Starting phenix.real_space_refine on Wed Feb 4 17:56:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k4f_62057/02_2026/9k4f_62057.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k4f_62057/02_2026/9k4f_62057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k4f_62057/02_2026/9k4f_62057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k4f_62057/02_2026/9k4f_62057.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k4f_62057/02_2026/9k4f_62057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k4f_62057/02_2026/9k4f_62057.map" } resolution = 3.27 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= 0.007 sd= 0.128 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: 5 Type Number sf(0) Gaussians P 130 5.49 5 S 19 5.16 5 C 7192 2.51 5 N 2118 2.21 5 O 2607 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 12066 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1136, 9268 Classifications: {'peptide': 1136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 1104} Chain breaks: 2 Chain: "B" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 560 Classifications: {'DNA': 27} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 26} Chain: "C" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 305 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "D" Number of atoms: 1933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1933 Classifications: {'RNA': 91} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 42, 'rna3p_pyr': 38} Link IDs: {'rna2p': 11, 'rna3p': 79} Time building chain proxies: 2.44, per 1000 atoms: 0.20 Number of scatterers: 12066 At special positions: 0 Unit cell: (129.21, 106.215, 148.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 130 15.00 O 2607 8.00 N 2118 7.00 C 7192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 497.6 milliseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 7 sheets defined 56.0% alpha, 10.1% beta 50 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.715A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 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 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.641A 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 196 removed outlier: 3.807A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 217 through 228 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 283 Processing helix chain 'A' and resid 286 through 306 removed outlier: 4.346A pdb=" N ASP A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 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 382 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.807A pdb=" N ASN A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.108A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 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 526 removed outlier: 4.066A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 553 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 703 through 712 Processing helix chain 'A' and resid 720 through 726 removed outlier: 3.844A pdb=" N ILE A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 751 Processing helix chain 'A' and resid 926 through 940 Processing helix chain 'A' and resid 959 through 970 removed outlier: 4.073A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.530A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1088 removed outlier: 3.580A pdb=" N ASP A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1177 through 1185 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 1281 Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1317 removed outlier: 3.731A pdb=" N HIS A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR A1314 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU A1315 " --> pdb=" O HIS A1311 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR A1316 " --> pdb=" O LEU A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.695A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) 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 954 through 957 removed outlier: 5.913A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N TYR A 5 " --> pdb=" O ASN A 758 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N VAL A 760 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 6.274A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.508A pdb=" N ALA A 538 " --> pdb=" O TYR A 529 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.522A pdb=" N GLU A1162 " --> pdb=" O VAL A1145 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.522A pdb=" N GLU A1162 " --> pdb=" O VAL A1145 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1326 462 hydrogen bonds defined for protein. 