Starting phenix.real_space_refine on Wed Aug 5 22:27:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eda_47942/08_2026/9eda_47942.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eda_47942/08_2026/9eda_47942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9eda_47942/08_2026/9eda_47942.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eda_47942/08_2026/9eda_47942.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eda_47942/08_2026/9eda_47942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eda_47942/08_2026/9eda_47942.map" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 138 5.49 5 S 17 5.16 5 C 7190 2.51 5 N 2110 2.21 5 O 2624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 12079 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1995 Classifications: {'RNA': 93} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 50, 'rna3p_pyr': 31} Link IDs: {'rna2p': 12, 'rna3p': 80} Chain: "C" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 346 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "D" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 332 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "c" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 239 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 9166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9166 Classifications: {'peptide': 1150} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 32, 'TRANS': 1117} Chain breaks: 4 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 12, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 122 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.60, per 1000 atoms: 0.22 Number of scatterers: 12079 At special positions: 0 Unit cell: (85.8196, 136.645, 124.147, 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 17 16.00 P 138 15.00 O 2624 8.00 N 2110 7.00 C 7190 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: 0.93 Conformation dependent library (CDL) restraints added in 396.9 milliseconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2188 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 54.4% alpha, 7.6% beta 51 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 59 through 95 removed outlier: 5.046A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.778A 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: 3.537A 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 229 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.556A pdb=" N PHE A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 286 through 304 removed outlier: 3.784A pdb=" N ASP A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 347 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: 3.724A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.129A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 4.017A 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: 3.984A pdb=" N MET A 495 " --> pdb=" O PHE A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 556 removed outlier: 3.684A pdb=" N PHE A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 removed outlier: 4.194A pdb=" N ARG A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) 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 663 through 668 removed outlier: 3.700A pdb=" N ILE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 703 through 714 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.582A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 940 Processing helix chain 'A' and resid 959 through 969 removed outlier: 3.822A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1001 Processing helix chain 'A' and resid 1078 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.685A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1186 Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1229 through 1240 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1263 through 1280 removed outlier: 4.335A pdb=" N ASP A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1312 Processing helix chain 'A' and resid 1313 through 1316 Processing helix chain 'A' and resid 1341 through 1344 Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 955 through 957 removed outlier: 6.211A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N GLU A 762 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU A 9 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 9.907A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.835A pdb=" N TYR A 529 " --> pdb=" O ALA A 538 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1063 through 1064 removed outlier: 3.967A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1167 Processing sheet with id=AA6, first strand: chain 'A' and resid 1324 through 1326 removed outlier: 3.587A pdb=" N PHE A1324 " --> pdb=" O ILE A1331 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 123 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 3.05 Time building geometry restraints manager: 1.30 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: 2562 1.33 - 1.46: 3593 1.46 - 1.58: 6131 1.58 - 1.70: 274 1.70 - 1.83: 32 Bond restraints: 12592 Sorted by residual: bond pdb=" C3' DC D 7 " pdb=" C2' DC D 7 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.85e+01 bond pdb=" C1' DC C -4 " pdb=" N1 DC C -4 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.34e+01 bond pdb=" C3' DC C -2 " pdb=" C2' DC C -2 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DT D 13 " pdb=" C2' DT D 13 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C5' DC D -1 " pdb=" C4' DC D -1 " ideal model delta sigma weight residual 1.512 1.534 -0.022 7.00e-03 2.04e+04 9.76e+00 ... (remaining 12587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 17078 2.58 - 5.15: 454 5.15 - 7.73: 78 7.73 - 10.31: 17 10.31 - 12.88: 8 Bond angle restraints: 17635 Sorted by residual: angle pdb=" CA LYS A1192 " pdb=" CB LYS A1192 " pdb=" CG LYS A1192 " ideal model delta sigma weight residual 114.10 124.86 -10.76 2.00e+00 2.50e-01 2.89e+01 angle pdb=" N3 DT C -3 " pdb=" C4 DT C -3 " pdb=" O4 DT C -3 " ideal model delta sigma weight residual 119.90 122.82 -2.92 6.00e-01 2.78e+00 2.36e+01 angle pdb=" CA GLN A1364 " pdb=" CB GLN A1364 " pdb=" CG GLN A1364 " ideal model delta sigma weight residual 114.10 123.73 -9.63 2.00e+00 2.50e-01 2.32e+01 angle pdb=" N GLU A 24 " pdb=" CA GLU A 24 " pdb=" C GLU A 24 " ideal model delta sigma weight residual 113.20 107.56 5.64 1.21e+00 6.83e-01 2.18e+01 angle pdb=" CA TYR A 451 " pdb=" CB TYR A 451 " pdb=" CG TYR A 451 " ideal model delta sigma weight residual 113.90 122.29 -8.39 1.80e+00 3.09e-01 2.17e+01 ... (remaining 17630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 6361 18.06 - 36.11: 736 36.11 - 54.17: 306 54.17 - 72.23: 139 72.23 - 90.28: 28 Dihedral angle restraints: 7570 sinusoidal: 4197 harmonic: 3373 Sorted by residual: dihedral pdb=" CA GLU A 627 " pdb=" C GLU A 627 " pdb=" N ASP A 628 " pdb=" CA ASP A 628 " ideal model delta harmonic sigma weight residual 180.00 153.75 26.25 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA PRO A 449 " pdb=" C PRO A 449 " pdb=" N TYR A 450 " pdb=" CA TYR A 450 " ideal model delta harmonic sigma weight residual 180.00 155.55 24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LEU A 625 " pdb=" C LEU A 625 " pdb=" N PHE A 626 " pdb=" CA PHE A 626 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 7567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 1951 0.126 - 0.252: 97 0.252 - 0.378: 2 0.378 - 0.503: 3 0.503 - 0.629: 7 Chirality restraints: 2060 Sorted by residual: chirality pdb=" P DT c 4 " pdb=" OP1 DT c 4 " pdb=" OP2 DT c 4 " pdb=" O5' DT c 4 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.63 2.00e-01 2.50e+01 9.90e+00 chirality pdb=" P DT c 9 " pdb=" OP1 DT c 9 " pdb=" OP2 DT c 9 " pdb=" O5' DT c 9 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.54 2.00e-01 2.50e+01 7.37e+00 chirality pdb=" P DA c 8 " pdb=" OP1 DA c 8 " pdb=" OP2 DA c 8 " pdb=" O5' DA c 8 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.54 2.00e-01 2.50e+01 7.32e+00 ... (remaining 2057 not shown) Planarity restraints: 1751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 655 " -0.480 9.50e-02 1.11e+02 2.15e-01 2.84e+01 pdb=" NE ARG A 655 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 655 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 655 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 655 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 661 " -0.361 9.50e-02 1.11e+02 1.62e-01 1.61e+01 pdb=" NE ARG A 661 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 661 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 661 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 661 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 518 " -0.012 2.00e-02 2.50e+03 2.33e-02 9.53e+00 pdb=" CG PHE A 518 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE A 518 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 518 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE A 518 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 518 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 518 " 0.004 2.00e-02 2.50e+03 ... (remaining 1748 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 892 2.73 - 3.28: 11375 3.28 - 3.82: 21732 3.82 - 4.36: 26854 4.36 - 4.90: 40655 Nonbonded interactions: 101508 Sorted by model distance: nonbonded pdb=" OH TYR A 451 " pdb=" OD2 ASP A 628 " model vdw 2.193 3.040 nonbonded pdb=" O2' A B 47 " pdb=" O LEU A 101 " model vdw 2.207 3.040 nonbonded pdb=" OG SER A 512 " pdb=" OE2 GLU A 617 " model vdw 2.217 3.040 nonbonded pdb=" O ILE A 667 " pdb=" OG1 THR A 678 " model vdw 2.225 3.040 nonbonded pdb=" CG2 VAL A 530 " pdb=" CB PRO A 537 " model vdw 2.241 3.860 ... (remaining 101503 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: 8.570 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 13.420 Find NCS groups from input model: 0.050 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:5.