Starting phenix.real_space_refine on Wed Aug 5 21:29:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k4e_62056/08_2026/9k4e_62056.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k4e_62056/08_2026/9k4e_62056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k4e_62056/08_2026/9k4e_62056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k4e_62056/08_2026/9k4e_62056.map" model { file = "/net/cci-nas-00/data/ceres_data/9k4e_62056/08_2026/9k4e_62056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k4e_62056/08_2026/9k4e_62056.cif" } resolution = 3.3 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= 0.006 sd= 0.154 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 112 5.49 5 S 19 5.16 5 C 7001 2.51 5 N 2044 2.21 5 O 2491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11667 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1134, 9247 Classifications: {'peptide': 1134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 1103} Chain breaks: 2 Chain: "B" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 282 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "C" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 286 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "D" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1852 Classifications: {'RNA': 87} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 42, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 75} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.59, per 1000 atoms: 0.22 Number of scatterers: 11667 At special positions: 0 Unit cell: (118.26, 105.12, 130.305, 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 112 15.00 O 2491 8.00 N 2044 7.00 C 7001 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: 0.85 Conformation dependent library (CDL) restraints added in 467.0 milliseconds 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 7 sheets defined 55.8% alpha, 8.6% beta 37 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.701A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.790A 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: 3.776A 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 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 247 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 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 396 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.522A pdb=" N ASN A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.055A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.587A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (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 496 removed outlier: 3.529A pdb=" N THR A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 removed outlier: 4.230A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 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 654 Processing helix chain 'A' and resid 664 through 669 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 723 through 727 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: 4.054A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1001 Processing helix chain 'A' and resid 1076 through 1088 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 1313 removed outlier: 3.898A pdb=" N HIS A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 4.010A 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: 4.178A pdb=" N ASN A 758 " --> pdb=" O TYR A 5 " (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: 6.384A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 507 through 509 removed outlier: 5.432A pdb=" N LEU A 508 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.552A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 3.809A 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 464 hydrogen bonds defined for protein. 1356 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 94 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 2.90 Time building geometry restraints manager: 1.11 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: 2664 1.33 - 1.45: 2956 1.45 - 1.57: 6242 1.57 - 1.69: 224 1.69 - 1.81: 36 Bond restraints: 12122 Sorted by residual: bond pdb=" C3' DG B 7 " pdb=" C2' DG B 7 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.89e+00 bond pdb=" C3' DG B 12 " pdb=" C2' DG B 12 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.27e+00 bond pdb=" C3' DG C 3 " pdb=" C2' DG C 3 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.17e+00 bond pdb=" C3' DC B 14 " pdb=" C2' DC B 14 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.87e+00 bond pdb=" C3' DT C 9 " pdb=" C2' DT C 9 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.69e+00 ... (remaining 12117 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 16454 1.91 - 3.82: 391 3.82 - 5.72: 10 5.72 - 7.63: 1 7.63 - 9.54: 1 Bond angle restraints: 16857 Sorted by residual: angle pdb=" N3 DT B 10 " pdb=" C4 DT B 10 " pdb=" O4 DT B 10 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT C 12 " pdb=" C4 DT C 12 " pdb=" O4 DT C 12 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT B 6 " pdb=" C4 DT B 6 " pdb=" O4 DT B 6 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 angle pdb=" N3 DT B 4 " pdb=" C4 DT B 4 " pdb=" O4 DT B 4 " ideal model delta sigma weight residual 119.90 122.30 -2.40 6.00e-01 