1353 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 127 hydrogen bonds 250 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2773 1.33 - 1.45: 3140 1.45 - 1.57: 6362 1.57 - 1.69: 260 1.69 - 1.81: 36 Bond restraints: 12571 Sorted by residual: bond pdb=" N ASP A 718 " pdb=" CA ASP A 718 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.36e+00 bond pdb=" O4' DT B 17 " pdb=" C1' DT B 17 " ideal model delta sigma weight residual 1.414 1.396 0.018 2.00e-02 2.50e+03 8.39e-01 bond pdb=" O4' DC B 16 " pdb=" C1' DC B 16 " ideal model delta sigma weight residual 1.414 1.396 0.018 2.00e-02 2.50e+03 8.22e-01 bond pdb=" O4' DG B 12 " pdb=" C1' DG B 12 " ideal model delta sigma weight residual 1.414 1.398 0.016 2.00e-02 2.50e+03 6.14e-01 bond pdb=" O4' DC C 5 " pdb=" C1' DC C 5 " ideal model delta sigma weight residual 1.414 1.398 0.016 2.00e-02 2.50e+03 6.05e-01 ... (remaining 12566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 17196 1.45 - 2.89: 314 2.89 - 4.34: 32 4.34 - 5.78: 7 5.78 - 7.23: 1 Bond angle restraints: 17550 Sorted by residual: angle pdb=" C SER A 719 " pdb=" N LEU A 720 " pdb=" CA LEU A 720 " ideal model delta sigma weight residual 121.54 127.04 -5.50 1.91e+00 2.74e-01 8.30e+00 angle pdb=" C ASP A 718 " pdb=" CA ASP A 718 " pdb=" CB ASP A 718 " ideal model delta sigma weight residual 110.42 115.82 -5.40 1.99e+00 2.53e-01 7.36e+00 angle pdb=" C ALA A1227 " pdb=" N LEU A1228 " pdb=" CA LEU A1228 " ideal model delta sigma weight residual 120.97 113.74 7.23 2.84e+00 1.24e-01 6.48e+00 angle pdb=" N GLN A 709 " pdb=" CA GLN A 709 " pdb=" CB GLN A 709 " ideal model delta sigma weight residual 110.28 113.78 -3.50 1.55e+00 4.16e-01 5.10e+00 angle pdb=" N ILE A 410 " pdb=" CA ILE A 410 " pdb=" C ILE A 410 " ideal model delta sigma weight residual 107.76 109.91 -2.15 1.01e+00 9.80e-01 4.55e+00 ... (remaining 17545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.80: 7164 28.80 - 57.59: 352 57.59 - 86.39: 106 86.39 - 115.18: 0 115.18 - 143.98: 1 Dihedral angle restraints: 7623 sinusoidal: 4286 harmonic: 3337 Sorted by residual: dihedral pdb=" CA SER A 719 " pdb=" C SER A 719 " pdb=" N LEU A 720 " pdb=" CA LEU A 720 " ideal model delta harmonic sigma weight residual -180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA ASN A 497 " pdb=" C ASN A 497 " pdb=" N PHE A 498 " pdb=" CA PHE A 498 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" C4' DG B 7 " pdb=" C3' DG B 7 " pdb=" O3' DG B 7 " pdb=" P DA B 8 " ideal model delta sinusoidal sigma weight residual 220.00 76.02 143.98 1 3.50e+01 8.16e-04 1.42e+01 ... (remaining 7620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1355 0.028 - 0.057: 466 0.057 - 0.085: 129 0.085 - 0.113: 61 0.113 - 0.142: 8 Chirality restraints: 2019 Sorted by residual: chirality pdb=" CA TYR A1201 " pdb=" N TYR A1201 " pdb=" C TYR A1201 " pdb=" CB TYR A1201 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE A 761 " pdb=" N ILE A 761 " pdb=" C ILE A 761 " pdb=" CB ILE A 761 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE A 48 " pdb=" N ILE A 48 " pdb=" C ILE A 48 " pdb=" CB ILE A 48 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 2016 not shown) Planarity restraints: 1757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G D 56 " 0.018 2.00e-02 2.50e+03 8.20e-03 2.02e+00 pdb=" N9 G D 56 " -0.021 2.00e-02 2.50e+03 pdb=" C8 G D 56 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G D 56 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G D 56 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G