Starting phenix.real_space_refine on Thu Jul 2 14:33:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mn9_48417/07_2026/9mn9_48417_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mn9_48417/07_2026/9mn9_48417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mn9_48417/07_2026/9mn9_48417_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mn9_48417/07_2026/9mn9_48417_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mn9_48417/07_2026/9mn9_48417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mn9_48417/07_2026/9mn9_48417.map" } resolution = 2.74 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= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 47 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 5406 2.51 5 N 1579 2.21 5 O 1661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 8742 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 7801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 7801 Classifications: {'peptide': 977} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 64, 'TRANS': 912} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain breaks: 1 Chain: "R" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 196 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 8} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 386 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CH1': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.79, per 1000 atoms: 0.20 Number of scatterers: 8742 At special positions: 0 Unit cell: (94.952, 101.526, 113.942, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 47 15.00 Mg 1 11.99 O 1661 8.00 N 1579 7.00 C 5406 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 285.3 milliseconds 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1862 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 7 sheets defined 55.4% alpha, 3.9% beta 14 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'E' and resid 221 through 235 removed outlier: 3.659A pdb=" N LEU E 227 " --> pdb=" O GLN E 223 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA E 228 " --> pdb=" O GLN E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 251 Processing helix chain 'E' and resid 261 through 274 Processing helix chain 'E' and resid 277 through 291 removed outlier: 4.664A pdb=" N ALA E 290 " --> pdb=" O MET E 286 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLY E 291 " --> pdb=" O VAL E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 308 Processing helix chain 'E' and resid 311 through 313 No H-bonds generated for 'chain 'E' and resid 311 through 313' Processing helix chain 'E' and resid 319 through 326 Processing helix chain 'E' and resid 330 through 335 Processing helix chain 'E' and resid 341 through 352 Processing helix chain 'E' and resid 393 through 408 Processing helix chain 'E' and resid 425 through 461 Processing helix chain 'E' and resid 468 through 471 No H-bonds generated for 'chain 'E' and resid 468 through 471' Processing helix chain 'E' and resid 476 through 488 Processing helix chain 'E' and resid 497 through 520 removed outlier: 3.605A pdb=" N VAL E 514 " --> pdb=" O SER E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 535 removed outlier: 4.553A pdb=" N CYS E 535 " --> pdb=" O ARG E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 555 Processing helix chain 'E' and resid 569 through 586 Processing helix chain 'E' and resid 625 through 634 removed outlier: 3.788A pdb=" N GLN E 629 " --> pdb=" O PRO E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 643 through 645 No H-bonds generated for 'chain 'E' and resid 643 through 645' Processing helix chain 'E' and resid 679 through 686 Processing helix chain 'E' and resid 689 through 691 No H-bonds generated for 'chain 'E' and resid 689 through 691' Processing helix chain 'E' and resid 693 through 703 Processing helix chain 'E' and resid 711 through 722 Processing helix chain 'E' and resid 758 through 788 removed outlier: 3.630A pdb=" N GLU E 778 " --> pdb=" O SER E 774 " (cutoff:3.500A) Processing helix chain 'E' and resid 819 through 824 Processing helix chain 'E' and resid 837 through 849 Processing helix