2.78e+00 1.60e+01 angle pdb=" N3 DT C 9 " pdb=" C4 DT C 9 " pdb=" O4 DT C 9 " ideal model delta sigma weight residual 119.90 122.30 -2.40 6.00e-01 2.78e+00 1.59e+01 ... (remaining 16852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.03: 6992 30.03 - 60.06: 329 60.06 - 90.10: 69 90.10 - 120.13: 0 120.13 - 150.16: 1 Dihedral angle restraints: 7391 sinusoidal: 4060 harmonic: 3331 Sorted by residual: dihedral pdb=" CA MET A 495 " pdb=" C MET A 495 " pdb=" N THR A 496 " pdb=" CA THR A 496 " ideal model delta harmonic sigma weight residual 180.00 -160.61 -19.39 0 5.00e+00 4.00e-02 1.50e+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 69.84 150.16 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" CG ARG A1359 " pdb=" CD ARG A1359 " pdb=" NE ARG A1359 " pdb=" CZ ARG A1359 " ideal model delta sinusoidal sigma weight residual -180.00 -135.21 -44.79 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 7388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1165 0.028 - 0.056: 465 0.056 - 0.084: 142 0.084 - 0.112: 76 0.112 - 0.140: 93 Chirality restraints: 1941 Sorted by residual: chirality pdb=" C2' G D 35 " pdb=" C3' G D 35 " pdb=" O2' G D 35 " pdb=" C1' G D 35 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" C2' G D 75 " pdb=" C3' G D 75 " pdb=" O2' G D 75 " pdb=" C1' G D 75 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" C2' U D 27 " pdb=" C3' U D 27 " pdb=" O2' U D 27 " pdb=" C1' U D 27 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 1938 not shown) Planarity restraints: 1735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A D 44 " 0.019 2.00e-02 2.50e+03 9.13e-03 2.29e+00 pdb=" N9 A D 44 " -0.022 2.00e-02 2.50e+03 pdb=" C8 A D 44 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A D 44 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A D 44 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A D 44 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A D 44 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A D 44 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A D 44 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A D 44 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A D 44 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 49 " 0.016 2.00e-02 2.50e+03 7.54e-03 1.57e+00 pdb=" N9 A D 49 " -0.018 2.00e-02 2.50e+03 pdb=" C8 A D 49 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A D 49 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A D 49 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A D 49 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A D 49 " 0.005 2.00e-02 2.50e+03 pdb=" N1 A D 49 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A D 49 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A D 49 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A D 49 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 76 " -0.015 2.00e-02 2.50e+03 7.05e-03 1.37e+00 pdb=" N9 A D 76 " 0.018 2.00e-02 2.50e+03 pdb=" C8 A D 76 " -0.000 2.00e-02 2.50e+03 pdb=" N7 A D 76 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A D 76 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A D 76 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A D 76 " -0.004 2.00e-02 2.50e+03 pdb=" N1 A D 76 " -0.000 2.00e-02 2.50e+03 pdb=" C2 A D 76 " 0.000 2.00e-02 2.50e+03 pdb=" N3 A D 76 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A D 76 " 0.001 2.00e-02 2.50e+03 ... (remaining 1732 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 2 2.02 - 2.74: 969 2.74 - 3.46: 15587 3.46 - 4.18: 28908 4.18 - 4.90: 48785 Nonbonded interactions: 94251 Sorted by model distance: nonbonded pdb=" NZ LYS A 742 " pdb=" OP1 C D 69 " model vdw 1.296 3.120 nonbonded pdb=" NH1 ARG A 71 " pdb=" N4 C D 20 " model vdw 1.351 3.200 nonbonded pdb=" NH2 ARG A 400 " pdb=" OD2 ASP A 406 " model vdw 2.137 3.120 nonbonded pdb=" O ILE A 305 " pdb=" OG SER A 320 " model vdw 2.150 3.040 nonbonded pdb=" NH1 ARG A 71 " pdb=" C4 C D 20 " model vdw 2.153 3.340 ... (remaining 94246 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: 0.570 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.920 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 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 0.030 12122 Z= 0.240 Angle : 0.592 9.540 16857 Z= 0.426 Chirality : 0.045 0.140 1941 Planarity : 0.003 0.028 1735 Dihedral : 16.207 150.162 5235 Min Nonbonded Distance : 1.296 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.95 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.25), residues: 1128 helix: 1.47 (0.22), residues: 597 sheet: 0.88 (0.55), residues: 87 loop : 0.40 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 324 TYR 0.018 0.001 TYR A 451 PHE 0.018 0.001 PHE A 491 TRP 0.008 0.001 TRP A1126 HIS 0.005 0.001 HIS A 985 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.24 (12122) covalent geometry : angle 0.59209 / 0.43 (16857) hydrogen bonds : bond 0.15571 / 10.38 ( 558) hydrogen bonds : angle 5.99214 / 4.18 ( 1540) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8079 (tttt) cc_final: 0.7819 (tptt) REVERT: A 84 GLU cc_start: 0.8097 (tt0) cc_final: 0.7665 (tp30) REVERT: A 147 ASP cc_start: 0.7878 (m-30) cc_final: 0.7430 (p0) REVERT: A 183 LYS cc_start: 0.6233 (tttt) cc_final: 0.5908 (mmtm) REVERT: A 202 ASN cc_start: 0.7897 (t0) cc_final: 0.7587 (p0) REVERT: A 273 ASP cc_start: 0.8324 (m-30) cc_final: 0.7752 (p0) REVERT: A 314 LYS cc_start: 0.8387 (mttt) cc_final: 0.7795 (mtmt) REVERT: A 334 LEU cc_start: 0.8226 (tp) cc_final: 0.7840 (tt) REVERT: A 516 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7501 (mt-10) REVERT: A 534 MET cc_start: 0.4246 (mtp) cc_final: 0.3171 (ptm) REVERT: A 570 LYS cc_start: 0.8821 (tttt) cc_final: 0.8290 (tppt) REVERT: A 696 LEU cc_start: 0.8493 (mt) cc_final: 0.8107 (mm) REVERT: A 751 MET cc_start: 0.8551 (mmm) cc_final: 0.8347 (mmm) REVERT: A 959 LYS cc_start: 0.6670 (mmpt) cc_final: 0.6312 (mttp) REVERT: A 977 GLU cc_start: 0.7710 (mp0) cc_final: 0.7256 (mp0) REVERT: A 999 LYS cc_start: 0.8404 (mmtm) cc_final: 0.7414 (ttpp) REVERT: A 1170 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8485 (mt-10) REVERT: A 1188 LYS cc_start: 0.8347 (mttt) cc_final: 0.8080 (mmmt) REVERT: A 1256 GLN cc_start: 0.7232 (mt0) cc_final: 0.6799 (mm110) REVERT: A 1258 PHE cc_start: 0.7389 (t80) cc_final: 0.6925 (t80) REVERT: A 1263 LYS cc_start: 0.8379 (tttt) cc_final: 0.7720 (mtmt) REVERT: A 1264 HIS cc_start: 0.6106 (p-80) cc_final: 0.5881 (p-80) REVERT: A 1272 GLN cc_start: 0.7071 (mt0) cc_final: 0.6710 (mm-40) REVERT: A 1307 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7319 (mt-10) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1236 time to fit residues: 43.6720 Evaluate side-chains 134 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 40.0000 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 117 optimal weight: 50.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 GLN A 716 GLN A 930 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.157286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.104200 restraints weight = 16814.646| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.50 r_work: 0.3125 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 12122 Z= 0.261 Angle : 0.611 9.565 16857 Z= 0.333 Chirality : 0.044 0.257 1941 Planarity : 0.005 0.060 1735 Dihedral : 18.539 150.882 2843 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.68 % Favored : 98.23 % Rotamer: Outliers : 1.68 % Allowed : 7.50 % Favored : 90.83 % 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: 0.94 (0.25), residues: 1128 helix: 1.18 (0.21), residues: 603 sheet: -0.04 (0.49), residues: 111 loop : 0.15 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1303 TYR 0.016 0.002 TYR A1141 PHE 0.019 0.002 PHE A 491 TRP 0.005 0.001 TRP A 464 HIS 0.008 0.001 HIS A 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.26 (12122) covalent geometry : angle 0.61136 / 0.33 (16857) hydrogen bonds : bond 0.05369 / 3.59 ( 558) hydrogen bonds : angle 5.00100 / 3.51 ( 1540) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8309 (tttt) cc_final: 0.7940 (tptt) REVERT: A 84 GLU cc_start: 0.8070 (tt0) cc_final: 0.7729 (tp30) REVERT: A 89 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7080 (tp30) REVERT: A 147 ASP cc_start: 0.8003 (m-30) cc_final: 0.7591 (p0) REVERT: A 183 LYS cc_start: 0.6126 (tttt) cc_final: 0.5781 (ttpp) REVERT: A 202 ASN cc_start: 0.8084 (t0) cc_final: 0.7707 (p0) REVERT: A 215 ARG cc_start: 0.7277 (mmm160) cc_final: 0.7035 (mmm160) REVERT: A 234 LYS cc_start: 0.8690 (pttt) cc_final: 0.8352 (ptmm) REVERT: A 252 PHE cc_start: 0.7485 (m-80) cc_final: 0.7187 (m-80) REVERT: A 273 ASP cc_start: 0.8227 (m-30) cc_final: 0.7952 (p0) REVERT: A 314 LYS cc_start: 0.8561 (mttt) cc_final: 0.7980 (mtmt) REVERT: A 353 ASP cc_start: 0.8291 (t0) cc_final: 0.8024 (t0) REVERT: A 356 LYS cc_start: 0.8555 (mmtt) cc_final: 0.8252 (mptt) REVERT: A 534 MET cc_start: 0.4297 (mtp) cc_final: 0.3076 (ptm) REVERT: A 751 MET cc_start: 0.8610 (mmm) cc_final: 0.8288 (mmm) REVERT: A 926 GLN cc_start: 0.7556 (mp10) cc_final: 0.7287 (mm-40) REVERT: A 929 LYS cc_start: 0.8292 (mtpt) cc_final: 0.7311 (tptt) REVERT: A 933 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.6979 (pm20) REVERT: A 953 VAL cc_start: 0.8915 (t) cc_final: 0.8659 (t) REVERT: A 959 LYS cc_start: 0.7046 (mmpt) cc_final: 0.6531 (mttp) REVERT: A 977 GLU cc_start: 0.7849 (mp0) cc_final: 0.7418 (mp0) REVERT: A 999 LYS cc_start: 0.8393 (mmtm) cc_final: 0.7407 (ttpp) REVERT: A 1170 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8580 (mt-10) REVERT: A 1188 LYS cc_start: 0.8551 (mttt) cc_final: 0.8326 (mmmt) REVERT: A 1242 TYR cc_start: 0.7481 (t80) cc_final: 0.7190 (t80) REVERT: A 1258 PHE cc_start: 0.7203 (t80) cc_final: 0.6755 (t80) REVERT: A 1263 LYS cc_start: 0.8248 (tttt) cc_final: 0.7642 (mtmt) REVERT: A 1307 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7321 (mt-10) outliers start: 17 outliers final: 12 residues processed: 156 average time/residue: 0.1317 time to fit residues: 27.2950 Evaluate side-chains 136 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1280 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 5 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.157949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.104884 restraints weight = 16972.657| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.51 r_work: 0.3141 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12122 Z= 0.167 Angle : 0.505 5.335 16857 Z= 0.281 Chirality : 0.039 0.268 1941 Planarity : 0.004 0.054 1735 Dihedral : 18.612 151.869 2843 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.86 % Favored : 98.05 % Rotamer: Outliers : 2.07 % Allowed : 9.17 % Favored : 88.76 % 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: 1128 helix: 1.32 (0.21), residues: 603 sheet: -0.22 (0.48), residues: 111 loop : 0.02 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 425 TYR 0.020 0.002 TYR A1242 PHE 0.016 0.002 PHE A 569 TRP 0.006 0.001 TRP A 476 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (12122) covalent geometry : angle 0.50510 / 0.28 (16857) hydrogen bonds : bond 0.04752 / 3.11 ( 558) hydrogen bonds : angle 4.65170 / 3.28 ( 1540) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8308 (tttt) cc_final: 0.7926 (tptt) REVERT: A 84 GLU cc_start: 0.8027 (tt0) cc_final: 0.7662 (tp30) REVERT: A 147 ASP cc_start: 0.8012 (m-30) cc_final: 0.7633 (p0) REVERT: A 202 ASN cc_start: 0.8100 (t0) cc_final: 0.7701 (p0) REVERT: A 273 ASP cc_start: 0.8166 (m-30) cc_final: 0.7918 (p0) REVERT: A 314 LYS cc_start: 0.8493 (mttt) cc_final: 0.7887 (mtmt) REVERT: A 321 MET cc_start: 0.8645 (mmt) cc_final: 0.8408 (mmt) REVERT: A 339 VAL cc_start: 0.8163 (p) cc_final: 0.7913 (p) REVERT: A 353 ASP cc_start: 0.8311 (t0) cc_final: 0.8032 (t0) REVERT: A 356 LYS cc_start: 0.8544 (mmtt) cc_final: 0.8226 (mptt) REVERT: A 495 MET cc_start: 0.8368 (ppp) cc_final: 0.8147 (ppp) REVERT: A 534 MET cc_start: 0.4386 (mtp) cc_final: 0.3175 (ptm) REVERT: A 628 ASP cc_start: 0.8004 (t0) cc_final: 0.7740 (t0) REVERT: A 682 PHE cc_start: 0.7551 (m-10) cc_final: 0.6997 (m-10) REVERT: A 929 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7682 (tptt) REVERT: A 959 LYS cc_start: 0.7031 (mmpt) cc_final: 0.6493 (mttp) REVERT: A 977 GLU cc_start: 0.7862 (mp0) cc_final: 0.7494 (mp0) REVERT: A 999 LYS cc_start: 0.8361 (mmtm) cc_final: 0.7424 (ttpp) REVERT: A 1170 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8487 (mt-10) REVERT: A 1188 LYS cc_start: 0.8566 (mttt) cc_final: 0.8353 (mmmt) REVERT: A 1213 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8473 (mtm) REVERT: A 1242 TYR cc_start: 0.7472 (t80) cc_final: 0.6987 (t80) REVERT: A 1258 PHE cc_start: 0.7165 (t80) cc_final: 0.6694 (t80) REVERT: A 1263 LYS cc_start: 0.8173 (tttt) cc_final: 0.7648 (mtmt) REVERT: A 1303 ARG cc_start: 0.6148 (mtp-110) cc_final: 0.5893 (mtp-110) REVERT: A 1307 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7284 (mt-10) outliers start: 21 outliers final: 12 residues processed: 155 average time/residue: 0.1552 time to fit residues: 32.0135 Evaluate side-chains 130 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1280 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 113 optimal weight: 40.0000 chunk 84 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS A 194 GLN A 369 GLN A 698 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.155984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102660 restraints weight = 17023.635| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.52 r_work: 0.3109 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12122 Z= 0.215 Angle : 0.547 5.607 16857 Z= 0.297 Chirality : 0.041 0.271 1941 Planarity : 0.004 0.052 1735 Dihedral : 18.653 151.383 2843 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.39 % Favored : 97.52 % Rotamer: Outliers : 1.97 % Allowed : 10.85 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.25), residues: 1128 helix: 1.24 (0.21), residues: 604 sheet: -0.37 (0.47), residues: 111 loop : -0.12 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 671 TYR 0.015 0.002 TYR A 450 PHE 0.025 0.002 PHE A 491 TRP 0.006 0.001 TRP A 476 HIS 0.005 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (12122) covalent geometry : angle 0.54692 / 0.30 (16857) hydrogen bonds : bond 0.04806 / 3.22 ( 558) hydrogen bonds : angle 4.63652 / 3.29 ( 1540) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8350 (tttt) cc_final: 0.7961 (tptt) REVERT: A 84 GLU cc_start: 0.8081 (tt0) cc_final: 0.7693 (tp30) REVERT: A 147 ASP cc_start: 0.8070 (m-30) cc_final: 0.7733 (p0) REVERT: A 196 PHE cc_start: 0.7413 (m-80) cc_final: 0.7206 (m-80) REVERT: A 202 ASN cc_start: 0.8043 (t0) cc_final: 0.7661 (p0) REVERT: A 273 ASP cc_start: 0.8121 (m-30) cc_final: 0.7844 (p0) REVERT: A 286 TYR cc_start: 0.6721 (m-10) cc_final: 0.6456 (m-10) REVERT: A 314 LYS cc_start: 0.8533 (mttt) cc_final: 0.7940 (mtmt) REVERT: A 353 ASP cc_start: 0.8358 (t0) cc_final: 0.8091 (t0) REVERT: A 356 LYS cc_start: 0.8472 (mmtt) cc_final: 0.8203 (mptt) REVERT: A 495 MET cc_start: 0.8375 (ppp) cc_final: 0.8119 (ppp) REVERT: A 518 PHE cc_start: 0.7988 (t80) cc_final: 0.7708 (t80) REVERT: A 534 MET cc_start: 0.4366 (mtp) cc_final: 0.3195 (ptm) REVERT: A 610 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7758 (mt-10) REVERT: A 628 ASP cc_start: 0.8154 (t0) cc_final: 0.7886 (t0) REVERT: A 661 ARG cc_start: 0.7368 (mtp85) cc_final: 0.7029 (mtp85) REVERT: A 926 GLN cc_start: 0.7577 (mp10) cc_final: 0.7210 (mm-40) REVERT: A 929 LYS cc_start: 0.8317 (mtpt) cc_final: 0.7673 (tptt) REVERT: A 959 LYS cc_start: 0.7064 (mmpt) cc_final: 0.6542 (mttp) REVERT: A 977 GLU cc_start: 0.7929 (mp0) cc_final: 0.7587 (mp0) REVERT: A 988 TYR cc_start: 0.7877 (t80) cc_final: 0.7608 (t80) REVERT: A 1170 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8602 (mt-10) REVERT: A 1188 LYS cc_start: 0.8577 (mttt) cc_final: 0.8336 (mmmt) REVERT: A 1263 LYS cc_start: 0.8210 (tttt) cc_final: 0.7632 (mtmt) REVERT: A 1307 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7373 (mt-10) REVERT: A 1332 ASP cc_start: 0.8283 (m-30) cc_final: 0.7841 (t0) outliers start: 20 outliers final: 15 residues processed: 141 average time/residue: 0.1523 time to fit residues: 28.8422 Evaluate side-chains 127 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1280 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 118 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 40 optimal weight: 0.0770 chunk 48 optimal weight: 2.9990 chunk 122 optimal weight: 30.0000 chunk 97 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 overall best weight: 2.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 GLN ** A1254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.156103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.103228 restraints weight = 16929.364| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.50 r_work: 0.3119 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12122 Z= 0.181 Angle : 0.518 7.244 16857 Z= 0.284 Chirality : 0.040 0.276 1941 Planarity : 0.004 0.052 1735 Dihedral : 18.688 152.504 2843 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.66 % Favored : 97.25 % Rotamer: Outliers : 1.87 % Allowed : 11.05 % Favored : 87.08 % 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: 0.83 (0.25), residues: 1128 helix: 1.29 (0.21), residues: 604 sheet: -0.38 (0.47), residues: 111 loop : -0.17 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 691 TYR 0.013 0.001 TYR A 155 PHE 0.042 0.002 PHE A1327 TRP 0.006 0.001 TRP A 476 HIS 0.005 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (12122) covalent geometry : angle 0.51785 / 0.28 (16857) hydrogen bonds : bond 0.04541 / 3.00 ( 558) hydrogen bonds : angle 4.53727 / 3.22 ( 1540) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8307 (tttt) cc_final: 0.7921 (tptt) REVERT: A 84 GLU cc_start: 0.8059 (tt0) cc_final: 0.7680 (tp30) REVERT: A 90 MET cc_start: 0.8626 (mmm) cc_final: 0.8325 (tpt) REVERT: A 147 ASP cc_start: 0.8072 (m-30) cc_final: 0.7741 (p0) REVERT: A 196 PHE cc_start: 0.7497 (m-80) cc_final: 0.7248 (m-80) REVERT: A 202 ASN cc_start: 0.8047 (t0) cc_final: 0.7683 (p0) REVERT: A 273 ASP cc_start: 0.8114 (m-30) cc_final: 0.7858 (p0) REVERT: A 314 LYS cc_start: 0.8511 (mttt) cc_final: 0.7906 (mtmt) REVERT: A 353 ASP cc_start: 0.8353 (t0) cc_final: 0.8042 (t0) REVERT: A 356 LYS cc_start: 0.8495 (mmtt) cc_final: 0.8229 (mptt) REVERT: A 495 MET cc_start: 0.8324 (ppp) cc_final: 0.8064 (ppp) REVERT: A 518 PHE cc_start: 0.7997 (t80) cc_final: 0.7752 (t80) REVERT: A 610 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7728 (mt-10) REVERT: A 628 ASP cc_start: 0.8210 (t0) cc_final: 0.7874 (t0) REVERT: A 661 ARG cc_start: 0.7348 (mtp85) cc_final: 0.7036 (mtp85) REVERT: A 926 GLN cc_start: 0.7565 (mp10) cc_final: 0.7125 (mm-40) REVERT: A 959 LYS cc_start: 0.7010 (mmpt) cc_final: 0.6495 (mttp) REVERT: A 977 GLU cc_start: 0.7935 (mp0) cc_final: 0.7595 (mp0) REVERT: A 988 TYR cc_start: 0.7784 (t80) cc_final: 0.7544 (t80) REVERT: A 1170 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8510 (mt-10) REVERT: A 1188 LYS cc_start: 0.8538 (mttt) cc_final: 0.8286 (mmmt) REVERT: A 1213 MET cc_start: 0.8779 (mtp) cc_final: 0.8457 (mtm) REVERT: A 1263 LYS cc_start: 0.8213 (tttt) cc_final: 0.7647 (mtmt) REVERT: A 1294 TYR cc_start: 0.8301 (t80) cc_final: 0.7196 (t80) REVERT: A 1303 ARG cc_start: 0.6898 (mmm160) cc_final: 0.6585 (mmm160) REVERT: A 1307 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7197 (mt-10) REVERT: A 1327 PHE cc_start: 0.7627 (m-10) cc_final: 0.7411 (m-80) REVERT: A 1332 ASP cc_start: 0.8274 (m-30) cc_final: 0.7831 (t0) outliers start: 19 outliers final: 13 residues processed: 132 average time/residue: 0.1439 time to fit residues: 25.6441 Evaluate side-chains 124 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1280 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 54 optimal weight: 0.0770 chunk 120 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 GLN A 726 ASN A1254 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.157762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.105202 restraints weight = 16972.771| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.52 r_work: 0.3149 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 12122 Z= 0.122 Angle : 0.488 16.548 16857 Z= 0.263 Chirality : 0.037 0.271 1941 Planarity : 0.003 0.052 1735 Dihedral : 18.686 153.785 2843 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.57 % Favored : 97.34 % Rotamer: Outliers : 1.58 % Allowed : 11.74 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.25), residues: 1128 helix: 1.45 (0.22), residues: 604 sheet: -0.21 (0.48), residues: 110 loop : -0.15 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 691 TYR 0.011 0.001 TYR A 155 PHE 0.020 0.001 PHE A1327 TRP 0.006 0.001 TRP A 476 HIS 0.004 0.001 HIS A 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (12122) covalent geometry : angle 0.48758 / 0.26 (16857) hydrogen bonds : bond 0.04043 / 2.62 ( 558) hydrogen bonds : angle 4.43951 / 3.18 ( 1540) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8265 (tttt) cc_final: 0.7877 (tptt) REVERT: A 84 GLU cc_start: 0.8050 (tt0) cc_final: 0.7683 (tp30) REVERT: A 147 ASP cc_start: 0.8055 (m-30) cc_final: 0.7741 (p0) REVERT: A 202 ASN cc_start: 0.8047 (t0) cc_final: 0.7683 (p0) REVERT: A 314 LYS cc_start: 0.8479 (mttt) cc_final: 0.7834 (mtmt) REVERT: A 339 VAL cc_start: 0.8025 (p) cc_final: 0.7798 (p) REVERT: A 353 ASP cc_start: 0.8347 (t0) cc_final: 0.8030 (t0) REVERT: A 356 LYS cc_start: 0.8503 (mmtt) cc_final: 0.8250 (mptt) REVERT: A 534 MET cc_start: 0.3429 (OUTLIER) cc_final: 0.2996 (ptm) REVERT: A 610 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7676 (mt-10) REVERT: A 661 ARG cc_start: 0.7319 (mtp85) cc_final: 0.7013 (mtp85) REVERT: A 926 GLN cc_start: 0.7590 (mp10) cc_final: 0.7153 (mm-40) REVERT: A 959 LYS cc_start: 0.6973 (mmpt) cc_final: 0.6458 (mttp) REVERT: A 977 GLU cc_start: 0.7918 (mp0) cc_final: 0.7603 (mp0) REVERT: A 988 TYR cc_start: 0.7717 (t80) cc_final: 0.7487 (t80) REVERT: A 1129 LYS cc_start: 0.9135 (mttt) cc_final: 0.8696 (mmmt) REVERT: A 1170 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8466 (mt-10) REVERT: A 1188 LYS cc_start: 0.8495 (mttt) cc_final: 0.8226 (mmmt) REVERT: A 1213 MET cc_start: 0.8764 (mtp) cc_final: 0.8464 (mtm) REVERT: A 1258 PHE cc_start: 0.7396 (t80) cc_final: 0.7059 (t80) REVERT: A 1263 LYS cc_start: 0.8168 (tttt) cc_final: 0.7620 (mtmt) REVERT: A 1307 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7368 (mt-10) REVERT: A 1332 ASP cc_start: 0.8269 (m-30) cc_final: 0.7814 (t0) outliers start: 16 outliers final: 10 residues processed: 130 average time/residue: 0.1459 time to fit residues: 25.5124 Evaluate side-chains 120 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1160 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 18 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 108 optimal weight: 0.0000 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 GLN ** A1254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.157156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.104525 restraints weight = 16899.170| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.49 r_work: 0.3136 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12122 Z= 0.143 Angle : 0.495 12.729 16857 Z= 0.268 Chirality : 0.038 0.269 1941 Planarity : 0.003 0.051 1735 Dihedral : 18.648 153.749 2843 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.75 % Favored : 97.16 % Rotamer: Outliers : 1.38 % Allowed : 11.64 % Favored : 86.98 % 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: 0.99 (0.25), residues: 1128 helix: 1.47 (0.22), residues: 604 sheet: -0.22 (0.48), residues: 110 loop : -0.18 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 671 TYR 0.013 0.001 TYR A 450 PHE 0.019 0.001 PHE A1327 TRP 0.005 0.001 TRP A 476 HIS 0.006 0.001 HIS A1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (12122) covalent geometry : angle 0.49513 / 0.27 (16857) hydrogen bonds : bond 0.04051 / 2.65 ( 558) hydrogen bonds : angle 4.41262 / 3.15 ( 1540) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8314 (tttt) cc_final: 0.7929 (tptt) REVERT: A 84 GLU cc_start: 0.8056 (tt0) cc_final: 0.7630 (tp30) REVERT: A 147 ASP cc_start: 0.8090 (m-30) cc_final: 0.7799 (p0) REVERT: A 196 PHE cc_start: 0.7645 (m-80) cc_final: 0.7238 (m-80) REVERT: A 202 ASN cc_start: 0.8088 (t0) cc_final: 0.7728 (p0) REVERT: A 314 LYS cc_start: 0.8472 (mttt) cc_final: 0.7868 (mtmt) REVERT: A 339 VAL cc_start: 0.8025 (p) cc_final: 0.7802 (p) REVERT: A 353 ASP cc_start: 0.8356 (t0) cc_final: 0.8021 (t0) REVERT: A 356 LYS cc_start: 0.8516 (mmtt) cc_final: 0.8255 (mptt) REVERT: A 495 MET cc_start: 0.8270 (ppp) cc_final: 0.7948 (ppp) REVERT: A 534 MET cc_start: 0.3486 (OUTLIER) cc_final: 0.3030 (ptm) REVERT: A 610 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7707 (mt-10) REVERT: A 661 ARG cc_start: 0.7249 (mtp85) cc_final: 0.6954 (mtp85) REVERT: A 926 GLN cc_start: 0.7657 (mp10) cc_final: 0.7203 (mm-40) REVERT: A 959 LYS cc_start: 0.6973 (mmpt) cc_final: 0.6466 (mttp) REVERT: A 977 GLU cc_start: 0.7955 (mp0) cc_final: 0.7667 (mp0) REVERT: A 988 TYR cc_start: 0.7754 (t80) cc_final: 0.7499 (t80) REVERT: A 1129 LYS cc_start: 0.9099 (mttt) cc_final: 0.8708 (mmmt) REVERT: A 1170 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8471 (mt-10) REVERT: A 1188 LYS cc_start: 0.8502 (mttt) cc_final: 0.8227 (mmmt) REVERT: A 1263 LYS cc_start: 0.8163 (tttt) cc_final: 0.7598 (mtmt) REVERT: A 1298 ARG cc_start: 0.7768 (tpp-160) cc_final: 0.7566 (tpp-160) REVERT: A 1307 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7312 (mt-10) REVERT: A 1327 PHE cc_start: 0.7583 (m-80) cc_final: 0.7379 (m-80) REVERT: A 1332 ASP cc_start: 0.8298 (m-30) cc_final: 0.7843 (t0) outliers start: 14 outliers final: 11 residues processed: 128 average time/residue: 0.1472 time to fit residues: 25.4177 Evaluate side-chains 126 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 936 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 44 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 71 optimal weight: 0.0670 chunk 54 optimal weight: 6.