D 56 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G D 56 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G D 56 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G D 56 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G D 56 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G D 56 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G D 56 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 44 " 0.018 2.00e-02 2.50e+03 7.92e-03 1.72e+00 pdb=" N9 A D 44 " -0.017 2.00e-02 2.50e+03 pdb=" C8 A D 44 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A D 44 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A D 44 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A D 44 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A D 44 " 0.005 2.00e-02 2.50e+03 pdb=" N1 A D 44 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A D 44 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A D 44 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A D 44 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 730 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO A 731 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 731 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 731 " -0.017 5.00e-02 4.00e+02 ... (remaining 1754 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 3 2.02 - 2.74: 1020 2.74 - 3.46: 16157 3.46 - 4.18: 30616 4.18 - 4.90: 50323 Nonbonded interactions: 98119 Sorted by model distance: nonbonded pdb=" NZ LYS A1340 " pdb=" OP2 DA B 8 " model vdw 1.297 3.120 nonbonded pdb=" NZ LYS A 44 " pdb=" O6 G D 94 " model vdw 1.297 3.120 nonbonded pdb=" NH1 ARG A 71 " pdb=" N4 C D 20 " model vdw 1.352 3.200 nonbonded pdb=" CE LYS A1340 " pdb=" OP2 DA B 8 " model vdw 2.067 3.440 nonbonded pdb=" NH1 ARG A 71 " pdb=" C4 C D 20 " model vdw 2.080 3.340 ... (remaining 98114 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: 0.650 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.310 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 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 : 0.003 0.024 12571 Z= 0.147 Angle : 0.503 7.227 17550 Z= 0.290 Chirality : 0.035 0.142 2019 Planarity : 0.003 0.032 1757 Dihedral : 16.450 143.976 5463 Min Nonbonded Distance : 1.297 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.57 (0.25), residues: 1130 helix: 1.69 (0.22), residues: 575 sheet: 0.79 (0.54), residues: 87 loop : 0.40 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 74 TYR 0.012 0.001 TYR A 155 PHE 0.012 0.001 PHE A1204 TRP 0.014 0.002 TRP A1074 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00309 (12571) covalent geometry : angle 0.50282 (17550) hydrogen bonds : bond 0.15131 ( 579) hydrogen bonds : angle 5.42549 ( 1603) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8173 (m-30) cc_final: 0.7784 (m-30) REVERT: A 327 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7358 (tt0) REVERT: A 498 PHE cc_start: 0.8167 (m-10) cc_final: 0.7754 (m-80) REVERT: A 534 MET cc_start: -0.0229 (mtp) cc_final: -0.1429 (mmt) REVERT: A 596 ASP cc_start: 0.7182 (m-30) cc_final: 0.6940 (m-30) REVERT: A 629 ARG cc_start: 0.7573 (mtt180) cc_final: 0.7199 (ppt170) REVERT: A 648 MET cc_start: 0.7113 (mmm) cc_final: 0.6851 (mmt) REVERT: A 751 MET cc_start: 0.8818 (mmm) cc_final: 0.8432 (mmt) REVERT: A 929 LYS cc_start: 0.7532 (mttt) cc_final: 0.7257 (mmtm) REVERT: A 1129 LYS cc_start: 0.8703 (mttt) cc_final: 0.8457 (mttm) REVERT: A 1157 LEU cc_start: 0.7644 (mt) cc_final: 0.7284 (mp) REVERT: A 1255 LYS cc_start: 0.6711 (mttt) cc_final: 0.6287 (mttm) REVERT: A 1325 LYS cc_start: 0.8828 (mttt) cc_final: 0.8402 (ttmm) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1310 time to fit residues: 33.0962 Evaluate side-chains 97 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN A 712 GLN A 723 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.167192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.121560 restraints weight = 18734.638| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 3.10 r_work: 0.3313 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12571 