Starting phenix.real_space_refine on Fri Jul 3 04:26:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eda_47942/07_2026/9eda_47942.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eda_47942/07_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_47942/07_2026/9eda_47942.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eda_47942/07_2026/9eda_47942.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eda_47942/07_2026/9eda_47942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eda_47942/07_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-dev-6108/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: 2.21, per 1000 atoms: 0.18 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: 0.74 Conformation dependent library (CDL) restraints added in 357.5 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: 1.36 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: 2.65 Time building geometry restraints manager: 1.07 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: 17154 2.58 - 5.15: 378 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: 2006 0.126 - 0.252: 42 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: 10.880 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: 0.040 Set scattering table: 0.020 Process input model: 11.390 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:5.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.180 ------------------------------------------------------------------------------- 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= 0.370 Angle : 0.997 12.883 17635 Z= 0.629 Chirality : 0.062 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 0.00583 / 0.37 (12592) covalent geometry : angle 0.99677 / 0.63 (17635) hydrogen bonds : bond 0.14734 / 14.29 ( 567) hydrogen bonds : angle 6.22377 / 7.82 ( 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 : 0.315 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: 0.4567 time to fit residues: 60.6968 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 : 0.291 ------------------------------------------------------------------------------- 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: 2.9990 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 = 0.4072 r_free = 0.4072 target = 0.146966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.107989 restraints weight = 21907.974| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.32 r_work: 0.3399 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12592 Z= 0.144 Angle : 0.591 8.629 17635 Z= 0.333 Chirality : 0.040 0.226 2060 Planarity : 0.004 0.037 1751 Dihedral : 19.253 90.658 3126 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.68 % Allowed : 23.03 % Favored : 73.29 % 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: -0.38 (0.24), residues: 1140 helix: 0.43 (0.21), residues: 569 sheet: -0.40 (0.48), residues: 117 loop : -0.98 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 586 TYR 0.034 0.002 TYR A 451 PHE 0.014 0.002 PHE A 606 TRP 0.014 0.001 TRP A1074 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (12592) covalent geometry : angle 0.59082 / 0.33 (17635) hydrogen bonds : bond 0.04660 / 4.61 ( 567) hydrogen bonds : angle 4.60174 / 5.65 ( 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 146 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.6941 (mtpp) cc_final: 0.6689 (ptpp) REVERT: A 118 ILE cc_start: 0.7592 (mm) cc_final: 0.7362 (mm) REVERT: A 122 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7412 (mp) REVERT: A 161 MET cc_start: 0.8062 (mtt) cc_final: 0.7465 (mtt) REVERT: A 209 LYS cc_start: 0.8908 (ttmm) cc_final: 0.8556 (tptp) REVERT: A 288 ASP cc_start: 0.8773 (m-30) cc_final: 0.8447 (t0) REVERT: A 290 PHE cc_start: 0.7857 (m-80) cc_final: 0.7620 (m-80) REVERT: A 383 MET cc_start: 0.7536 (mtp) cc_final: 0.7073 (mtm) REVERT: A 465 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8442 (ttp) REVERT: A 599 LYS cc_start: 0.8847 (mptt) cc_final: 0.8602 (mmtm) REVERT: A 618 ASP cc_start: 0.8262 (t0) cc_final: 0.7769 (t0) REVERT: A 648 MET cc_start: 0.7735 (mtm) cc_final: 0.7515 (mtt) REVERT: A 762 GLU cc_start: 0.7318 (pt0) cc_final: 0.6695 (tt0) REVERT: A 1170 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8248 (mt-10) REVERT: A 1176 LYS cc_start: 0.8593 (ttmm) cc_final: 0.8045 (tmmt) REVERT: A 1261 GLN cc_start: 0.8816 (pt0) cc_final: 0.8550 (pt0) outliers start: 36 outliers final: 11 residues processed: 138 average time/residue: 0.3984 time to fit residues: 60.9085 Evaluate side-chains 106 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 465 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 614 ASP 