chain 'E' and resid 857 through 866 Processing helix chain 'E' and resid 868 through 876 Processing helix chain 'E' and resid 884 through 887 Processing helix chain 'E' and resid 891 through 905 Processing helix chain 'E' and resid 926 through 935 Processing helix chain 'E' and resid 938 through 943 Processing helix chain 'E' and resid 955 through 972 Processing helix chain 'E' and resid 976 through 981 removed outlier: 4.106A pdb=" N LEU E 981 " --> pdb=" O VAL E 977 " (cutoff:3.500A) Processing helix chain 'E' and resid 987 through 999 removed outlier: 5.000A pdb=" N GLN E 992 " --> pdb=" O LYS E 988 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N THR E 993 " --> pdb=" O VAL E 989 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL E 998 " --> pdb=" O VAL E 994 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N TYR E 999 " --> pdb=" O MET E 995 " (cutoff:3.500A) Processing helix chain 'E' and resid 1003 through 1015 Processing helix chain 'E' and resid 1022 through 1033 removed outlier: 3.743A pdb=" N VAL E1025 " --> pdb=" O GLN E1022 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N TRP E1026 " --> pdb=" O GLU E1023 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU E1027 " --> pdb=" O PHE E1024 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL E1033 " --> pdb=" O HIS E1030 " (cutoff:3.500A) Processing helix chain 'E' and resid 1045 through 1064 removed outlier: 3.666A pdb=" N MET E1064 " --> pdb=" O LEU E1060 " (cutoff:3.500A) Processing helix chain 'E' and resid 1112 through 1142 Proline residue: E1120 - end of helix removed outlier: 3.877A pdb=" N LYS E1142 " --> pdb=" O HIS E1138 " (cutoff:3.500A) Processing helix chain 'E' and resid 1160 through 1175 removed outlier: 3.676A pdb=" N LEU E1174 " --> pdb=" O GLN E1170 " (cutoff:3.500A) Processing helix chain 'E' and resid 1179 through 1191 Processing helix chain 'E' and resid 1199 through 1208 Processing helix chain 'E' and resid 1219 through 1224 Processing sheet with id= A, first strand: chain 'E' and resid 411 through 415 Processing sheet with id= B, first strand: chain 'E' and resid 588 through 590 Processing sheet with id= C, first strand: chain 'E' and resid 606 through 610 Processing sheet with id= D, first strand: chain 'E' and resid 707 through 709 Processing sheet with id= E, first strand: chain 'E' and resid 798 through 800 Processing sheet with id= F, first strand: chain 'E' and resid 919 through 922 Processing sheet with id= G, first strand: chain 'E' and resid 1069 through 1071 373 hydrogen bonds defined for protein. 1059 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 33 hydrogen bonds 66 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1301 1.30 - 1.43: 2544 1.43 - 1.55: 5027 1.55 - 1.68: 93 1.68 - 1.81: 72 Bond restraints: 9037 Sorted by residual: bond pdb=" C2' CH1 R 14 " pdb=" C3' CH1 R 14 " ideal model delta sigma weight residual 1.537 1.316 0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C4' CH1 R 14 " pdb=" O4' CH1 R 14 " ideal model delta sigma weight residual 1.469 1.298 0.171 2.00e-02 2.50e+03 7.32e+01 bond pdb=" O1B CH1 R 14 " pdb=" PB CH1 R 14 " ideal model delta sigma weight residual 1.667 1.501 0.166 2.00e-02 2.50e+03 6.86e+01 bond pdb=" O1A CH1 R 14 " pdb=" PA CH1 R 14 " ideal model delta sigma weight residual 1.668 1.508 0.160 2.00e-02 2.50e+03 6.39e+01 bond pdb=" O2B CH1 R 14 " pdb=" PB CH1 R 14 " ideal model delta sigma weight residual 1.662 1.505 0.157 2.00e-02 2.50e+03 6.18e+01 ... (remaining 9032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.10: 12440 11.10 - 22.20: 3 22.20 - 33.30: 5 33.30 - 44.40: 0 44.40 - 55.51: 2 Bond angle restraints: 12450 Sorted by residual: angle pdb=" O1B CH1 R 14 " pdb=" PB CH1 R 14 " pdb=" O2B CH1 R 14 " ideal model delta sigma weight residual 54.66 110.17 -55.51 3.00e+00 1.11e-01 3.42e+02 angle pdb=" O1G CH1 R 14 " pdb=" PG CH1 R 14 " pdb=" O3G CH1 R 14 " ideal model delta sigma weight residual 55.38 109.53 -54.15 3.00e+00 1.11e-01 3.26e+02 angle pdb=" PB CH1 R 14 " pdb=" O3B CH1 R 14 " pdb=" PG CH1 R 14 " ideal model delta sigma weight residual 147.88 120.49 27.39 3.00e+00 