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 999 removed outlier: 4.185A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 998 " --> pdb=" O GLY A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1087 removed outlier: 3.597A pdb=" N LYS A1085 " --> pdb=" O ALA A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.538A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 removed outlier: 3.585A pdb=" N LYS A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1280 removed outlier: 4.383A pdb=" N ILE A1270 " --> pdb=" O LEU A1266 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A1271 " --> pdb=" O ASP A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1310 removed outlier: 3.540A pdb=" N ASN A1308 " --> pdb=" O GLU A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1315 removed outlier: 3.577A pdb=" N THR A1314 " --> pdb=" O HIS A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1344 removed outlier: 3.836A pdb=" N LEU A1343 " --> pdb=" O THR A1339 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP A1344 " --> pdb=" O LYS A1340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1339 through 1344' Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 10 removed outlier: 6.236A pdb=" N ALA A 50 " --> pdb=" O VAL A1095 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.828A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA5, first strand: chain 'A' and resid 759 through 760 removed outlier: 6.670A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1163 removed outlier: 3.581A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1156 through 1163 removed outlier: 3.578A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1324 through 1326 394 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 122 hydrogen bonds 240 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 6.42 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10802 1.03 - 1.23: 80 1.23 - 1.42: 5503 1.42 - 1.62: 6891 1.62 - 1.81: 34 Bond restraints: 23310 Sorted by residual: bond pdb=" ND2 ASN A 121 " pdb="HD22 ASN A 121 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" ND2 ASN A 121 " pdb="HD21 ASN A 121 " ideal model delta sigma weight residual 0.860 0.977 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" CA ASP A 936 " pdb=" C ASP A 936 " ideal model delta sigma weight residual 1.522 1.490 0.033 1.40e-02 5.10e+03 5.46e+00 bond pdb=" C ILE A 122 " pdb=" O ILE A 122 " ideal model delta sigma weight residual 1.236 1.213 0.023 1.11e-02 8.12e+03 4.45e+00 bond pdb=" CB PRO A 378 " pdb=" CG PRO A 378 " ideal model delta sigma weight residual 1.492 1.586 -0.094 5.00e-02 4.00e+02 3.53e+00 ... (remaining 23305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 40687 1.52 - 3.03: 1405 3.03 - 4.55: 88 4.55 - 6.06: 16 6.06 - 7.58: 1 Bond angle restraints: 42197 Sorted by residual: angle pdb=" CA PRO A 378 " pdb=" N PRO A 378 " pdb=" CD PRO A 378 " ideal model delta sigma weight residual 112.00 107.16 4.84 1.40e+00 5.10e-01 1.19e+01 angle pdb=" N ILE A 282 " pdb=" CA ILE A 282 " pdb=" C ILE A 282 " ideal model delta sigma weight residual 113.53 110.21 3.32 9.80e-01 1.04e+00 1.15e+01 angle pdb=" CA PRO A1090 " pdb=" N PRO A1090 " pdb=" CD PRO A1090 " ideal model delta sigma weight residual 112.00 107.58 4.42 1.40e+00 5.10e-01 9.95e+00 angle pdb=" CA ARG A1298 " pdb=" C ARG A1298 " pdb=" N ASP A1299 " ideal model delta sigma weight residual 118.15 123.64 -5.49 1.80e+00 3.09e-01 9.29e+00 angle pdb=" CA LYS A1191 " pdb=" CB LYS A1191 " pdb=" CG LYS A1191 " ideal model delta sigma weight residual 114.10 119.60 -5.50 2.00e+00 2.50e-01 7.56e+00 ... (remaining 42192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 9266 17.94 - 35.87: 894 35.87 - 53.81: 392 53.81 - 71.74: 172 71.74 - 89.68: 36 Dihedral angle restraints: 10760 sinusoidal: 6886 harmonic: 3874 Sorted by residual: dihedral pdb=" CA SER A1216 " pdb=" C SER A1216 " pdb=" N ALA A1217 " pdb=" CA ALA A1217 " ideal model delta harmonic sigma weight residual 180.00 152.00 28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA GLU A1243 " pdb=" C GLU A1243 " pdb=" N LYS A1244 " pdb=" CA LYS A1244 " ideal model delta harmonic sigma weight residual 180.00 153.02 26.98 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA GLU A 505 " pdb=" C GLU A 505 " pdb=" N LYS A 506 " pdb=" CA LYS A 506 " ideal model delta harmonic sigma weight residual -180.00 -153.34 -26.66 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 10757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1285 0.035 - 0.070: 550 0.070 - 0.105: 131 0.105 - 0.139: 42 0.139 - 0.174: 13 Chirality restraints: 2021 Sorted by residual: chirality pdb=" CB ILE A 118 " pdb=" CA ILE A 118 " pdb=" CG1 ILE A 118 " pdb=" CG2 ILE A 118 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA VAL A1092 " pdb=" N VAL A1092 " pdb=" C VAL A1092 " pdb=" CB VAL A1092 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.53e-01 chirality pdb=" C1' A