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 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: 10.0000 chunk 53 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4005 r_free = 0.4005 target = 0.141454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.101121 restraints weight = 21788.492| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.26 r_work: 0.3287 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12592 Z= 0.182 Angle : 0.596 9.865 17635 Z= 0.330 Chirality : 0.041 0.268 2060 Planarity : 0.004 0.040 1751 Dihedral : 19.394 92.296 3122 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.09 % Allowed : 22.21 % 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: -0.11 (0.25), residues: 1140 helix: 0.61 (0.21), residues: 574 sheet: -0.34 (0.49), residues: 117 loop : -0.77 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 403 TYR 0.025 0.002 TYR A 271 PHE 0.020 0.002 PHE A1105 TRP 0.010 0.001 TRP A1074 HIS 0.009 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (12592) covalent geometry : angle 0.59647 / 0.33 (17635) hydrogen bonds : bond 0.04627 / 4.45 ( 567) hydrogen bonds : angle 4.49167 / 5.56 ( 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 142 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.6900 (mtpp) cc_final: 0.6566 (ptpp) REVERT: A 103 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6410 (pt0) REVERT: A 122 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7954 (tp) REVERT: A 209 LYS cc_start: 0.8878 (ttmm) cc_final: 0.8532 (tptp) REVERT: A 288 ASP cc_start: 0.8836 (m-30) cc_final: 0.8525 (t0) REVERT: A 290 PHE cc_start: 0.7814 (m-80) cc_final: 0.7599 (m-80) REVERT: A 331 ASP cc_start: 0.8914 (t0) cc_final: 0.8692 (t0) REVERT: A 383 MET cc_start: 0.7642 (mtp) cc_final: 0.7093 (mtm) REVERT: A 618 ASP cc_start: 0.8481 (t0) cc_final: 0.7959 (t0) REVERT: A 762 GLU cc_start: 0.7487 (pt0) cc_final: 0.6951 (tt0) REVERT: A 976 ARG cc_start: 0.7971 (ptp90) cc_final: 0.7448 (ptp90) REVERT: A 1151 LYS cc_start: 0.8557 (ttmm) cc_final: 0.8229 (mtpp) REVERT: A 1170 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8443 (mt-10) REVERT: A 1177 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.7836 (p0) REVERT: A 1256 GLN cc_start: 0.6649 (OUTLIER) cc_final: 0.6297 (pp30) REVERT: A 1261 GLN cc_start: 0.8799 (pt0) cc_final: 0.8571 (pt0) REVERT: A 1307 GLU cc_start: 0.6717 (tt0) cc_final: 0.6213 (pt0) outliers start: 40 outliers final: 18 residues processed: 131 average time/residue: 0.4128 time to fit residues: 59.6718 Evaluate side-chains 103 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 189 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 308 VAL 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 1177 ASN Chi-restraints excluded: chain A residue 1256 GLN 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: 0.0170 chunk 29 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 116 optimal weight: 0.0770 chunk 110 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.142974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.102507 restraints weight = 21630.121| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.23 r_work: 0.3324 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12592 Z= 0.126 Angle : 0.525 6.647 17635 Z= 0.293 Chirality : 0.038 0.221 2060 Planarity : 0.003 0.031 1751 Dihedral : 19.362 92.200 3122 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.48 % Allowed : 22.93 % 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: 0.29 (0.25), residues: 1140 helix: 0.95 (0.22), residues: 574 sheet: 0.68 (0.57), residues: 82 loop : -0.75 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 307 TYR 0.013 0.001 TYR A 451 PHE 0.012 0.001 PHE A1105 TRP 0.006 0.001 TRP A1074 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 (12592) covalent geometry : angle 0.52461 / 0.29 (17635) hydrogen bonds : bond 0.03940 / 3.82 ( 567) hydrogen bonds : angle 4.26910 / 5.34 ( 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 127 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.6860 (mtpp) cc_final: 0.6530 (ptpp) REVERT: A 103 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6293 (pt0) REVERT: A 118 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7971 (mm) REVERT: A 209 LYS cc_start: 0.8886 (ttmm) cc_final: 0.8556 (tptp) REVERT: A 288 ASP cc_start: 0.8751 (m-30) cc_final: 0.8482 (t0) REVERT: A 290 PHE cc_start: 0.7860 (m-80) cc_final: 0.7609 (m-80) REVERT: A 331 ASP cc_start: 0.8878 (t0) cc_final: 0.8600 (t0) REVERT: A 383 MET cc_start: 0.7537 (mtp) cc_final: 0.6946 (mtm) REVERT: A 434 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8079 (ttpt) REVERT: A 599 LYS