1.11e-01 8.34e+01 angle pdb=" O1A CH1 R 14 " pdb=" PA CH1 R 14 " pdb=" O3A CH1 R 14 " ideal model delta sigma weight residual 81.79 109.04 -27.25 3.00e+00 1.11e-01 8.25e+01 angle pdb=" PA CH1 R 14 " pdb=" O3A CH1 R 14 " pdb=" PB CH1 R 14 " ideal model delta sigma weight residual 98.38 125.25 -26.87 3.00e+00 1.11e-01 8.02e+01 ... (remaining 12445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 5206 35.19 - 70.38: 197 70.38 - 105.57: 6 105.57 - 140.76: 0 140.76 - 175.95: 3 Dihedral angle restraints: 5412 sinusoidal: 2551 harmonic: 2861 Sorted by residual: dihedral pdb=" CA ARG E 318 " pdb=" C ARG E 318 " pdb=" N CYS E 319 " pdb=" CA CYS E 319 " ideal model delta harmonic sigma weight residual -180.00 -150.96 -29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA VAL E1149 " pdb=" C VAL E1149 " pdb=" N HIS E1150 " pdb=" CA HIS E1150 " ideal model delta harmonic sigma weight residual 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA GLN E 493 " pdb=" C GLN E 493 " pdb=" N GLY E 494 " pdb=" CA GLY E 494 " ideal model delta harmonic sigma weight residual -180.00 -156.28 -23.72 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 5409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1260 0.087 - 0.174: 119 0.174 - 0.260: 10 0.260 - 0.347: 1 0.347 - 0.434: 1 Chirality restraints: 1391 Sorted by residual: chirality pdb=" C2' CH1 R 14 " pdb=" C1' CH1 R 14 " pdb=" C3' CH1 R 14 " pdb=" O2' CH1 R 14 " both_signs ideal model delta sigma weight residual False -2.84 -2.41 -0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CG LEU E 408 " pdb=" CB LEU E 408 " pdb=" CD1 LEU E 408 " pdb=" CD2 LEU E 408 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB VAL E1001 " pdb=" CA VAL E1001 " pdb=" CG1 VAL E1001 " pdb=" CG2 VAL E1001 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1388 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 920 " -0.020 2.00e-02 2.50e+03 2.29e-02 7.88e+00 pdb=" CG HIS E 920 " 0.049 2.00e-02 2.50e+03 pdb=" ND1 HIS E 920 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS E 920 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 HIS E 920 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS E 920 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E1165 " -0.013 2.00e-02 2.50e+03 2.72e-02 7.38e+00 pdb=" C GLN E1165 " 0.047 2.00e-02 2.50e+03 pdb=" O GLN E1165 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL E1166 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS E1167 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.23e+00 pdb=" C CYS E1167 " -0.047 2.00e-02 2.50e+03 pdb=" O CYS E1167 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG E1168 " 0.016 2.00e-02 2.50e+03 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 183 2.68 - 3.24: 7889 3.24 - 3.79: 14321 3.79 - 4.35: 18754 4.35 - 4.90: 29802 Nonbonded interactions: 70949 Sorted by model distance: nonbonded pdb=" OD2 ASP E 922 " pdb="MG MG M 1 " model vdw 2.130 2.170 nonbonded pdb=" O GLN E 992 " pdb=" OG1 THR E 996 " model vdw 2.225 3.040 nonbonded pdb=" O GLY E 923 " pdb="MG MG M 1 " model vdw 2.277 2.170 nonbonded pdb=" OH TYR E 530 " pdb=" O PRO E 651 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR E 378 " pdb=" OD2 ASP E 697 " model vdw 2.301 3.040 ... (remaining 70944 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.460 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: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.350 Find NCS groups from input model: 0.030 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:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5710 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 : 0.008 0.221 9037 Z= 0.444 Angle : 1.338 55.505 12450 Z= 0.660 Chirality : 0.055 0.434 1391 Planarity : 0.009 0.092 1448 Dihedral : 17.002 175.946 3550 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.24), residues: 971 helix: -0.17 (0.19), residues: 572 sheet: -0.52 (0.62), residues: 59 loop : -0.89 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 511 TYR 0.030 0.003 TYR E 931 PHE 0.035 0.003 PHE E 465 TRP 0.023 0.003 TRP E 271 HIS 0.026 0.002 HIS E 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00824 / 0.44 ( 9037) covalent geometry : angle 1.33816 / 0.66 (12450) hydrogen bonds : bond 0.08779 / 6.05 ( 406) hydrogen bonds : angle 4.47902 / 3.28 ( 1125) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.316 Fit side-chains REVERT: E 385 SER cc_start: 0.7535 (m) cc_final: 0.7295 (m) REVERT: E 401 GLU cc_start: 0.6148 (mm-30) cc_final: 0.5937 (mm-30) REVERT: E 528 ASN cc_start: 0.6572 (m-40) cc_final: 0.6200 (m-40) REVERT: E 581 GLU cc_start: 0.6659 (mt-10) cc_final: 0.6420 (mt-10) REVERT: E 642 GLU cc_start: 0.6550 (pt0) cc_final: 0.5843 (pt0) REVERT: E 645 ASP cc_start: 0.6892 (m-30) cc_final: 0.6475 (m-30) REVERT: E 682 GLU cc_start: 0.6259 (tm-30) cc_final: 0.5933 (tm-30) REVERT: E 768 VAL cc_start: 0.7081 (p) cc_final: 0.6863 (p) REVERT: E 883 LYS cc_start: 0.7996 (mtmm) cc_final: 0.7757 (mtmm) REVERT: E 937 ASP cc_start: 0.6524 (m-30) cc_final: 0.6321 (m-30) REVERT: E 1019 ASP cc_start: 0.6549 (t0) cc_final: 0.6334 (t0) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.6241 time to fit residues: 120.3405 Evaluate side-chains 168 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 265 ASN E 304 GLN E 405 HIS E 493 GLN E 522 GLN E 616 GLN E 680 HIS E 773 HIS ** E 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1030 HIS E1080 GLN E1111 ASN E1125 HIS E1156 HIS E1181 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.157590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.130305 restraints weight = 11793.993| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.61 r_work: 0.3556 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9037 Z= 0.182 Angle : 0.645 7.321 12450 Z= 0.344 Chirality : 0.042 0.184 1391 Planarity : 0.006 0.045 1448 Dihedral : 17.551 173.055 1600 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.00 % Allowed : 8.23 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.26), residues: 971 helix: 0.79 (0.21), residues: 571 sheet: -0.49 (0.63), residues: 59 loop : -0.59 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 987 TYR 0.022 0.002 TYR E1227 PHE 0.016 0.002 PHE E 465 TRP 0.011 0.002 TRP E1070 HIS 0.013 0.002 HIS E 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 ( 9037) covalent geometry : angle 0.64535 / 0.34 (12450) hydrogen bonds : bond 0.04735 / 3.21 ( 406) hydrogen bonds : angle 3.68516 / 2.66 ( 1125) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.215 Fit side-chains REVERT: E 447 ARG cc_start: 0.8589 (mtm-85) cc_final: 0.8292 (mtm-85) REVERT: E 642 GLU cc_start: 0.7509 (pt0) cc_final: 0.7100 (pt0) REVERT: E 645 ASP cc_start: 0.7529 (m-30) cc_final: 0.7203 (m-30) REVERT: E 682 GLU cc_start: 0.7364 (tm-30) cc_final: 0.6977 (tm-30) REVERT: E 1003 ARG cc_start: 0.7603 (mmt180) cc_final: 0.7394 (mmt180) outliers start: 17 outliers final: 5 residues processed: 178 average time/residue: 0.6579 time to fit residues: 123.4345 Evaluate side-chains 175 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 1114 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 80 optimal weight: 0.0070 chunk 83 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 405 HIS ** E 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1035 GLN ** E1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.156293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.129078 restraints weight = 11697.333| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.61 r_work: 0.3540 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9037 Z= 0.177 Angle : 0.613 7.852 12450 Z= 0.329 Chirality : 0.042 0.208 1391 Planarity : 0.006 0.044 1448 Dihedral : 17.359 171.773 1600 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.35 % Allowed : 11.28 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.26), residues: 971 helix: 1.22 (0.21), residues: 572 sheet: -0.08 (0.74), residues: 49 loop : -0.53 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 464 TYR 0.022 0.002 TYR E 468 PHE 0.018 0.002 PHE E1186 TRP 0.011 0.002 TRP E 707 HIS 0.012 0.001 HIS E1150 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 ( 9037) covalent geometry : angle 0.61348 / 0.33 (12450) hydrogen bonds : bond 0.04504 / 3.06 ( 406) hydrogen bonds : angle 3.52975 / 2.55 ( 1125) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.321 Fit side-chains REVERT: E 447 ARG cc_start: 0.8602 (mtm-85) cc_final: 0.8304 (mtm-85) REVERT: E 464 ARG cc_start: 0.8231 (ptp90) cc_final: 0.7795 (ptp90) REVERT: E 573 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7199 (mtt) REVERT: E 577 LYS cc_start: 0.8195 (mttm) cc_final: 0.7707 (mttm) REVERT: E 642 GLU cc_start: 0.7464 (pt0) cc_final: 0.7002 (pt0) REVERT: E 645 ASP cc_start: 0.7583 (m-30) cc_final: 0.7208 (m-30) REVERT: E 682 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7143 (tm-30) REVERT: E 1003 ARG cc_start: 0.7634 (mmt180) cc_final: 0.7416 (mmt180) REVERT: E 1019 ASP cc_start: 0.8233 (t0) cc_final: 0.8013 (t70) outliers start: 20 outliers final: 9 residues processed: 184 average time/residue: 0.6499 time to fit residues: 126.3699 Evaluate side-chains 181 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 443 LYS Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 573 MET Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 1130 SER Chi-restraints excluded: chain E residue 1132 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 87 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 3 optimal weight: 0.0970 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 224 GLN E 405 HIS E 454 ASN E 597 HIS E 844 HIS E 920 HIS ** E1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1156 HIS E1221 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.156454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.129408 restraints weight = 11908.746| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.62 r_work: 0.3539 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9037 Z= 0.157 Angle : 0.590 7.858 12450 Z= 0.318 Chirality : 0.041 0.203 1391 Planarity : 0.005 0.042 1448 Dihedral : 17.326 171.562 1600 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.47 % Allowed : 13.04 % Favored : 84.49 % 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: 0.97 (0.26), residues: 971 helix: 1.42 (0.21), residues: 572 sheet: -0.16 (0.72), residues: 49 loop : -0.47 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E1224 TYR 0.019 0.002 TYR E 468 PHE 0.018 0.002 PHE E 465 TRP 0.012 0.002 TRP E 567 HIS 0.008 0.001 HIS E1150 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 ( 9037) covalent geometry : angle 0.58972 / 0.32 (12450) hydrogen bonds : bond 0.04317 / 2.92 ( 406) hydrogen bonds : angle 3.42845 / 2.48 ( 1125) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.227 Fit side-chains REVERT: E 447 ARG cc_start: 0.8582 (mtm-85) cc_final: 0.8311 (mtm-85) REVERT: E 464 ARG cc_start: 0.8235 (ptp90) cc_final: 0.7724 (ptp90) REVERT: E 573 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7161 (mtt) REVERT: E 577 LYS cc_start: 0.8136 (mttm) cc_final: 0.7695 (mttm) REVERT: E 642 GLU cc_start: 0.7464 (pt0) cc_final: 0.6980 (pt0) REVERT: E 645 ASP cc_start: 0.7629 (m-30) cc_final: 0.7229 (m-30) REVERT: E 682 GLU cc_start: 0.7392 (tm-30) cc_final: 0.7083 (tm-30) REVERT: E 1019 ASP cc_start: 0.8210 (t0) cc_final: 0.8008 (t70) outliers start: 21 outliers final: 12 residues processed: 179 average time/residue: 0.6036 time to fit residues: 114.5380 Evaluate side-chains 187 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 443 LYS Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 573 MET Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain E residue 899 MET Chi-restraints excluded: chain E residue 979 GLN Chi-restraints excluded: chain E residue 1008 LEU Chi-restraints excluded: chain E residue 1033 VAL Chi-restraints excluded: chain E residue 1130 SER Chi-restraints excluded: chain E residue 1132 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 0.0980 chunk 88 optimal weight: 0.5980 chunk 14 optimal weight: 0.0470 chunk 89 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 0.0020 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 overall best weight: 0.2686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 331 GLN E 405 HIS E 454 ASN E 597 HIS E1111 ASN