B 42 " pdb=" O4' A B 42 " pdb=" C2' A B 42 " pdb=" N9 A B 42 " both_signs ideal model delta sigma weight residual False 2.46 2.30 0.16 2.00e-01 2.50e+01 6.26e-01 ... (remaining 2018 not shown) Planarity restraints: 2931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 121 " 0.195 2.00e-02 2.50e+03 1.97e-01 5.80e+02 pdb=" CG ASN A 121 " -0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN A 121 " -0.186 2.00e-02 2.50e+03 pdb=" ND2 ASN A 121 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 121 " -0.282 2.00e-02 2.50e+03 pdb="HD22 ASN A 121 " 0.283 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A1089 " -0.071 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO A1090 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO A1090 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A1090 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 377 " -0.049 5.00e-02 4.00e+02 7.20e-02 8.29e+00 pdb=" N PRO A 378 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 378 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 378 " -0.040 5.00e-02 4.00e+02 ... (remaining 2928 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 574 2.11 - 2.73: 38010 2.73 - 3.35: 64007 3.35 - 3.98: 83029 3.98 - 4.60: 129030 Nonbonded interactions: 314650 Sorted by model distance: nonbonded pdb=" OE1 GLU A 427 " pdb=" H GLU A 427 " model vdw 1.482 2.450 nonbonded pdb="HH22 ARG A 400 " pdb=" OD2 ASP A 406 " model vdw 1.525 2.450 nonbonded pdb="HH11 ARG A 967 " pdb=" OD1 ASP A 986 " model vdw 1.533 2.450 nonbonded pdb=" HH TYR A 373 " pdb=" O LEU A 398 " model vdw 1.552 2.450 nonbonded pdb=" HG SER A 512 " pdb=" OE2 GLU A 617 " model vdw 1.552 2.450 ... (remaining 314645 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 0.400 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 26.260 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 12506 Z= 0.270 Angle : 0.667 7.577 17471 Z= 0.387 Chirality : 0.042 0.174 2021 Planarity : 0.005 0.106 1740 Dihedral : 18.629 89.678 5447 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.06 % Favored : 92.85 % Rotamer: Outliers : 0.40 % Allowed : 11.82 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.24), residues: 1119 helix: -0.82 (0.22), residues: 516 sheet: -2.07 (0.51), residues: 90 loop : -1.45 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 40 TYR 0.014 0.002 TYR A1336 PHE 0.027 0.002 PHE A1080 TRP 0.010 0.002 TRP A 476 HIS 0.008 0.002 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00559 (12506) covalent geometry : angle 0.66673 (17471) hydrogen bonds : bond 0.18472 ( 508) hydrogen bonds : angle 7.10092 ( 1359) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 219 time to evaluate : 0.577 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: 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 outliers start: 4 outliers final: 3 residues processed: 222 average time/residue: 1.4492 time to fit residues: 345.4379 Evaluate side-chains 107 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 1310 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 489 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.120767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.082741 restraints weight = 74482.433| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.79 r_work: 0.3255 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 12506 Z= 0.264 Angle : 0.652 5.373 17471 Z= 0.359 Chirality : 0.041 0.178 2021 Planarity : 0.005 0.068 1740 Dihedral : 18.758 93.659 3082 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.90 % Favored : 94.01 % Rotamer: Outliers : 2.48 % Allowed : 17.38 % Favored : 80.14 % 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: -1.45 (0.24), residues: 1119 helix: -0.34 (0.22), residues: 534 sheet: -1.94 (0.44), residues: 117 loop : -1.29 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 976 TYR 0.019 0.002 TYR A 155 PHE 0.019 0.002 PHE A1258 TRP 0.009 0.002 TRP A 18 HIS 0.006 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00568 (12506) covalent geometry : angle 0.65172 (17471) hydrogen bonds : bond 0.05292 ( 508) hydrogen bonds : angle 4.93969 ( 1359) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.594 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8395 (tttt) REVERT: A 648 MET cc_start: 0.6658 (tmm) cc_final: 0.6053 (tmm) REVERT: A 661 ARG cc_start: 0.8466 (mmm-85) cc_final: 0.8232 (mpp80) REVERT: A 704 PHE cc_start: 0.7905 (m-10) cc_final: 0.7686 (m-10) REVERT: A 933 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8611 (tm130) outliers start: 25 outliers final: 8 residues processed: 129 average time/residue: 1.3465 time to fit residues: 188.0352 Evaluate side-chains 99 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1298 ARG Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 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 = 0.4066 r_free = 0.4066 target = 0.120948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.082222 