cc_start: 0.8884 (mptt) cc_final: 0.8658 (mmtt) REVERT: A 618 ASP cc_start: 0.8478 (t0) cc_final: 0.7974 (t0) REVERT: A 677 LYS cc_start: 0.6717 (mtmt) cc_final: 0.6338 (mtmt) REVERT: A 681 ASP cc_start: 0.8513 (t70) cc_final: 0.8182 (p0) REVERT: A 762 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6886 (tt0) REVERT: A 976 ARG cc_start: 0.7875 (ptp90) cc_final: 0.7357 (ptp90) REVERT: A 1151 LYS cc_start: 0.8486 (ttmm) cc_final: 0.8091 (mtpp) REVERT: A 1261 GLN cc_start: 0.8800 (pt0) cc_final: 0.8560 (pt0) REVERT: A 1262 HIS cc_start: 0.7532 (m-70) cc_final: 0.7200 (m-70) REVERT: A 1307 GLU cc_start: 0.6639 (tt0) cc_final: 0.6151 (pt0) outliers start: 34 outliers final: 13 residues processed: 117 average time/residue: 0.4261 time to fit residues: 55.2190 Evaluate side-chains 102 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 54 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1262 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.140420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.099519 restraints weight = 21722.147| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.22 r_work: 0.3274 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12592 Z= 0.169 Angle : 0.551 8.114 17635 Z= 0.305 Chirality : 0.039 0.229 2060 Planarity : 0.004 0.059 1751 Dihedral : 19.351 92.996 3122 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.99 % Allowed : 22.72 % Favored : 73.29 % 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: 0.29 (0.25), residues: 1140 helix: 0.97 (0.22), residues: 574 sheet: 0.32 (0.54), residues: 92 loop : -0.74 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 467 TYR 0.016 0.002 TYR A 639 PHE 0.019 0.002 PHE A 518 TRP 0.011 0.001 TRP A1074 HIS 0.011 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (12592) covalent geometry : angle 0.55084 / 0.31 (17635) hydrogen bonds : bond 0.04146 / 3.99 ( 567) hydrogen bonds : angle 4.25568 / 5.30 ( 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 127 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 88 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.6951 (mtpp) cc_final: 0.6562 (ptpp) REVERT: A 103 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6535 (pt0) REVERT: A 118 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8241 (mm) REVERT: A 179 SER cc_start: 0.8225 (p) cc_final: 0.7994 (m) REVERT: A 209 LYS cc_start: 0.8821 (ttmm) cc_final: 0.8508 (tptp) REVERT: A 288 ASP cc_start: 0.8755 (m-30) cc_final: 0.8502 (t0) REVERT: A 290 PHE cc_start: 0.7876 (m-80) cc_final: 0.7607 (m-80) REVERT: A 331 ASP cc_start: 0.8871 (t0) cc_final: 0.8549 (t0) REVERT: A 404 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.7966 (p) REVERT: A 406 ASP cc_start: 0.8745 (m-30) cc_final: 0.8493 (m-30) REVERT: A 434 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8067 (ttpt) REVERT: A 599 LYS cc_start: 0.8844 (mptt) cc_final: 0.8549 (mmtm) REVERT: A 618 ASP cc_start: 0.8523 (t0) cc_final: 0.8032 (t0) REVERT: A 663 SER cc_start: 0.8764 (p) cc_final: 0.8499 (t) REVERT: A 762 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6998 (tt0) REVERT: A 976 ARG cc_start: 0.7917 (ptp90) cc_final: 0.7403 (ptp90) REVERT: A 1105 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7628 (p90) REVERT: A 1151 LYS cc_start: 0.8492 (ttmm) cc_final: 0.8077 (mttp) REVERT: A 1307 GLU cc_start: 0.6684 (tt0) cc_final: 0.6324 (pt0) outliers start: 39 outliers final: 15 residues processed: 115 average time/residue: 0.4105 time to fit residues: 52.4497 Evaluate side-chains 104 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 308 VAL 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 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 1105 PHE Chi-restraints excluded: chain A residue 1135 ASP 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 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: 1.9990 chunk 49 optimal weight: 0.0050 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.140439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.099658 restraints weight = 21672.632| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.23 r_work: 0.3274 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12592 Z= 0.148 Angle : 0.518 7.307 17635 Z= 0.289 Chirality : 0.038 0.219 2060 Planarity : 0.004 0.076 1751 Dihedral : 19.353 93.310 3122 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % 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: 0.35 (0.25), residues: 1140 helix: 1.06 (0.22), residues: 577 sheet: 0.60 (0.57), residues: 82 loop : -0.80 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 221 TYR 0.013 0.001 TYR A 155 PHE 0.015 0.002 PHE A1105 TRP 0.010 