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 12592 Z= 0.375 Angle : 1.036 12.883 17635 Z= 0.669 Chirality : 0.067 0.629 2060 Planarity : 0.009 0.215 1751 Dihedral : 19.256 90.285 5382 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.41 % Allowed : 27.33 % Favored : 72.26 % 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: -1.21 (0.23), residues: 1140 helix: -0.50 (0.20), residues: 560 sheet: -0.30 (0.48), residues: 117 loop : -1.16 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 586 TYR 0.041 0.003 TYR A 271 PHE 0.052 0.003 PHE A 518 TRP 0.024 0.002 TRP A 659 HIS 0.012 0.002 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.38 (12592) covalent geometry : angle 1.03582 / 0.67 (17635) hydrogen bonds : bond 0.14734 / 15.80 ( 567) hydrogen bonds : angle 6.22377 / 8.09 ( 1535) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7204 (mtpp) cc_final: 0.6886 (ptpp) REVERT: A 209 LYS cc_start: 0.8911 (ttmm) cc_final: 0.8536 (tptp) REVERT: A 284 ASP cc_start: 0.8286 (p0) cc_final: 0.7728 (t0) REVERT: A 288 ASP cc_start: 0.8716 (m-30) cc_final: 0.8301 (t0) REVERT: A 383 MET cc_start: 0.7425 (mtp) cc_final: 0.7040 (mtm) REVERT: A 599 LYS cc_start: 0.8904 (mptt) cc_final: 0.8596 (mmtm) REVERT: A 618 ASP cc_start: 0.8019 (t0) cc_final: 0.7609 (t0) REVERT: A 702 LEU cc_start: 0.6082 (mm) cc_final: 0.5767 (mm) REVERT: A 762 GLU cc_start: 0.7398 (pt0) cc_final: 0.6698 (tt0) REVERT: A 1151 LYS cc_start: 0.8043 (ttmm) cc_final: 0.7777 (mttm) REVERT: A 1170 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8091 (mt-10) REVERT: A 1176 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8104 (tmmt) REVERT: A 1177 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8142 (t0) REVERT: A 1258 PHE cc_start: 0.6027 (t80) cc_final: 0.5687 (t80) REVERT: A 1261 GLN cc_start: 0.8830 (pt0) cc_final: 0.8570 (pt0) outliers start: 4 outliers final: 1 residues processed: 121 average time/residue: 0.5353 time to fit residues: 70.8965 Evaluate side-chains 94 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 1177 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.3980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.0050 overall best weight: 0.3732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN A 709 GLN A1364 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.147025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.108113 restraints weight = 21870.506| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.30 r_work: 0.3401 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12592 Z= 0.143 Angle : 0.601 8.908 17635 Z= 0.335 Chirality : 0.040 0.239 2060 Planarity : 0.004 0.043 1751 Dihedral : 19.207 89.243 3126 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.68 % Allowed : 23.23 % Favored : 73.08 % 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: -0.44 (0.24), residues: 1140 helix: 0.37 (0.21), residues: 569 sheet: -0.40 (0.48), residues: 117 loop : -1.00 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 586 TYR 0.033 0.002 TYR A 451 PHE 0.015 0.002 PHE A 518 TRP 0.014 0.001 TRP A1074 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (12592) covalent geometry : angle 0.60050 / 0.34 (17635) hydrogen bonds : bond 0.05030 / 5.45 ( 567) hydrogen bonds : angle 4.66076 / 5.93 ( 1535) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.392 Fit side-chains REVERT: A 26 LYS cc_start: 0.6954 (mtpp) cc_final: 0.6691 (ptpp) REVERT: A 118 ILE cc_start: 0.7583 (mm) cc_final: 0.7374 (mm) REVERT: A 122 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7427 (mp) REVERT: A 161 MET cc_start: 0.8036 (mtt) cc_final: 0.7450 (mtt) REVERT: A 209 LYS cc_start: 0.8906 (ttmm) cc_final: 0.8493 (tptp) REVERT: A 288 ASP cc_start: 0.8771 (m-30) cc_final: 0.8423 (t0) REVERT: A 383 MET cc_start: 0.7542 (mtp) cc_final: 0.6981 (mtm) REVERT: A 599 LYS cc_start: 0.8856 (mptt) cc_final: 0.8593 (mmtm) REVERT: A 618 ASP cc_start: 0.8216 (t0) cc_final: 0.7726 (t70) REVERT: A 648 MET cc_start: 0.7739 (mtm) cc_final: 0.7504 (mtt) REVERT: A 702 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5653 (mm) REVERT: A 762 GLU cc_start: 0.7343 (pt0) cc_final: 0.6721 (tt0) REVERT: A 1151 LYS cc_start: 0.8248 (ttmm) cc_final: 0.7883 (mttp) REVERT: A 1170 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8236 (mt-10) REVERT: A 1176 LYS cc_start: 0.8606 (ttmm) cc_final: 0.8066 (tmmt) REVERT: A 1261 GLN cc_start: 0.8823 (pt0) cc_final: 0.8556 (pt0) outliers start: 36 outliers final: 9 residues processed: 140 average time/residue: 0.4460 time to fit residues: 69.3356 Evaluate side-chains 100 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1339 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 35 optimal weight: 8.9990 chunk 53 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 29 optimal weight: 0.0970 chunk 49 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 ASN A1177 ASN A1256 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.143596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.103836 restraints weight = 21834.154| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.26 r_work: 0.3327 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12592 Z= 0.152 Angle : 0.575 8.236 17635 Z= 0.317 Chirality : 0.040 0.265 2060 Planarity : 0.004 0.038 1751 Dihedral : 19.291 90.284 3122 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.89 % Allowed : 22.52 % Favored : 73.59 % 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: 0.01 (0.24), residues: 1140 helix: 0.77 (0.21), residues: 570 sheet: -0.35 (0.49), residues: 117 loop : -0.78 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 976 TYR 0.021 0.002 TYR A 271 PHE 0.016 0.002 PHE A1258 TRP 0.009 0.001 TRP A1074 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (12592) covalent geometry : angle 0.57451 / 0.32 (17635) hydrogen bonds : bond 0.04347 / 4.60 ( 567) hydrogen bonds : angle 4.42775 / 5.72 ( 1535) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 101 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.6844 (mtpp) cc_final: 0.6532 (ptpp) REVERT: A 103 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6228 (pt0) REVERT: A 122 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7889 (tp) REVERT: A 209 LYS cc_start: 0.8900 (ttmm) cc_final: 0.8538 (tptp) REVERT: A 288 ASP cc_start: 0.8765 (m-30) cc_final: 0.8468 (t0) REVERT: A 290 PHE cc_start: 0.7784 (m-80) cc_final: 0.7529 (m-80) REVERT: A 383 MET cc_start: 0.7568 (mtp) cc_final: 0.7042 (mtm) REVERT: A 618 ASP cc_start: 0.8389 (t0) cc_final: 0.7811 (t0) REVERT: A 762 GLU cc_start: 0.7320 (pt0) cc_final: 0.6788 (tt0) REVERT: A 976 ARG cc_start: 0.7955 (ptp90) cc_final: 0.7089 (ptp90) REVERT: A 1170 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8289 (mt-10) REVERT: A 1176 LYS cc_start: 0.8564 (ttmm) cc_final: 0.8110 (tmmt) REVERT: A 1256 GLN cc_start: 0.6671 (OUTLIER) cc_final: 0.6325 (pp30) REVERT: A 1261 GLN cc_start: 0.8807 (pt0) cc_final: 0.8584 (pt0) REVERT: A 1307 GLU cc_start: 0.6566 (tt0) cc_final: 0.6085 (pt0) REVERT: A 1357 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7167 (pt0) outliers start: 38 outliers final: 18 residues processed: 131 average time/residue: 0.4781 time to fit residues: 69.5174 Evaluate side-chains 108 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 652 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1256 GLN Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1357 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 101 optimal weight: 0.7980 chunk 29 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 116 optimal weight: 0.1980 chunk 110 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 113 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1177 ASN A1262 HIS A1364 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.142631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.102748 restraints weight = 21674.965| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.26 r_work: 0.3316 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12592 Z= 0.136 Angle : 0.531 6.720 17635 Z= 0.296 Chirality : 0.038 0.227 2060 Planarity : 0.003 0.031 1751 Dihedral : 19.296 90.543 3122 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.68 % Allowed : 22.62 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.25), residues: 1140 helix: 0.96 (0.22), residues: 573 sheet: -0.30 (0.49), residues: 117 loop : -0.64 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 307 TYR 0.015 0.001 TYR A 521 PHE 0.019 0.002 PHE A 518 TRP 0.007 0.001 TRP A1074 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (12592) covalent geometry : angle 0.53116 / 0.30 (17635) hydrogen bonds : bond 0.04077 / 4.32 ( 567) hydrogen bonds : angle 4.26039 / 5.50 ( 1535) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.6849 (mtpp) cc_final: 0.6551 (ptpp) REVERT: A 103 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6187 (pt0) REVERT: A 118 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7828 (mm) REVERT: A 122 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7909 (tp) REVERT: A 209 LYS cc_start: 0.8871 (ttmm) cc_final: 0.8519 (tptp) REVERT: A 269 ASP cc_start: 0.7830 (p0) cc_final: 0.7378 (p0) REVERT: A 288 ASP cc_start: 0.8745 (m-30) cc_final: 0.8462 (t0) REVERT: A 290 PHE cc_start: 0.7793 (m-80) cc_final: 0.7564 (m-80) REVERT: A 341 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8267 (tm-30) REVERT: A 383 MET cc_start: 0.7533 (mtp) cc_final: 0.6954 (mtm) REVERT: A 599 LYS cc_start: 0.8872 (mptt) cc_final: 0.8650 (mmtt) REVERT: A 618 ASP cc_start: 0.8404 (t0) cc_final: 0.7873 (t0) REVERT: A 762 GLU cc_start: 0.7294 (pt0) cc_final: 0.6792 (tt0) REVERT: A 976 ARG cc_start: 0.7838 (ptp90) cc_final: 0.7277 (ptp90) REVERT: A 1177 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.7837 (p0) REVERT: A 1307 GLU cc_start: 0.6562 (tt0) cc_final: 0.6094 (pt0) REVERT: A 1357 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7225 (pt0) outliers start: 36 outliers final: 16 residues processed: 121 average time/residue: 0.4250 time to fit residues: 57.1155 Evaluate side-chains 111 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 652 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1177 ASN Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1357 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 54 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.139631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.099125 restraints weight = 21663.934| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.24 r_work: 0.3252 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12592 Z= 0.188 Angle : 0.563 6.777 17635 Z= 0.312 Chirality : 0.040 0.228 2060 Planarity : 0.004 0.086 1751 Dihedral : 19.326 91.420 3122 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.71 % Allowed : 21.90 % Favored : 73.39 % 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: 0.23 (0.25), residues: 1140 helix: 0.89 (0.22), residues: 576 sheet: 0.56 (0.57), residues: 82 loop : -0.77 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 221 TYR 0.017 0.002 TYR A 155 PHE 0.021 0.002 PHE A1105 TRP 0.011 0.001 TRP A1074 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (12592) covalent geometry : angle 0.56297 / 0.31 (17635) hydrogen bonds : bond 0.04349 / 4.55 ( 567) hydrogen bonds : angle 4.28090 / 5.55 ( 1535) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 92 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.6944 (mtpp) cc_final: 0.6578 (ptpp) REVERT: A 103 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6562 (pt0) REVERT: A 118 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8210 (mm) REVERT: A 209 LYS cc_start: 0.8825 (ttmm) cc_final: 0.8540 (tptp) REVERT: A 288 ASP cc_start: 0.8771 (m-30) cc_final: 0.8512 (t0) REVERT: A 290 PHE cc_start: 0.7881 (m-80) cc_final: 0.7650 (m-80) REVERT: A 331 ASP cc_start: 0.8904 (t0) cc_final: 0.8617 (t0) REVERT: A 341 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8365 (tm-30) REVERT: A 404 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.7995 (p) REVERT: A 434 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8089 (ttpt) REVERT: A 599 LYS cc_start: 0.8884 (mptt) cc_final: 0.8634 (mmtm) REVERT: A 618 ASP cc_start: 0.8503 (t0) cc_final: 0.8000 (t0) REVERT: A 642 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7641 (tp) REVERT: A 681 ASP cc_start: 0.8622 (t70) cc_final: 0.8343 (p0) REVERT: A 762 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6980 (tt0) REVERT: A 976 ARG cc_start: 0.7891 (ptp90) cc_final: 0.7372 (ptp90) REVERT: A 1177 ASN cc_start: 0.8760 (OUTLIER) cc_final: 0.8022 (p0) REVERT: A 1307 GLU cc_start: 0.6639 (tt0) cc_final: 0.6280 (pt0) outliers start: 46 outliers final: 18 residues processed: 123 average time/residue: 0.3914 time to fit residues: 53.6987 Evaluate side-chains 115 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 652 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1177 ASN Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1357 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 11 optimal weight: 4.9990 chunk 118 optimal weight: 0.3980 chunk 49 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.140253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.099850 restraints weight = 21666.973| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.24 r_work: 0.3267 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12592 Z= 0.137 Angle : 0.518 6.619 17635 Z= 0.290 Chirality : 0.038 0.225 2060 Planarity : 0.004 0.087 1751 Dihedral : 19.322 91.359 3122 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.17 % Allowed : 23.23 % Favored : 73.59 % 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: 0.33 (0.25), residues: 1140 helix: 1.05 (0.22), residues: 576 sheet: 0.63 (0.58), residues: 82 loop : -0.84 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 221 TYR 0.013 0.001 TYR A 271 PHE 0.022 0.002 PHE A 518 TRP 0.009 0.001 TRP A1074 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (12592) covalent geometry : angle 0.51821 / 0.29 (17635) hydrogen bonds : bond 0.03946 / 4.13 ( 567) hydrogen bonds : angle 4.19617 / 5.48 ( 1535) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.6965 (mtpp) cc_final: 0.6553 (ptpp) REVERT: A 103 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6502 (pt0) REVERT: A 209 LYS cc_start: 0.8811 (ttmm) cc_final: 0.8504 (tptp) REVERT: A 288 ASP cc_start: 0.8769 (m-30) cc_final: 0.8518 (t0) REVERT: A 290 PHE cc_start: 0.7894 (m-80) cc_final: 0.7656 (m-80) REVERT: A 331 ASP cc_start: 0.8883 (t0) cc_final: 0.8573 (t0) REVERT: A 406 ASP cc_start: 0.8669 (m-30) cc_final: 0.8440 (m-30) REVERT: A 434 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8063 (ttpt) REVERT: A 599 LYS cc_start: 0.8873 (mptt) cc_final: 0.8595 (mmtm) REVERT: A 618 ASP cc_start: 0.8562 (t0) cc_final: 0.8057 (t0) REVERT: A 663 SER cc_start: 0.8774 (p) cc_final: 0.8538 (t) REVERT: A 762 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6909 (tt0) REVERT: A 976 ARG cc_start: 0.7883 (ptp90) cc_final: 0.7355 (ptp90) REVERT: A 1177 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.7890 (p0) REVERT: A 1307 GLU cc_start: 0.6637 (tt0) cc_final: 0.6141 (pt0) outliers start: 31 outliers final: 13 residues processed: 114 average time/residue: 0.4598 time to fit residues: 57.9664 Evaluate side-chains 104 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 652 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1177 ASN Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 92 optimal weight: 0.3980 chunk 101 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.139545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.098843 restraints weight = 21637.214| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.24 r_work: 0.3254 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12592 Z= 0.159 Angle : 0.533 6.621 17635 Z= 0.297 Chirality : 0.039 0.224 2060 Planarity : 0.004 0.048 1751 Dihedral : 19.316 91.676 3122 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.97 % Allowed : 23.54 % Favored : 73.49 % 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: 0.35 (0.25), residues: 1140 helix: 1.06 (0.22), residues: 576 sheet: 0.09 (0.54), residues: 98 loop : -0.72 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 221 TYR 0.015 0.001 TYR A 155 PHE 0.017 0.002 PHE A 606 TRP 0.009 0.001 TRP A1074 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (12592) covalent geometry : angle 0.53342 / 0.30 (17635) hydrogen bonds : bond 0.03981 / 4.15 ( 567) hydrogen bonds : angle 4.21481 / 5.51 ( 1535) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.325 Fit side-chains REVERT: A 26 LYS cc_start: 0.6965 (mtpp) cc_final: 0.6427 (ptpp) REVERT: A 103 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6637 (pt0) REVERT: A 209 LYS cc_start: 0.8818 (ttmm) cc_final: 0.8515 (tptp) REVERT: A 288 ASP cc_start: 0.8778 (m-30) cc_final: 0.8528 (t0) REVERT: A 290 PHE cc_start: 0.7910 (m-80) cc_final: 0.7649 (m-80) REVERT: A 331 ASP cc_start: 0.8884 (t0) cc_final: 0.8496 (t0) REVERT: A 404 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.7981 (p) REVERT: A 406 ASP cc_start: 0.8711 (m-30) cc_final: 0.8433 (m-30) REVERT: A 434 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8084 (ttpt) REVERT: A 479 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8437 (mp0) REVERT: A 599 LYS cc_start: 0.8857 (mptt) cc_final: 0.8567 (mmtm) REVERT: A 618 ASP cc_start: 0.8628 (t0) cc_final: 0.8135 (t0) REVERT: A 642 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7592 (tp) REVERT: A 663 SER cc_start: 0.8775 (p) cc_final: 0.8551 (t) REVERT: A 681 ASP cc_start: 0.8629 (t0) cc_final: 0.8271 (p0) REVERT: A 702 LEU cc_start: 0.5954 (OUTLIER) cc_final: 0.5504 (mm) REVERT: A 709 GLN cc_start: 0.7885 (mm110) cc_final: 0.7684 (mm-40) REVERT: A 762 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6932 (tt0) REVERT: A 976 ARG cc_start: 0.7879 (ptp90) cc_final: 0.7352 (ptp90) REVERT: A 1089 MET cc_start: 0.8772 (ttm) cc_final: 0.8547 (ttm) REVERT: A 1177 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.7951 (p0) REVERT: A 1307 GLU cc_start: 0.6671 (tt0) cc_final: 0.6182 (pt0) outliers start: 29 outliers final: 13 residues processed: 113 average time/residue: 0.4691 time to fit residues: 58.4632 Evaluate side-chains 110 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 652 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1177 ASN Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1338 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 