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 GLN A 674 GLN ** A1254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.157791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.105193 restraints weight = 16904.821| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.51 r_work: 0.3147 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12122 Z= 0.123 Angle : 0.483 11.927 16857 Z= 0.262 Chirality : 0.037 0.266 1941 Planarity : 0.003 0.050 1735 Dihedral : 18.633 154.166 2843 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.57 % Favored : 97.34 % Rotamer: Outliers : 1.28 % Allowed : 12.03 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.25), residues: 1128 helix: 1.58 (0.22), residues: 604 sheet: -0.19 (0.49), residues: 107 loop : -0.19 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 671 TYR 0.023 0.001 TYR A 286 PHE 0.017 0.001 PHE A1258 TRP 0.005 0.001 TRP A 476 HIS 0.006 0.001 HIS A1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (12122) covalent geometry : angle 0.48284 / 0.26 (16857) hydrogen bonds : bond 0.03862 / 2.50 ( 558) hydrogen bonds : angle 4.37731 / 3.12 ( 1540) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8313 (tttt) cc_final: 0.7928 (tptt) REVERT: A 84 GLU cc_start: 0.8050 (tt0) cc_final: 0.7642 (tp30) REVERT: A 147 ASP cc_start: 0.8081 (m-30) cc_final: 0.7792 (p0) REVERT: A 196 PHE cc_start: 0.7648 (m-80) cc_final: 0.7214 (m-80) REVERT: A 202 ASN cc_start: 0.8081 (t0) cc_final: 0.7747 (p0) REVERT: A 314 LYS cc_start: 0.8445 (mttt) cc_final: 0.7849 (mtmt) REVERT: A 353 ASP cc_start: 0.8368 (t0) cc_final: 0.8074 (t0) REVERT: A 356 LYS cc_start: 0.8510 (mmtt) cc_final: 0.8253 (mptt) REVERT: A 495 MET cc_start: 0.8240 (ppp) cc_final: 0.7904 (ppp) REVERT: A 534 MET cc_start: 0.3625 (OUTLIER) cc_final: 0.3132 (ptm) REVERT: A 610 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7751 (mt-10) REVERT: A 661 ARG cc_start: 0.7260 (mtp85) cc_final: 0.6974 (mtp85) REVERT: A 926 GLN cc_start: 0.7599 (mp10) cc_final: 0.7137 (mm-40) REVERT: A 959 LYS cc_start: 0.7015 (mmpt) cc_final: 0.6364 (mttp) REVERT: A 977 GLU cc_start: 0.7966 (mp0) cc_final: 0.7665 (mp0) REVERT: A 988 TYR cc_start: 0.7722 (t80) cc_final: 0.7479 (t80) REVERT: A 1129 LYS cc_start: 0.9095 (mttt) cc_final: 0.8704 (mmmt) REVERT: A 1170 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8481 (mt-10) REVERT: A 1188 LYS cc_start: 0.8480 (mttt) cc_final: 0.8210 (mmmt) REVERT: A 1263 LYS cc_start: 0.8174 (tttt) cc_final: 0.7616 (mtmt) REVERT: A 1303 ARG cc_start: 0.6953 (mmm160) cc_final: 0.6477 (mmm160) REVERT: A 1307 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7140 (mt-10) REVERT: A 1332 ASP cc_start: 0.8288 (m-30) cc_final: 0.7835 (t0) outliers start: 13 outliers final: 10 residues processed: 132 average time/residue: 0.1551 time to fit residues: 27.3007 Evaluate side-chains 124 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 936 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 53 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 78 optimal weight: 0.0000 chunk 84 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN A 194 GLN ** A1254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.159358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.107187 restraints weight = 16810.448| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.50 r_work: 0.3173 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12122 Z= 0.102 Angle : 0.474 10.431 16857 Z= 0.257 Chirality : 0.036 0.262 1941 Planarity : 0.003 0.051 1735 Dihedral : 18.617 154.752 2843 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.66 % Favored : 97.25 % Rotamer: Outliers : 1.08 % Allowed : 12.33 % Favored : 86.59 % 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: 1.28 (0.25), residues: 1128 helix: 1.71 (0.22), residues: 603 sheet: 0.61 (0.54), residues: 87 loop : -0.25 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 671 TYR 0.017 0.001 TYR A 286 PHE 0.014 0.001 PHE A 693 TRP 0.005 0.001 TRP A 476 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (12122) covalent geometry : angle 0.47425 / 0.26 (16857) hydrogen bonds : bond 0.03571 / 2.26 ( 558) hydrogen bonds : angle 4.26993 / 3.04 ( 1540) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8277 (tttt) cc_final: 0.7895 (tptt) REVERT: A 84 GLU cc_start: 0.8074 (tt0) cc_final: 0.7722 (tp30) REVERT: A 147 ASP cc_start: 0.8066 (m-30) cc_final: 0.7802 (p0) REVERT: A 202 ASN cc_start: 0.8061 (t0) cc_final: 0.7728 (p0) REVERT: A 286 TYR cc_start: 0.6793 (m-10) cc_final: 0.6567 (m-10) REVERT: A 314 LYS cc_start: 0.8389 (mttt) cc_final: 0.7795 (mtmt) REVERT: A 353 ASP cc_start: 0.8368 (t0) cc_final: 0.8029 (t0) REVERT: A 356 LYS cc_start: 0.8487 (mmtt) cc_final: 0.8221 (mmtp) REVERT: A 495 MET cc_start: 0.8237 (ppp) cc_final: 0.7943 (ppp) REVERT: A 534 MET cc_start: 0.3628 (OUTLIER) cc_final: 0.3057 (ptm) REVERT: A 610 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7741 (mt-10) REVERT: A 661 ARG cc_start: 0.7260 (mtp85) cc_final: 0.7000 (mtp85) REVERT: A 926 GLN cc_start: 0.7606 (mp10) cc_final: 0.7174 (mm-40) REVERT: A 959 LYS cc_start: 0.6979 (mmpt) cc_final: 0.6361 (mttp) REVERT: A 977 GLU cc_start: 0.7945 (mp0) cc_final: 0.7649 (mp0) REVERT: A 988 TYR cc_start: 0.7683 (t80) cc_final: 0.7472 (t80) REVERT: A 1129 LYS cc_start: 0.9098 (mttt) cc_final: 0.8714 (mmmt) REVERT: A 1170 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8439 (mt-10) REVERT: A 1188 LYS cc_start: 0.8460 (mttt) cc_final: 