0.001 TRP A1074 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (12592) covalent geometry : angle 0.51831 / 0.29 (17635) hydrogen bonds : bond 0.03877 / 3.73 ( 567) hydrogen bonds : angle 4.18940 / 5.25 ( 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 125 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 87 time to evaluate : 0.352 Fit side-chains REVERT: A 26 LYS cc_start: 0.6948 (mtpp) cc_final: 0.6483 (ptpp) REVERT: A 103 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6561 (pt0) REVERT: A 179 SER cc_start: 0.8205 (p) cc_final: 0.7963 (m) REVERT: A 209 LYS cc_start: 0.8794 (ttmm) cc_final: 0.8485 (tptp) REVERT: A 288 ASP cc_start: 0.8773 (m-30) cc_final: 0.8524 (t0) REVERT: A 290 PHE cc_start: 0.7898 (m-80) cc_final: 0.7656 (m-80) REVERT: A 331 ASP cc_start: 0.8856 (t0) cc_final: 0.8459 (t0) REVERT: A 404 THR cc_start: 0.8338 (OUTLIER) cc_final: 0.7915 (p) REVERT: A 406 ASP cc_start: 0.8733 (m-30) cc_final: 0.8458 (m-30) REVERT: A 434 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8037 (ttpt) REVERT: A 479 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8446 (mp0) REVERT: A 599 LYS cc_start: 0.8805 (mptt) cc_final: 0.8512 (mmtm) REVERT: A 618 ASP cc_start: 0.8613 (t0) cc_final: 0.8118 (t0) REVERT: A 642 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7759 (tp) REVERT: A 702 LEU cc_start: 0.5951 (OUTLIER) cc_final: 0.5505 (mm) REVERT: A 709 GLN cc_start: 0.7904 (mm110) cc_final: 0.7701 (mm-40) REVERT: A 762 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6952 (tt0) REVERT: A 976 ARG cc_start: 0.7898 (ptp90) cc_final: 0.7391 (ptp90) REVERT: A 1307 GLU cc_start: 0.6668 (tt0) cc_final: 0.6167 (pt0) outliers start: 38 outliers final: 12 residues processed: 117 average time/residue: 0.4318 time to fit residues: 56.1162 Evaluate side-chains 101 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 267 SER 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 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 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 1163 LEU 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: 0.9980 chunk 8 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 101 optimal weight: 0.2980 chunk 11 optimal weight: 5.9990 chunk 56 optimal weight: 0.3980 chunk 65 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 50 optimal weight: 0.0370 chunk 102 optimal weight: 0.7980 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 = 0.4004 r_free = 0.4004 target = 0.140892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.100128 restraints weight = 21588.979| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.22 r_work: 0.3298 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12592 Z= 0.129 Angle : 0.511 7.170 17635 Z= 0.284 Chirality : 0.038 0.216 2060 Planarity : 0.004 0.087 1751 Dihedral : 19.321 93.421 3122 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.66 % Allowed : 23.75 % 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: 0.55 (0.25), residues: 1140 helix: 1.21 (0.22), residues: 577 sheet: 0.66 (0.58), residues: 82 loop : -0.68 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 221 TYR 0.014 0.001 TYR A 155 PHE 0.024 0.001 PHE A 518 TRP 0.008 0.001 TRP A1074 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (12592) covalent geometry : angle 0.51051 / 0.28 (17635) hydrogen bonds : bond 0.03725 / 3.58 ( 567) hydrogen bonds : angle 4.11743 / 5.16 ( 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 117 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7028 (mtpp) cc_final: 0.6522 (ptpp) REVERT: A 103 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6538 (pt0) REVERT: A 209 LYS cc_start: 0.8800 (ttmm) cc_final: 0.8503 (tptp) REVERT: A 288 ASP cc_start: 0.8754 (m-30) cc_final: 0.8527 (t0) REVERT: A 290 PHE cc_start: 0.7905 (m-80) cc_final: 0.7670 (m-80) REVERT: A 331 ASP cc_start: 0.8896 (t0) cc_final: 0.8638 (m-30) REVERT: A 404 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.7903 (p) REVERT: A 406 ASP cc_start: 0.8706 (m-30) cc_final: 0.8446 (m-30) REVERT: A 434 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8057 (ttpt) REVERT: A 479 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8471 (mp0) REVERT: A 599 LYS cc_start: 0.8837 (mptt) cc_final: 0.8525 (mmtm) REVERT: A 618 ASP cc_start: 0.8627 (t0) cc_final: 0.8134 (t0) REVERT: A 681 ASP cc_start: 0.8620 (t0) cc_final: 0.8307 (p0) REVERT: A 682 PHE cc_start: 0.6744 (m-80) cc_final: 0.6501 (m-10) REVERT: A 702 LEU cc_start: 0.5983 (OUTLIER) cc_final: 0.5528 (mm) REVERT: A 709 GLN cc_start: 0.8034 (mm110) cc_final: 0.7810 (mm-40) REVERT: A 762 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6932 (tt0) REVERT: A 976 ARG cc_start: 0.7919 (ptp90) cc_final: 0.7396 (ptp90) REVERT: A 1307 GLU cc_start: 0.6623 (tt0) cc_final: 0.6149 (pt0) outliers start: 26 outliers final: 11 residues processed: 111 average time/residue: 0.4665 time to fit residues: 57.0035 Evaluate side-chains 100 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 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 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 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: 0.9980 chunk 35 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.138333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.097226 restraints weight = 21463.019| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.22 r_work: 0.3219 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12592 Z= 0.193 Angle : 0.557 8.621 17635 Z= 0.308 Chirality : 0.040 0.218 2060 Planarity : 0.004 0.080 1751 Dihedral : 19.378 94.449 3122 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.07 % Allowed : 23.75 % 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: 0.40 (0.25), residues: 1140 helix: 1.11 (0.22), residues: 576 sheet: 0.11 (0.55), residues: 92 loop : -0.69 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 221 TYR 0.018 0.002 TYR A 155 PHE 0.025 0.002 PHE A 606 TRP 0.012 0.002 TRP A1074 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (12592) covalent geometry : angle 0.55664 / 0.31 (17635) hydrogen bonds : bond 0.04219 / 4.01 ( 567) hydrogen bonds : angle 4.19412 / 5.23 ( 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 116 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7093 (mtpp) cc_final: 0.6483 (ptpp) REVERT: A 103 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6717 (pt0) REVERT: A 209 LYS cc_start: 0.8817 (ttmm) cc_final: 0.8525 (tptp) REVERT: A 288 ASP cc_start: 0.8776 (m-30) cc_final: 0.8545 (t0) REVERT: A 331 ASP cc_start: 0.8917 (t0) cc_final: 0.8649 (m-30) REVERT: A 404 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.7973 (p) REVERT: A 479 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8489 (mp0) REVERT: A 642 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7692 (tp) REVERT: A 702 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5622 (mm) REVERT: A 708 ILE cc_start: 0.8115 (pt) cc_final: 0.7871 (pp) REVERT: A 762 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7034 (tt0) REVERT: A 976 ARG cc_start: 0.7887 (ptp90) cc_final: 0.7370 (ptp90) REVERT: A 1307 GLU cc_start: 0.6718 (tt0) cc_final: 0.6323 (mt-10) outliers start: 30 outliers final: 13 residues processed: 109 average time/residue: 0.4939 time to fit residues: 58.9979 Evaluate side-chains 98 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 267 SER 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 1135 ASP 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 85 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 102 optimal weight: 0.0970 chunk 80 optimal weight: 0.0060 chunk 9 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 709 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.139345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.098417 restraints weight = 21394.894| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.22 r_work: 0.3257 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12592 Z= 0.141 Angle : 0.533 11.233 17635 Z= 0.292 Chirality : 0.038 0.217 2060 Planarity : 0.004 0.077 1751 Dihedral : 19.381 94.240 3122 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.56 % Allowed : 24.46 % Favored : 72.98 % 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: 0.49 (0.25), residues: 1140 helix: 1.22 (0.22), residues: 577 sheet: -0.22 (0.53), residues: 100 loop : -0.63 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 221 TYR 0.013 0.001 TYR A 155 PHE 0.015 0.001 PHE A1105 TRP 0.009 0.001 TRP A1074 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (12592) covalent geometry : angle 0.53280 / 0.29 (17635) hydrogen bonds : bond 0.03896 / 3.71 ( 567) hydrogen bonds : angle 4.11544 / 5.14 ( 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 108 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.346 Fit side-chains REVERT: A 26 LYS cc_start: 0.7094 (mtpp) cc_final: 0.6463 (ptpp) REVERT: A 103 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6676 (pt0) REVERT: A 209 LYS cc_start: 0.8829 (ttmm) cc_final: 0.8544 (tptp) REVERT: A 288 ASP cc_start: 0.8745 (m-30) cc_final: 0.8544 (t0) REVERT: A 331 ASP cc_start: 0.8917 (t0) cc_final: 0.8693 (m-30) REVERT: A 404 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.7897 (p) REVERT: A 479 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8503 (mp0) REVERT: A 642 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7677 (tp) REVERT: A 681 ASP cc_start: 0.8651 (t0) cc_final: 0.8354 (p0) REVERT: A 702 LEU cc_start: 0.6171 (OUTLIER) cc_final: 0.5657 (mm) REVERT: A 762 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7021 (tt0) REVERT: A 976 ARG cc_start: 0.7901 (ptp90) cc_final: 0.7372 (ptp90) REVERT: A 1089 MET cc_start: 0.8802 (ttm) cc_final: 0.8552 (ttm) REVERT: A 1307 GLU cc_start: 0.6635 (tt0) cc_final: 0.6166 (pt0) outliers start: 25 outliers final: 12 residues processed: 102 average time/residue: 0.4618 time to fit residues: 52.0710 Evaluate side-chains 98 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 145 SER Chi-restraints excluded: chain A residue 264 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 1135 ASP Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1312 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: 8.9990 chunk 98 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 0.0870 chunk 121 optimal weight: 0.6980 chunk 118 optimal weight: 0.2980 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.139371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.098491 restraints weight = 21657.344| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.23 r_work: 0.3257 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12592 Z= 0.146 Angle : 0.549 10.743 17635 Z= 0.299 Chirality : 0.038 0.214 2060 Planarity : 0.004 0.078 1751 Dihedral : 19.361 94.242 3122 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.05 % Allowed : 25.38 % Favored : 72.57 % 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: 1.21 (0.22), residues: 578 sheet: -0.22 (0.53), residues: 100 loop : -0.63 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 221 TYR 0.013 0.001 TYR A 155 PHE 0.024 0.002 PHE A 518 TRP 0.009 0.001 TRP A1074 HIS 0.008 0.001 HIS A 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (12592) covalent geometry : angle 0.54875 / 0.30 (17635) hydrogen bonds : bond 0.03886 / 3.69 ( 567) hydrogen bonds : angle 4.12040 / 5.16 ( 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 102 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7137 (mtpp) cc_final: 0.6540 (ptpp) REVERT: A 103 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6688 (pt0) REVERT: A 145 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8173 (t) REVERT: A 209 LYS cc_start: 0.8832 (ttmm) cc_final: 0.8546 (tptp) REVERT: A 331 ASP cc_start: 0.8925 (t0) cc_final: 0.8718 (m-30) REVERT: A 404 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.7897 (p) REVERT: A 479 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8503 (mp0) REVERT: A 642 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7686 (tp) REVERT: A 702 LEU cc_start: 0.6213 (OUTLIER) cc_final: 0.5707 (mm) REVERT: A 762 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7025 (tt0) REVERT: A 976 ARG cc_start: 0.7908 (ptp90) cc_final: 0.7374 (ptp90) REVERT: A 1089 MET cc_start: 0.8791 (ttm) cc_final: 0.8549 (ttm) REVERT: A 1262 HIS cc_start: 0.7791 (m90) cc_final: 0.6503 (m90) REVERT: A 1307 GLU cc_start: 0.6616 (tt0) cc_final: 0.6247 (mt-10) outliers start: 20 outliers final: 11 residues processed: 98 average time/residue: 0.4503 time to fit residues: 48.9362 Evaluate side-chains 96 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 145 SER 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 1213 MET Chi-restraints excluded: chain A residue 1312 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: 0.8980 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.138514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097544 restraints weight = 21624.207| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.23 r_work: 0.3241 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12592 Z= 0.174 Angle : 0.575 13.288 17635 Z= 0.310 Chirality : 0.039 0.215 2060 Planarity : 0.004 0.075 1751 Dihedral : 19.363 94.464 3122 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.35 % Allowed : 24.77 % Favored : 72.88 % 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: 1.20 (0.22), residues: 578 sheet: -0.24 (0.53), residues: 100 loop : -0.66 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 221 TYR 0.015 0.001 TYR A 155 PHE 0.036 0.002 PHE A 682 TRP 0.010 0.001 TRP A1074 HIS 0.011 0.001 HIS A 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (12592) covalent geometry : angle 0.57500 / 0.31 (17635) hydrogen bonds : bond 0.03969 / 3.77 ( 567) hydrogen bonds : angle 4.15190 / 5.21 ( 1535) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3954.41 seconds wall clock time: 68 minutes 8.54 seconds (4088.54 seconds total)