50 optimal weight: 0.6980 chunk 35 optimal weight: 0.0040 chunk 36 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 104 optimal weight: 0.0060 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 83 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.3808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.141411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.100851 restraints weight = 21498.706| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.21 r_work: 0.3298 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12592 Z= 0.120 Angle : 0.505 7.015 17635 Z= 0.283 Chirality : 0.037 0.222 2060 Planarity : 0.004 0.067 1751 Dihedral : 19.292 91.585 3122 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.35 % Allowed : 24.56 % Favored : 73.08 % 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: 0.49 (0.25), residues: 1140 helix: 1.17 (0.22), residues: 577 sheet: 0.17 (0.54), residues: 98 loop : -0.66 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 221 TYR 0.013 0.001 TYR A 271 PHE 0.025 0.001 PHE A 518 TRP 0.007 0.001 TRP A1074 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (12592) covalent geometry : angle 0.50522 / 0.28 (17635) hydrogen bonds : bond 0.03772 / 3.95 ( 567) hydrogen bonds : angle 4.14763 / 5.44 ( 1535) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.6946 (mtpp) cc_final: 0.6440 (ptpp) REVERT: A 103 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6486 (pt0) REVERT: A 209 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8478 (tptp) REVERT: A 288 ASP cc_start: 0.8755 (m-30) cc_final: 0.8510 (t0) REVERT: A 290 PHE cc_start: 0.7902 (m-80) cc_final: 0.7645 (m-80) REVERT: A 331 ASP cc_start: 0.8886 (t0) cc_final: 0.8615 (m-30) REVERT: A 404 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.7876 (p) REVERT: A 434 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8031 (ttpt) REVERT: A 479 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8472 (mp0) REVERT: A 599 LYS cc_start: 0.8848 (mptt) cc_final: 0.8555 (mmtm) REVERT: A 618 ASP cc_start: 0.8606 (t0) cc_final: 0.8114 (t0) REVERT: A 642 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7573 (tp) REVERT: A 702 LEU cc_start: 0.5944 (OUTLIER) cc_final: 0.5509 (mm) REVERT: A 709 GLN cc_start: 0.7959 (mm110) cc_final: 0.7753 (mm-40) REVERT: A 762 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6891 (tt0) REVERT: A 976 ARG cc_start: 0.7895 (ptp90) cc_final: 0.7373 (ptp90) REVERT: A 1307 GLU cc_start: 0.6602 (tt0) cc_final: 0.6120 (pt0) outliers start: 23 outliers final: 10 residues processed: 109 average time/residue: 0.4371 time to fit residues: 52.7420 Evaluate side-chains 99 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 652 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 85 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 102 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.139902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.099128 restraints weight = 21349.430| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.20 r_work: 0.3265 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12592 Z= 0.151 Angle : 0.527 7.066 17635 Z= 0.293 Chirality : 0.038 0.221 2060 Planarity : 0.004 0.073 1751 Dihedral : 19.278 92.181 3122 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.66 % Allowed : 24.16 % Favored : 73.18 % 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: 0.47 (0.25), residues: 1140 helix: 1.18 (0.22), residues: 575 sheet: -0.08 (0.53), residues: 100 loop : -0.63 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 221 TYR 0.015 0.001 TYR A 155 PHE 0.016 0.002 PHE A1105 TRP 0.010 0.001 TRP A1074 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (12592) covalent geometry : angle 0.52666 / 0.29 (17635) hydrogen bonds : bond 0.03926 / 4.08 ( 567) hydrogen bonds : angle 4.14378 / 5.37 ( 1535) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7040 (mtpp) cc_final: 0.6480 (ptpp) REVERT: A 103 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6635 (pt0) REVERT: A 209 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8472 (tptp) REVERT: A 288 ASP cc_start: 0.8756 (m-30) cc_final: 0.8513 (t0) REVERT: A 290 PHE cc_start: 0.7931 (m-80) cc_final: 0.7707 (m-80) REVERT: A 331 ASP cc_start: 0.8906 (t0) cc_final: 0.8641 (m-30) REVERT: A 404 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.7861 (p) REVERT: A 406 ASP cc_start: 0.8700 (m-30) cc_final: 0.8455 (m-30) REVERT: A 479 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8472 (mp0) REVERT: A 599 LYS cc_start: 0.8879 (mptt) cc_final: 0.8523 (mmtm) REVERT: A 642 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7553 (tp) REVERT: A 702 LEU cc_start: 0.6065 (OUTLIER) cc_final: 0.5539 (mm) REVERT: A 708 