0.8186 (mmmt) REVERT: A 1211 LYS cc_start: 0.8698 (mttt) cc_final: 0.8361 (mtmt) REVERT: A 1263 LYS cc_start: 0.8143 (tttt) cc_final: 0.7607 (mtmt) REVERT: A 1303 ARG cc_start: 0.7069 (mmm160) cc_final: 0.6610 (mmm160) REVERT: A 1307 GLU cc_start: 0.7495 (mt-10) cc_final: 0.6995 (mt-10) REVERT: A 1332 ASP cc_start: 0.8266 (m-30) cc_final: 0.7815 (t0) outliers start: 11 outliers final: 9 residues processed: 128 average time/residue: 0.1411 time to fit residues: 24.3034 Evaluate side-chains 121 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 936 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 121 optimal weight: 30.0000 chunk 22 optimal weight: 5.9990 chunk 50 optimal weight: 0.0040 chunk 116 optimal weight: 10.9990 chunk 96 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 113 optimal weight: 50.0000 chunk 0 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN A 194 GLN A1261 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.156468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.103891 restraints weight = 16878.071| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.48 r_work: 0.3127 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12122 Z= 0.172 Angle : 0.527 9.517 16857 Z= 0.281 Chirality : 0.039 0.265 1941 Planarity : 0.004 0.048 1735 Dihedral : 18.586 153.796 2843 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.39 % Favored : 97.52 % Rotamer: Outliers : 1.18 % Allowed : 12.62 % Favored : 86.19 % 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: 1.12 (0.25), residues: 1128 helix: 1.63 (0.22), residues: 605 sheet: -0.04 (0.50), residues: 101 loop : -0.28 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 671 TYR 0.022 0.001 TYR A 286 PHE 0.030 0.002 PHE A 682 TRP 0.005 0.001 TRP A 476 HIS 0.006 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (12122) covalent geometry : angle 0.52676 / 0.28 (16857) hydrogen bonds : bond 0.04149 / 2.72 ( 558) hydrogen bonds : angle 4.34717 / 3.11 ( 1540) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8323 (tttt) cc_final: 0.7965 (tptt) REVERT: A 84 GLU cc_start: 0.8108 (tt0) cc_final: 0.7698 (tp30) REVERT: A 147 ASP cc_start: 0.8075 (m-30) cc_final: 0.7797 (p0) REVERT: A 196 PHE cc_start: 0.7655 (m-80) cc_final: 0.7145 (m-80) REVERT: A 202 ASN cc_start: 0.8055 (t0) cc_final: 0.7748 (p0) REVERT: A 314 LYS cc_start: 0.8482 (mttt) cc_final: 0.7882 (mtmt) REVERT: A 353 ASP cc_start: 0.8379 (t0) cc_final: 0.8055 (t0) REVERT: A 356 LYS cc_start: 0.8518 (mmtt) cc_final: 0.8283 (mptt) REVERT: A 534 MET cc_start: 0.3653 (OUTLIER) cc_final: 0.3101 (ptm) REVERT: A 610 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7816 (mt-10) REVERT: A 661 ARG cc_start: 0.7308 (mtp85) cc_final: 0.7033 (mtp85) REVERT: A 707 ASP cc_start: 0.8288 (m-30) cc_final: 0.7975 (m-30) REVERT: A 926 GLN cc_start: 0.7758 (mp10) cc_final: 0.7324 (mm-40) REVERT: A 959 LYS cc_start: 0.7001 (mmpt) cc_final: 0.6379 (mttp) REVERT: A 977 GLU cc_start: 0.8010 (mp0) cc_final: 0.7725 (mp0) REVERT: A 988 TYR cc_start: 0.7882 (t80) cc_final: 0.7614 (t80) REVERT: A 1129 LYS cc_start: 0.9106 (mttt) cc_final: 0.8704 (mmmt) REVERT: A 1170 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8492 (mt-10) REVERT: A 1188 LYS cc_start: 0.8508 (mttt) cc_final: 0.8238 (mmmt) REVERT: A 1258 PHE cc_start: 0.7650 (t80) cc_final: 0.7360 (t80) REVERT: A 1303 ARG cc_start: 0.7101 (mmm160) cc_final: 0.6734 (mmm160) REVERT: A 1307 GLU cc_start: 0.7456 (mt-10) cc_final: 0.6944 (mt-10) REVERT: A 1332 ASP cc_start: 0.8297 (m-30) cc_final: 0.7845 (t0) outliers start: 12 outliers final: 9 residues processed: 128 average time/residue: 0.1425 time to fit residues: 24.7095 Evaluate side-chains 122 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 936 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 8 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 31 optimal weight: 0.0070 chunk 122 optimal weight: 30.0000 chunk 102 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 121 optimal weight: 30.0000 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 GLN ** A1254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.158156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.105600 restraints weight = 16963.323| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.51 r_work: 0.3152 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12122 Z= 0.116 Angle : 0.494 10.814 16857 Z= 0.267 Chirality : 0.037 0.264 1941 Planarity : 0.003 0.050 1735 Dihedral : 18.613 154.485 2843 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.75 % Favored : 97.16 % Rotamer: Outliers : 1.18 % Allowed : 12.72 % Favored : 86.09 % 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: 1.23 (0.25), residues: 1128 helix: 1.72 (0.22), residues: 603 sheet: 0.03 (0.51), residues: 101 loop : -0.23 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 671 TYR 0.024 0.001 TYR A 286 PHE 0.026 0.001 PHE A 682 TRP 0.006 0.001 TRP A 476 HIS 0.005 0.001 HIS A1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (12122) covalent geometry : angle 0.49404 / 0.27 (16857) hydrogen bonds : bond 0.03824 / 2.44 ( 558) hydrogen bonds : angle 4.29482 / 3.07 ( 1540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2767.88 seconds wall clock time: 48 minutes 19.17 seconds (2899.17 seconds total)