restraints weight = 75372.024| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.87 r_work: 0.3257 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12506 Z= 0.186 Angle : 0.573 5.296 17471 Z= 0.315 Chirality : 0.038 0.158 2021 Planarity : 0.004 0.072 1740 Dihedral : 18.617 96.054 3076 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 2.68 % Allowed : 17.28 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.25), residues: 1119 helix: -0.11 (0.22), residues: 538 sheet: -1.69 (0.45), residues: 112 loop : -1.09 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 63 TYR 0.014 0.001 TYR A 155 PHE 0.019 0.001 PHE A 256 TRP 0.006 0.001 TRP A 476 HIS 0.005 0.001 HIS A 595 Details of bonding type rmsd covalent geometry : bond 0.00400 (12506) covalent geometry : angle 0.57298 (17471) hydrogen bonds : bond 0.04524 ( 508) hydrogen bonds : angle 4.56430 ( 1359) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.533 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 447 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8341 (ttm170) REVERT: A 712 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8529 (tm-30) REVERT: A 758 ASN cc_start: 0.8459 (m-40) cc_final: 0.8174 (m110) REVERT: A 933 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8641 (tm130) REVERT: A 938 ARG cc_start: 0.8431 (mmm-85) cc_final: 0.7847 (tpp80) REVERT: A 1329 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8631 (t) outliers start: 27 outliers final: 7 residues processed: 107 average time/residue: 1.0857 time to fit residues: 127.4963 Evaluate side-chains 89 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 27 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 59 optimal weight: 20.0000 chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.120606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.081657 restraints weight = 75632.378| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.88 r_work: 0.3250 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12506 Z= 0.176 Angle : 0.553 5.091 17471 Z= 0.304 Chirality : 0.038 0.151 2021 Planarity : 0.004 0.055 1740 Dihedral : 18.572 98.688 3076 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.36 % Favored : 94.55 % Rotamer: Outliers : 2.18 % Allowed : 18.57 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.25), residues: 1119 helix: 0.04 (0.22), residues: 544 sheet: -1.67 (0.46), residues: 113 loop : -1.08 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 661 TYR 0.014 0.001 TYR A 155 PHE 0.014 0.001 PHE A 478 TRP 0.005 0.001 TRP A 476 HIS 0.005 0.001 HIS A1262 Details of bonding type rmsd covalent geometry : bond 0.00378 (12506) covalent geometry : angle 0.55275 (17471) hydrogen bonds : bond 0.04157 ( 508) hydrogen bonds : angle 4.34979 ( 1359) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.558 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 661 ARG cc_start: 0.8477 (mmm-85) cc_final: 0.8096 (mpp80) REVERT: A 758 ASN cc_start: 0.8480 (m-40) cc_final: 0.8195 (m110) REVERT: A 933 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8618 (tm130) REVERT: A 938 ARG cc_start: 0.8450 (mmm-85) cc_final: 0.7864 (tpp-160) outliers start: 22 outliers final: 6 residues processed: 102 average time/residue: 1.1257 time to fit residues: 125.2600 Evaluate side-chains 84 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 1099 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 105 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.119088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.079887 restraints weight = 75598.913| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.89 r_work: 0.3218 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12506 Z= 0.233 Angle : 0.578 6.083 17471 Z= 0.317 Chirality : 0.039 0.157 2021 Planarity : 0.004 0.054 1740 Dihedral : 18.612 101.272 3076 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.34 % Favored : 93.57 % Rotamer: Outliers : 2.58 % Allowed : 18.27 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.25), residues: 1119 helix: 0.07 (0.22), residues: 546 sheet: -1.72 (0.47), residues: 116 loop : -1.08 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 653 TYR 0.016 0.001 TYR A 155 PHE 0.015 0.001 PHE A 478 TRP 0.007 0.001 TRP A 18 HIS 0.007 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00499 (12506) covalent geometry : angle 0.57827 (17471) hydrogen bonds : bond 0.04448 ( 508) hydrogen bonds : angle 4.39644 ( 1359) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.433 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: A 661 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.8106 (mpp80) REVERT: A 758 ASN cc_start: 0.8433 (m-40) cc_final: 0.8147 (m110) REVERT: A 933 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8599 (tm130) REVERT: A 938 ARG cc_start: 0.8447 (mmm-85) cc_final: 0.7873 (tpp-160) outliers start: 26 outliers final: 12 residues processed: 95 average time/residue: 0.9969 time to fit residues: 