E1221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.157770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.130762 restraints weight = 11822.356| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.62 r_work: 0.3559 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9037 Z= 0.123 Angle : 0.564 7.938 12450 Z= 0.302 Chirality : 0.039 0.203 1391 Planarity : 0.005 0.041 1448 Dihedral : 17.247 171.095 1600 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.12 % Allowed : 15.63 % Favored : 82.26 % 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: 1.27 (0.27), residues: 971 helix: 1.67 (0.22), residues: 573 sheet: -0.07 (0.74), residues: 49 loop : -0.34 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1224 TYR 0.017 0.001 TYR E 468 PHE 0.013 0.001 PHE E1186 TRP 0.010 0.001 TRP E1070 HIS 0.008 0.001 HIS E 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 9037) covalent geometry : angle 0.56385 / 0.30 (12450) hydrogen bonds : bond 0.03970 / 2.68 ( 406) hydrogen bonds : angle 3.32235 / 2.40 ( 1125) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: E 447 ARG cc_start: 0.8599 (mtm-85) cc_final: 0.8330 (mtm-85) REVERT: E 464 ARG cc_start: 0.8249 (ptp90) cc_final: 0.7707 (ptp90) REVERT: E 573 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7174 (mtt) REVERT: E 577 LYS cc_start: 0.8111 (mttm) cc_final: 0.7682 (mttm) REVERT: E 642 GLU cc_start: 0.7458 (pt0) cc_final: 0.6912 (pt0) REVERT: E 645 ASP cc_start: 0.7617 (m-30) cc_final: 0.7184 (m-30) REVERT: E 682 GLU cc_start: 0.7376 (tm-30) cc_final: 0.7048 (tm-30) REVERT: E 1019 ASP cc_start: 0.8226 (t0) cc_final: 0.7942 (t70) outliers start: 18 outliers final: 13 residues processed: 180 average time/residue: 0.6139 time to fit residues: 116.6653 Evaluate side-chains 187 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 443 LYS Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 545 GLU Chi-restraints excluded: chain E residue 573 MET Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 899 MET Chi-restraints excluded: chain E residue 979 GLN Chi-restraints excluded: chain E residue 1008 LEU Chi-restraints excluded: chain E residue 1033 VAL Chi-restraints excluded: chain E residue 1130 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 89 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.0170 chunk 49 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 405 HIS E 454 ASN E 597 HIS E 616 GLN ** E1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.155977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.128376 restraints weight = 11851.787| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.64 r_work: 0.3531 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9037 Z= 0.164 Angle : 0.590 7.871 12450 Z= 0.315 Chirality : 0.041 0.206 1391 Planarity : 0.005 0.041 1448 Dihedral : 17.235 170.973 1600 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.12 % Allowed : 15.51 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.27), residues: 971 helix: 1.63 (0.22), residues: 575 sheet: -0.07 (0.73), residues: 49 loop : -0.40 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 968 TYR 0.022 0.002 TYR E 468 PHE 0.015 0.002 PHE E 465 TRP 0.009 0.001 TRP E 707 HIS 0.009 0.001 HIS E 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 9037) covalent geometry : angle 0.58953 / 0.31 (12450) hydrogen bonds : bond 0.04218 / 2.87 ( 406) hydrogen bonds : angle 3.37026 / 2.44 ( 1125) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.308 Fit side-chains REVERT: E 447 ARG cc_start: 0.8590 (mtm-85) cc_final: 0.8330 (mtm-85) REVERT: E 464 ARG cc_start: 0.8242 (ptp90) cc_final: 0.7677 (ptp90) REVERT: E 573 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7138 (mtt) REVERT: E 577 LYS cc_start: 0.8125 (mttm) cc_final: 0.7690 (mttm) REVERT: E 642 GLU cc_start: 0.7444 (pt0) cc_final: 0.6886 (pt0) REVERT: E 645 ASP cc_start: 0.7610 (m-30) cc_final: 0.7162 (m-30) REVERT: E 682 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7044 (tm-30) REVERT: E 1116 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7598 (tttp) outliers start: 18 outliers final: 12 residues processed: 181 average time/residue: 0.6614 time to fit residues: 