Z= 0.168 Angle : 0.540 10.011 17550 Z= 0.288 Chirality : 0.037 0.143 2019 Planarity : 0.004 0.053 1757 Dihedral : 18.699 144.874 3066 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.65 % Favored : 97.26 % Rotamer: Outliers : 1.28 % Allowed : 4.23 % Favored : 94.49 % 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 (0.25), residues: 1130 helix: 1.50 (0.22), residues: 596 sheet: 0.49 (0.54), residues: 87 loop : 0.12 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 71 TYR 0.028 0.002 TYR A 136 PHE 0.013 0.001 PHE A 626 TRP 0.007 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00376 (12571) covalent geometry : angle 0.54005 (17550) hydrogen bonds : bond 0.04397 ( 579) hydrogen bonds : angle 4.32162 ( 1603) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8245 (m-30) cc_final: 0.7773 (m-30) REVERT: A 76 LYS cc_start: 0.8091 (tttt) cc_final: 0.7749 (tptt) REVERT: A 498 PHE cc_start: 0.8184 (m-10) cc_final: 0.7769 (m-80) REVERT: A 534 MET cc_start: -0.0231 (mtp) cc_final: -0.0828 (mmm) REVERT: A 629 ARG cc_start: 0.7514 (mtt180) cc_final: 0.7271 (ppt170) REVERT: A 631 MET cc_start: 0.8188 (mtm) cc_final: 0.7625 (mtm) REVERT: A 929 LYS cc_start: 0.7702 (mttt) cc_final: 0.7396 (mmtm) REVERT: A 1129 LYS cc_start: 0.8763 (mttt) cc_final: 0.8532 (mttm) REVERT: A 1325 LYS cc_start: 0.8952 (mttt) cc_final: 0.8495 (ttmm) REVERT: A 1346 THR cc_start: 0.8664 (p) cc_final: 0.8420 (t) outliers start: 13 outliers final: 9 residues processed: 109 average time/residue: 0.1232 time to fit residues: 18.7274 Evaluate side-chains 96 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1277 SER Chi-restraints excluded: chain A residue 1303 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 62 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 650 GLN A 723 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.162369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.114759 restraints weight = 19007.429| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.26 r_work: 0.3207 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12571 Z= 0.221 Angle : 0.576 10.649 17550 Z= 0.306 Chirality : 0.039 0.131 2019 Planarity : 0.004 0.057 1757 Dihedral : 19.094 144.583 3066 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Rotamer: Outliers : 1.38 % Allowed : 6.10 % Favored : 92.52 % 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: 0.98 (0.25), residues: 1130 helix: 1.39 (0.21), residues: 594 sheet: -0.16 (0.49), residues: 103 loop : -0.05 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 71 TYR 0.028 0.002 TYR A 136 PHE 0.015 0.002 PHE A1258 TRP 0.010 0.002 TRP A1074 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00499 (12571) covalent geometry : angle 0.57585 (17550) hydrogen bonds : bond 0.04846 ( 579) hydrogen bonds : angle 4.33363 ( 1603) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8137 (tttt) cc_final: 0.7790 (tptt) REVERT: A 498 PHE cc_start: 0.8109 (m-10) cc_final: 0.7656 (m-80) REVERT: A 534 MET cc_start: -0.0305 (mtp) cc_final: -0.1354 (mmt) REVERT: A 629 ARG cc_start: 0.7401 (mtt180) cc_final: 0.7157 (ppt170) REVERT: A 929 LYS cc_start: 0.7654 (mttt) cc_final: 0.7352 (mmtm) REVERT: A 951 ARG cc_start: 0.8135 (ptp-110) cc_final: 0.7566 (ptm-80) REVERT: A 1129 LYS cc_start: 0.8796 (mttt) cc_final: 0.8525 (mttm) REVERT: A 1145 VAL cc_start: 0.8948 (t) cc_final: 0.8698 (p) REVERT: A 1191 LYS cc_start: 0.8461 (mtmm) cc_final: 0.7917 (mtmm) REVERT: A 1213 MET cc_start: 0.8614 (mtm) cc_final: 0.8202 (mtp) REVERT: A 1256 GLN cc_start: 0.8299 (mt0) cc_final: 0.7867 (mp10) REVERT: A 1325 LYS cc_start: 0.8918 (mttt) cc_final: 0.8430 (ttmm) outliers start: 14 outliers final: 11 residues processed: 108 average time/residue: 0.1211 time to fit residues: 18.2138 Evaluate side-chains 95 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1277 SER Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 56 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN A 650 GLN A 982 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.162127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.117289 