104.5183 Evaluate side-chains 83 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1309 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 28 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** 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 = 0.4042 r_free = 0.4042 target = 0.119115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.080079 restraints weight = 75850.273| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.87 r_work: 0.3221 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12506 Z= 0.204 Angle : 0.561 5.135 17471 Z= 0.307 Chirality : 0.038 0.147 2021 Planarity : 0.004 0.058 1740 Dihedral : 18.594 101.684 3076 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.26 % Favored : 93.66 % Rotamer: Outliers : 2.58 % Allowed : 18.77 % Favored : 78.65 % 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: -0.85 (0.25), residues: 1119 helix: 0.19 (0.22), residues: 547 sheet: -1.62 (0.47), residues: 111 loop : -1.09 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 653 TYR 0.015 0.001 TYR A 155 PHE 0.014 0.001 PHE A 518 TRP 0.005 0.001 TRP A 18 HIS 0.006 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00438 (12506) covalent geometry : angle 0.56103 (17471) hydrogen bonds : bond 0.04197 ( 508) hydrogen bonds : angle 4.26085 ( 1359) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.599 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: A 661 ARG cc_start: 0.8493 (mmm-85) cc_final: 0.8083 (mpp80) REVERT: A 758 ASN cc_start: 0.8378 (m-40) cc_final: 0.8089 (m110) REVERT: A 933 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8588 (tm130) outliers start: 26 outliers final: 15 residues processed: 94 average time/residue: 1.1709 time to fit residues: 120.4948 Evaluate side-chains 85 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1309 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 91 optimal weight: 0.0670 chunk 73 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 0.0020 overall best weight: 1.3930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.119970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.082099 restraints weight = 74996.965| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.80 r_work: 0.3254 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12506 Z= 0.140 Angle : 0.534 6.069 17471 Z= 0.290 Chirality : 0.036 0.142 2021 Planarity : 0.004 0.084 1740 Dihedral : 18.557 101.855 3076 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.65 % Favored : 95.26 % Rotamer: Outliers : 2.09 % Allowed : 18.77 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.25), residues: 1119 helix: 0.52 (0.23), residues: 540 sheet: -1.57 (0.48), residues: 108 loop : -0.79 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 925 TYR 0.013 0.001 TYR A1336 PHE 0.011 0.001 PHE A1258 TRP 0.005 0.001 TRP A 476 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00302 (12506) covalent geometry : angle 0.53357 (17471) hydrogen bonds : bond 0.03786 ( 508) hydrogen bonds : angle 4.07027 ( 1359) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.597 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 661 ARG cc_start: 0.8467 (mmm-85) cc_final: 0.8070 (mpp80) REVERT: A 758 ASN cc_start: 0.8397 (m-40) cc_final: 0.8093 (m110) REVERT: A 933 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8560 (tm130) outliers start: 21 outliers final: 10 residues processed: 94 average time/residue: 1.2050 time to fit residues: 124.3703 Evaluate side-chains 82 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1309 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 54 optimal weight: 8.9990 chunk 47 optimal weight: 0.0970 chunk 10 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 117 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN A 971 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.120154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.081520 restraints weight = 75548.574| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.88 r_work: 0.3253 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12506 Z= 0.138 Angle : 0.525 6.905 17471 Z= 0.287 Chirality : 0.036 0.140 2021 Planarity : 0.004 0.062 1740 Dihedral : 18.507 102.523 3076 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.81 % Favored : 94.10 % Rotamer: Outliers : 2.28 % Allowed : 19.07 % Favored : 78.65 % 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: -0.27 (0.26), residues: 1119 helix: 0.65 (0.23), residues: 540 sheet: -1.49 (0.49), residues: 107 loop : -0.72 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 653 TYR 0.012 0.001 TYR A 155 PHE 0.016 0.001 PHE A 704 TRP 0.005 0.001 TRP A 476 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00299 (12506) covalent geometry : angle 0.52477 (17471) hydrogen bonds : bond 0.03698 ( 508) hydrogen bonds : angle 3.99181 ( 1359) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.571 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 433 