ILE cc_start: 0.8066 (pt) cc_final: 0.7857 (pp) REVERT: A 762 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6962 (tt0) REVERT: A 976 ARG cc_start: 0.7873 (ptp90) cc_final: 0.7350 (ptp90) REVERT: A 1089 MET cc_start: 0.8763 (ttm) cc_final: 0.8241 (ttm) REVERT: A 1177 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.7913 (p0) REVERT: A 1307 GLU cc_start: 0.6658 (tt0) cc_final: 0.6271 (mt-10) outliers start: 26 outliers final: 11 residues processed: 111 average time/residue: 0.4099 time to fit residues: 50.3885 Evaluate side-chains 102 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 652 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1177 ASN Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1338 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 28 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 709 GLN A1177 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.139741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.098816 restraints weight = 21585.878| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.22 r_work: 0.3264 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12592 Z= 0.154 Angle : 0.539 8.520 17635 Z= 0.298 Chirality : 0.039 0.226 2060 Planarity : 0.004 0.063 1751 Dihedral : 19.287 92.260 3122 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.05 % Allowed : 25.18 % Favored : 72.77 % 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: 0.46 (0.25), residues: 1140 helix: 1.19 (0.22), residues: 576 sheet: -0.12 (0.53), residues: 100 loop : -0.67 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 221 TYR 0.016 0.001 TYR A 639 PHE 0.025 0.002 PHE A 518 TRP 0.010 0.001 TRP A1074 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (12592) covalent geometry : angle 0.53898 / 0.30 (17635) hydrogen bonds : bond 0.03915 / 4.08 ( 567) hydrogen bonds : angle 4.14359 / 5.40 ( 1535) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7115 (mtpp) cc_final: 0.6568 (ptpp) REVERT: A 103 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6654 (pt0) REVERT: A 209 LYS cc_start: 0.8778 (ttmm) cc_final: 0.8472 (tptp) REVERT: A 288 ASP cc_start: 0.8766 (m-30) cc_final: 0.8531 (t0) REVERT: A 290 PHE cc_start: 0.7943 (m-80) cc_final: 0.7715 (m-80) REVERT: A 331 ASP cc_start: 0.8910 (t0) cc_final: 0.8652 (m-30) REVERT: A 404 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.7902 (p) REVERT: A 406 ASP cc_start: 0.8697 (m-30) cc_final: 0.8464 (m-30) REVERT: A 479 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8478 (mp0) REVERT: A 599 LYS cc_start: 0.8876 (mptt) cc_final: 0.8567 (mmtm) REVERT: A 642 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7539 (tp) REVERT: A 681 ASP cc_start: 0.8653 (t0) cc_final: 0.8383 (p0) REVERT: A 702 LEU cc_start: 0.6092 (OUTLIER) cc_final: 0.5600 (mm) REVERT: A 762 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6960 (tt0) REVERT: A 976 ARG cc_start: 0.7885 (ptp90) cc_final: 0.7361 (ptp90) REVERT: A 1177 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8078 (p0) REVERT: A 1262 HIS cc_start: 0.7780 (m90) cc_final: 0.6841 (m-70) REVERT: A 1307 GLU cc_start: 0.6658 (tt0) cc_final: 0.6275 (mt-10) outliers start: 20 outliers final: 12 residues processed: 105 average time/residue: 0.5023 time to fit residues: 57.9685 Evaluate side-chains 104 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 652 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1177 ASN Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1338 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 21 optimal weight: 0.0040 chunk 5 optimal weight: 3.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.139706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.098818 restraints weight = 21559.181| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.22 r_work: 0.3246 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.225 12592 Z= 0.244 Angle : 0.967 61.546 17635 Z= 0.540 Chirality : 0.041 0.603 2060 Planarity : 0.004 0.077 1751 Dihedral : 19.291 92.261 3122 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.84 % Allowed : 25.08 % Favored : 73.08 % Cbeta Deviations : 0.18 % 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: 1140 helix: 1.18 (0.22), residues: 576 sheet: -0.13 (0.53), residues: 100 loop : -0.68 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 653 TYR 0.014 0.001 TYR A 155 PHE 0.016 0.001 PHE A1105 TRP 0.009 0.001 TRP A1074 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.24 (12592) covalent geometry : angle 0.96730 / 0.54 (17635) hydrogen bonds : bond 0.03907 / 4.07 ( 567) hydrogen bonds : angle 4.14298 / 5.40 ( 1535) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3766.29 seconds wall clock time: 64 minutes 59.95 seconds (3899.95 seconds total)