restraints weight = 19173.225| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.04 r_work: 0.3215 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 12571 Z= 0.300 Angle : 0.656 12.578 17550 Z= 0.344 Chirality : 0.042 0.158 2019 Planarity : 0.005 0.059 1757 Dihedral : 19.426 147.681 3066 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.19 % Favored : 96.73 % Rotamer: Outliers : 1.48 % Allowed : 7.19 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.24), residues: 1130 helix: 1.16 (0.21), residues: 586 sheet: -0.63 (0.48), residues: 100 loop : -0.56 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 165 TYR 0.029 0.002 TYR A 136 PHE 0.022 0.002 PHE A 164 TRP 0.009 0.002 TRP A1074 HIS 0.007 0.001 HIS A1349 Details of bonding type rmsd covalent geometry : bond 0.00679 (12571) covalent geometry : angle 0.65576 (17550) hydrogen bonds : bond 0.05626 ( 579) hydrogen bonds : angle 4.53024 ( 1603) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8270 (tttt) cc_final: 0.7991 (tptt) REVERT: A 498 PHE cc_start: 0.8125 (m-10) cc_final: 0.7676 (m-80) REVERT: A 534 MET cc_start: -0.0026 (mtp) cc_final: -0.1074 (mmt) REVERT: A 753 ARG cc_start: 0.8292 (mmt90) cc_final: 0.8033 (mmm-85) REVERT: A 925 ARG cc_start: 0.7013 (mmm-85) cc_final: 0.6503 (mmm-85) REVERT: A 929 LYS cc_start: 0.7676 (mttt) cc_final: 0.7435 (mmtm) REVERT: A 951 ARG cc_start: 0.8211 (ptp-110) cc_final: 0.7717 (ptm-80) REVERT: A 1129 LYS cc_start: 0.8796 (mttt) cc_final: 0.8521 (mttm) REVERT: A 1191 LYS cc_start: 0.8552 (mtmm) cc_final: 0.8036 (mtmm) REVERT: A 1213 MET cc_start: 0.8553 (mtm) cc_final: 0.8158 (mtp) REVERT: A 1325 LYS cc_start: 0.8991 (mttt) cc_final: 0.8520 (ttmm) outliers start: 15 outliers final: 13 residues processed: 96 average time/residue: 0.1176 time to fit residues: 15.5625 Evaluate side-chains 94 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 83 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 30.0000 chunk 53 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 71 optimal weight: 40.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.165187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.117137 restraints weight = 19658.108| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.44 r_work: 0.3260 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12571 Z= 0.160 Angle : 0.530 13.249 17550 Z= 0.281 Chirality : 0.037 0.168 2019 Planarity : 0.004 0.054 1757 Dihedral : 19.260 159.214 3066 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 2.07 % Allowed : 7.97 % Favored : 89.96 % 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: 0.71 (0.25), residues: 1130 helix: 1.45 (0.22), residues: 586 sheet: -0.70 (0.49), residues: 101 loop : -0.49 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 165 TYR 0.019 0.001 TYR A 136 PHE 0.020 0.001 PHE A1327 TRP 0.009 0.001 TRP A1074 HIS 0.006 0.001 HIS A 930 Details of bonding type rmsd covalent geometry : bond 0.00355 (12571) covalent geometry : angle 0.52977 (17550) hydrogen bonds : bond 0.04180 ( 579) hydrogen bonds : angle 4.18218 ( 1603) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8184 (tttt) cc_final: 0.7890 (tptt) REVERT: A 498 PHE cc_start: 0.8098 (m-10) cc_final: 0.7554 (m-80) REVERT: A 534 MET cc_start: -0.0110 (mtp) cc_final: -0.1102 (mmt) REVERT: A 929 LYS cc_start: 0.7674 (mttt) cc_final: 0.7450 (mmtm) REVERT: A 950 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.6998 (tp) REVERT: A 951 ARG cc_start: 0.8038 (ptp-110) cc_final: 0.7587 (ptm-80) REVERT: A 1129 LYS cc_start: 0.8808 (mttt) cc_final: 0.8514 (mttm) REVERT: A 1145 VAL cc_start: 0.8977 (t) cc_final: 0.8767 (p) REVERT: A 1213 MET cc_start: 0.8621 (mtm) cc_final: 0.8214 (mtp) REVERT: A 1325 LYS cc_start: 0.8960 (mttt) cc_final: 0.8462 (ttmm) outliers start: 21 outliers final: 12 residues processed: 105 average time/residue: 0.1182 time to fit residues: 17.5054 Evaluate side-chains 96 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1346 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 97 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 