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8162 (mp) REVERT: A 661 ARG cc_start: 0.8501 (mmm-85) cc_final: 0.8112 (mpp80) REVERT: A 758 ASN cc_start: 0.8381 (m-40) cc_final: 0.8099 (m110) REVERT: A 933 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8548 (tm130) outliers start: 23 outliers final: 14 residues processed: 95 average time/residue: 1.1283 time to fit residues: 118.5262 Evaluate side-chains 86 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1309 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 28 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 690 ASN A 721 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.117499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.078574 restraints weight = 76268.800| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.91 r_work: 0.3192 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 12506 Z= 0.308 Angle : 0.621 7.255 17471 Z= 0.337 Chirality : 0.041 0.149 2021 Planarity : 0.004 0.062 1740 Dihedral : 18.632 103.663 3076 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.06 % Favored : 92.85 % Rotamer: Outliers : 2.38 % Allowed : 19.27 % Favored : 78.35 % 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: -0.73 (0.25), residues: 1119 helix: 0.26 (0.22), residues: 546 sheet: -1.62 (0.48), residues: 115 loop : -0.96 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 925 TYR 0.017 0.002 TYR A 155 PHE 0.017 0.002 PHE A 478 TRP 0.011 0.002 TRP A 18 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00656 (12506) covalent geometry : angle 0.62070 (17471) hydrogen bonds : bond 0.04723 ( 508) hydrogen bonds : angle 4.29508 ( 1359) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8208 (mp) REVERT: A 661 ARG cc_start: 0.8541 (mmm-85) cc_final: 0.8144 (mpp80) REVERT: A 758 ASN cc_start: 0.8403 (m-40) cc_final: 0.8108 (m110) REVERT: A 933 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8575 (tm130) REVERT: A 938 ARG cc_start: 0.8483 (mmm-85) cc_final: 0.7844 (tpp-160) outliers start: 24 outliers final: 15 residues processed: 88 average time/residue: 1.0217 time to fit residues: 99.5166 Evaluate side-chains 82 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1309 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.118993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.080215 restraints weight = 76050.232| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.88 r_work: 0.3228 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12506 Z= 0.167 Angle : 0.546 6.475 17471 Z= 0.296 Chirality : 0.037 0.142 2021 Planarity : 0.004 0.066 1740 Dihedral : 18.627 102.823 3076 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 1.99 % Allowed : 19.66 % Favored : 78.35 % 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: -0.47 (0.26), residues: 1119 helix: 0.48 (0.23), residues: 546 sheet: -1.56 (0.47), residues: 114 loop : -0.83 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 925 TYR 0.014 0.001 TYR A1336 PHE 0.016 0.001 PHE A 704 TRP 0.005 0.001 TRP A 476 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00359 (12506) covalent geometry : angle 0.54589 (17471) hydrogen bonds : bond 0.03879 ( 508) hydrogen bonds : angle 4.05853 ( 1359) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.614 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: A 661 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.8125 (mpp80) REVERT: A 758 ASN cc_start: 0.8356 (m-40) cc_final: 0.8067 (m110) REVERT: A 933 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8534 (tm130) outliers start: 20 outliers final: 14 residues processed: 87 average time/residue: 1.0325 time to fit residues: 99.2979 Evaluate side-chains 81 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1309 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 22 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.118567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.079694 restraints weight = 75787.852| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.88 r_work: 0.3217 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12506 Z= 0.200 Angle : 0.560 7.011 17471 Z= 0.304 Chirality : 0.038 0.142 2021 Planarity : 0.004 0.062 1740 Dihedral : 18.634 103.159 3076 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.52 % Favored : 93.39 % Rotamer: Outliers : 1.79 % Allowed : 20.06 % Favored : 78.15 % 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: -0.50 (0.26), residues: 1119 helix: 0.48 (0.22), residues: 546 sheet: -1.61 (0.47), residues: 114 loop : -0.87 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 925 TYR 0.014 0.001 TYR A1336 PHE 0.012 0.001 PHE A 478 TRP 0.005 0.001 TRP A 476 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00429 (12506) covalent geometry : angle 0.56036 (17471) hydrogen bonds : bond 0.04006 ( 508) hydrogen bonds : angle 4.09106 ( 1359) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6570.51 seconds wall clock time: 111 minutes 57.16 seconds (6717.16 seconds total)