67 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.162459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.116646 restraints weight = 19734.282| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 3.48 r_work: 0.3200 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12571 Z= 0.246 Angle : 0.599 11.497 17550 Z= 0.315 Chirality : 0.040 0.152 2019 Planarity : 0.004 0.055 1757 Dihedral : 19.360 152.872 3066 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.19 % Favored : 96.73 % Rotamer: Outliers : 1.87 % Allowed : 8.86 % Favored : 89.27 % 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: 0.40 (0.24), residues: 1130 helix: 1.24 (0.22), residues: 586 sheet: -0.82 (0.47), residues: 100 loop : -0.73 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 165 TYR 0.022 0.002 TYR A 136 PHE 0.021 0.002 PHE A1327 TRP 0.009 0.002 TRP A1074 HIS 0.007 0.001 HIS A 982 Details of bonding type rmsd covalent geometry : bond 0.00556 (12571) covalent geometry : angle 0.59948 (17550) hydrogen bonds : bond 0.05109 ( 579) hydrogen bonds : angle 4.32200 ( 1603) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8306 (tttt) cc_final: 0.8050 (tptt) REVERT: A 498 PHE cc_start: 0.8151 (m-10) cc_final: 0.7669 (m-80) REVERT: A 534 MET cc_start: -0.0098 (mtp) cc_final: -0.1131 (mmt) REVERT: A 951 ARG cc_start: 0.8043 (ptp-110) cc_final: 0.7639 (ptm-80) REVERT: A 1129 LYS cc_start: 0.8760 (mttt) cc_final: 0.8447 (mtpt) REVERT: A 1191 LYS cc_start: 0.8577 (mtmm) cc_final: 0.7021 (mmmt) REVERT: A 1213 MET cc_start: 0.8615 (mtm) cc_final: 0.8246 (mtp) REVERT: A 1303 ARG cc_start: 0.8715 (ttp-170) cc_final: 0.8514 (mtp85) REVERT: A 1325 LYS cc_start: 0.8996 (mttt) cc_final: 0.8744 (mtpp) outliers start: 19 outliers final: 17 residues processed: 98 average time/residue: 0.1077 time to fit residues: 15.0255 Evaluate side-chains 94 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1256 GLN Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 42 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.166564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.119599 restraints weight = 19485.806| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 3.23 r_work: 0.3285 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12571 Z= 0.123 Angle : 0.488 9.990 17550 Z= 0.262 Chirality : 0.035 0.161 2019 Planarity : 0.003 0.057 1757 Dihedral : 19.172 158.043 3066 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.74 % Favored : 97.17 % Rotamer: Outliers : 1.77 % Allowed : 8.86 % Favored : 89.37 % 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: 0.77 (0.25), residues: 1130 helix: 1.59 (0.22), residues: 587 sheet: -0.74 (0.49), residues: 101 loop : -0.60 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 165 TYR 0.015 0.001 TYR A 136 PHE 0.018 0.001 PHE A1258 TRP 0.009 0.001 TRP A1074 HIS 0.006 0.001 HIS A 930 Details of bonding type rmsd covalent geometry : bond 0.00265 (12571) covalent geometry : angle 0.48840 (17550) hydrogen bonds : bond 0.03822 ( 579) hydrogen bonds : angle 4.04025 ( 1603) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7299 (mmmt) REVERT: A 76 LYS cc_start: 0.8202 (tttt) cc_final: 0.7932 (tptt) REVERT: A 498 PHE cc_start: 0.8074 (m-10) cc_final: 0.7571 (m-80) REVERT: A 534 MET cc_start: -0.0379 (mtp) cc_final: -0.1270 (mmt) REVERT: A 596 ASP cc_start: 0.6426 (m-30) cc_final: 0.6099 (m-30) REVERT: A 709 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7713 (mp10) REVERT: A 926 GLN cc_start: 0.8342 (tp40) cc_final: 0.8102 (tp40) REVERT: A 950 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.6851 (tp) REVERT: A 951 ARG cc_start: 0.7931 (ptp-110) cc_final: 0.7575 (ptm-80) REVERT: A 1129 LYS cc_start: 0.8766 (mttt) cc_final: 0.8466 (mttm) REVERT: A 1191 LYS cc_start: 0.8612 (mtmm) cc_final: 0.7106 (mmmt) REVERT: A 1213 MET cc_start: 0.8632 (mtm) cc_final: 0.8225 (mtp) REVERT: A 1325 LYS cc_start: 0.8954 (mttt) cc_final: 0.8689 (mtpp) outliers start: 18 outliers final: 9 residues processed: 109 average time/residue: 0.1209 time to fit residues: 18.2966 Evaluate side-chains 97 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1273 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 45 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 110 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.162970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.106568 restraints weight = 19676.509| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.08 r_work: 0.3242 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 12571 Z= 0.244 Angle : 0.592 11.247 17550 Z= 0.312 Chirality : 0.039 0.143 2019 Planarity : 0.004 0.055 1757 Dihedral : 19.333 151.761 3066 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.36 % Favored : 96.55 % Rotamer: Outliers : 1.67 % Allowed : 9.35 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.25), residues: 1130 helix: 1.31 (0.22), residues: 587 sheet: -0.86 (0.49), residues: 96 loop : -0.75 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 165 TYR 0.023 0.002 TYR A 136 PHE 0.021 0.002 PHE A1327 TRP 0.009 0.002 TRP A1074 HIS 0.007 0.001 HIS A 982 Details of bonding type rmsd covalent geometry : bond 0.00550 (12571) covalent geometry : angle 0.59183 (17550) hydrogen bonds : bond 0.04935 ( 579) hydrogen bonds : angle 4.25555 ( 1603) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LYS cc_start: 0.7808 (mmmt) cc_final: 0.7328 (mmmt) REVERT: A 76 LYS cc_start: 0.8250 (tttt) cc_final: 0.7981 (tptt) REVERT: A 222 LEU cc_start: 0.7834 (mt) cc_final: 0.7579 (mt) REVERT: A 498 PHE cc_start: 0.8118 (m-10) cc_final: 0.7571 (m-80) REVERT: A 534 MET cc_start: -0.0464 (mtp) cc_final: -0.1119 (mmp) REVERT: A 596 ASP cc_start: 0.6443 (m-30) cc_final: 0.6070 (m-30) REVERT: A 656 TYR cc_start: 0.7031 (m-80) cc_final: 0.6718 (m-80) REVERT: A 926 GLN cc_start: 0.8383 (tp40) cc_final: 0.8117 (tp40) REVERT: A 950 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.6790 (tp) REVERT: A 951 ARG cc_start: 0.7913 (ptp-110) cc_final: 0.7583 (ptm-80) REVERT: A 1129 LYS cc_start: 0.8725 (mttt) cc_final: 0.8523 (mtpt) REVERT: A 1191 LYS cc_start: 0.8624 (mtmm) cc_final: 0.7134 (mmmt) REVERT: A 1213 MET cc_start: 0.8615 (mtm) cc_final: 0.8230 (mtp) REVERT: A 1325 LYS cc_start: 0.8990 (mttt) cc_final: 0.8731 (mtpp) outliers start: 17 outliers final: 13 residues processed: 96 average time/residue: 0.1073 time to fit residues: 14.5389 Evaluate side-chains 96 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 78 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.164449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.118033 restraints weight = 19474.900| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 3.34 r_work: 0.3244 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12571 Z= 0.188 Angle : 0.546 11.698 17550 Z= 0.290 Chirality : 0.037 0.149 2019 Planarity : 0.004 0.056 1757 Dihedral : 19.310 154.742 3066 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.19 % Favored : 96.73 % Rotamer: Outliers : 1.38 % Allowed : 9.65 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.25), residues: 1130 helix: 1.38 (0.22), residues: 587 sheet: -0.80 (0.48), residues: 98 loop : -0.75 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 165 TYR 0.019 0.002 TYR A 136 PHE 0.025 0.001 PHE A1327 TRP 0.008 0.001 TRP A1074 HIS 0.006 0.001 HIS A 930 Details of bonding type rmsd covalent geometry : bond 0.00423 (12571) covalent geometry : angle 0.54557 (17550) hydrogen bonds : bond 0.04375 ( 579) hydrogen bonds : angle 4.17137 ( 1603) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8261 (tttt) cc_final: 0.7977 (tptt) REVERT: A 222 LEU cc_start: 0.7935 (mt) cc_final: 0.7700 (mt) REVERT: A 383 MET cc_start: 0.8007 (ttm) cc_final: 0.7718 (ttm) REVERT: A 498 PHE cc_start: 0.8017 (m-10) cc_final: 0.7433 (m-80) REVERT: A 534 MET cc_start: -0.0439 (mtp) cc_final: -0.1117 (mmp) REVERT: A 596 ASP cc_start: 0.6455 (m-30) cc_final: 0.6073 (m-30) REVERT: A 656 TYR cc_start: 0.6950 (m-80) cc_final: 0.6638 (m-80) REVERT: A 709 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7688 (mp10) REVERT: A 950 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.6829 (tp) REVERT: A 951 ARG cc_start: 0.7904 (ptp-110) cc_final: 0.7604 (ptm-80) REVERT: A 1129 LYS cc_start: 0.8750 (mttt) cc_final: 0.8448 (mttm) REVERT: A 1191 LYS cc_start: 0.8574 (mtmm) cc_final: 0.7057 (mmmt) REVERT: A 1213 MET cc_start: 0.8634 (mtm) cc_final: 0.8258 (mtp) REVERT: A 1325 LYS cc_start: 0.8998 (mttt) cc_final: 0.8747 (mtpp) outliers start: 14 outliers final: 11 residues processed: 98 average time/residue: 0.1239 time to fit residues: 16.8689 Evaluate side-chains 99 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 9 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.164019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.116961 restraints weight = 19657.900| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 3.66 r_work: 0.3223 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12571 Z= 0.203 Angle : 0.575 11.692 17550 Z= 0.303 Chirality : 0.038 0.145 2019 Planarity : 0.004 0.055 1757 Dihedral : 19.331 151.979 3066 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.45 % Favored : 96.46 % Rotamer: Outliers : 1.48 % Allowed : 9.74 % Favored : 88.78 % 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: 0.45 (0.25), residues: 1130 helix: 1.31 (0.22), residues: 587 sheet: -0.82 (0.48), residues: 98 loop : -0.76 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 165 TYR 0.020 0.002 TYR A 136 PHE 0.029 0.002 PHE A1327 TRP 0.008 0.001 TRP A1074 HIS 0.006 0.001 HIS A 982 Details of bonding type rmsd covalent geometry : bond 0.00458 (12571) covalent geometry : angle 0.57508 (17550) hydrogen bonds : bond 0.04618 ( 579) hydrogen bonds : angle 4.22729 ( 1603) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8040 (mmmt) cc_final: 0.7340 (mmmt) REVERT: A 76 LYS cc_start: 0.8245 (tttt) cc_final: 0.7953 (tptt) REVERT: A 222 LEU cc_start: 0.7957 (mt) cc_final: 0.7724 (mt) REVERT: A 383 MET cc_start: 0.8111 (ttm) cc_final: 0.7828 (ttm) REVERT: A 498 PHE cc_start: 0.8017 (m-10) cc_final: 0.7411 (m-80) REVERT: A 534 MET cc_start: -0.0373 (mtp) cc_final: -0.1115 (mmp) REVERT: A 596 ASP cc_start: 0.6448 (m-30) cc_final: 0.6094 (m-30) REVERT: A 656 TYR cc_start: 0.7041 (m-80) cc_final: 0.6762 (m-80) REVERT: A 950 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.6815 (tp) REVERT: A 951 ARG cc_start: 0.7904 (ptp-110) cc_final: 0.7593 (ptm-80) REVERT: A 1129 LYS cc_start: 0.8759 (mttt) cc_final: 0.8435 (mtpt) REVERT: A 1191 LYS cc_start: 0.8583 (mtmm) cc_final: 0.7156 (mmmt) REVERT: A 1213 MET cc_start: 0.8673 (mtm) cc_final: 0.8285 (mtp) REVERT: A 1302 ILE cc_start: 0.9103 (mt) cc_final: 0.8846 (tp) REVERT: A 1325 LYS cc_start: 0.9009 (mttt) cc_final: 0.8506 (ttmm) outliers start: 15 outliers final: 12 residues processed: 95 average time/residue: 0.1206 time to fit residues: 16.2686 Evaluate side-chains 96 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 54 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 79 optimal weight: 0.2980 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.163118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.115800 restraints weight = 19584.711| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 3.36 r_work: 0.3233 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12571 Z= 0.228 Angle : 0.605 11.519 17550 Z= 0.317 Chirality : 0.039 0.161 2019 Planarity : 0.004 0.055 1757 Dihedral : 19.420 150.933 3066 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.89 % Favored : 95.93 % Rotamer: Outliers : 1.57 % Allowed : 9.84 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.24), residues: 1130 helix: 1.23 (0.22), residues: 581 sheet: -0.92 (0.48), residues: 98 loop : -0.83 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 165 TYR 0.020 0.002 TYR A 136 PHE 0.029 0.002 PHE A1327 TRP 0.007 0.001 TRP A1074 HIS 0.007 0.001 HIS A 982 Details of bonding type rmsd covalent geometry : bond 0.00515 (12571) covalent geometry : angle 0.60468 (17550) hydrogen bonds : bond 0.04878 ( 579) hydrogen bonds : angle 4.29897 ( 1603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2898.42 seconds wall clock time: 50 minutes 17.53 seconds (3017.53 seconds total)