126.3091 Evaluate side-chains 189 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 443 LYS Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 573 MET Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 899 MET Chi-restraints excluded: chain E residue 1008 LEU Chi-restraints excluded: chain E residue 1033 VAL Chi-restraints excluded: chain E residue 1116 LYS Chi-restraints excluded: chain E residue 1130 SER Chi-restraints excluded: chain E residue 1132 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 26 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 265 ASN E 405 HIS E 454 ASN E 616 GLN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 962 GLN ** E1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.154177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.127099 restraints weight = 11806.652| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.61 r_work: 0.3510 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9037 Z= 0.216 Angle : 0.631 7.991 12450 Z= 0.337 Chirality : 0.043 0.211 1391 Planarity : 0.006 0.060 1448 Dihedral : 17.255 171.241 1600 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.23 % Allowed : 15.98 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.27), residues: 971 helix: 1.51 (0.21), residues: 573 sheet: -0.04 (0.73), residues: 49 loop : -0.44 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 550 TYR 0.035 0.002 TYR E 468 PHE 0.017 0.002 PHE E1186 TRP 0.011 0.002 TRP E 707 HIS 0.011 0.001 HIS E1150 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 ( 9037) covalent geometry : angle 0.63072 / 0.34 (12450) hydrogen bonds : bond 0.04583 / 3.13 ( 406) hydrogen bonds : angle 3.54670 / 2.57 ( 1125) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.330 Fit side-chains REVERT: E 402 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8078 (mttm) REVERT: E 464 ARG cc_start: 0.8253 (ptp90) cc_final: 0.7662 (ptp90) REVERT: E 577 LYS cc_start: 0.8127 (mttm) cc_final: 0.7714 (mttm) REVERT: E 642 GLU cc_start: 0.7434 (pt0) cc_final: 0.6860 (pt0) REVERT: E 645 ASP cc_start: 0.7564 (m-30) cc_final: 0.7097 (m-30) REVERT: E 682 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7081 (tm-30) REVERT: E 1116 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7624 (tttp) outliers start: 19 outliers final: 13 residues processed: 189 average time/residue: 0.6738 time to fit residues: 134.4196 Evaluate side-chains 195 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 402 LYS Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 545 GLU Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 800 MET Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 899 MET Chi-restraints excluded: chain E residue 1008 LEU Chi-restraints excluded: chain E residue 1033 VAL Chi-restraints excluded: chain E residue 1116 LYS Chi-restraints excluded: chain E residue 1130 SER Chi-restraints excluded: chain E residue 1132 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 51 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 405 HIS E 454 ASN E 616 GLN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.154900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.127737 restraints weight = 11732.110| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.60 r_work: 0.3520 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9037 Z= 0.171 Angle : 0.596 7.724 12450 Z= 0.319 Chirality : 0.041 0.211 1391 Planarity : 0.005 0.045 1448 Dihedral : 17.214 171.148 1600 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.88 % Allowed : 16.33 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.27), residues: 971 helix: 1.59 (0.21), residues: 573 sheet: -0.03 (0.73), residues: 49 loop : -0.40 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 455 TYR 0.036 0.002 TYR E 468 PHE 0.020 0.002 PHE E 465 TRP 0.010 0.002 TRP E 707 HIS 0.009 0.001 HIS E 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 9037) covalent geometry : angle 0.59590 / 0.32 (12450) hydrogen bonds : bond 0.04351 / 2.96 ( 406) hydrogen bonds : angle 3.46955 / 2.52 ( 1125) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.350 Fit side-chains REVERT: E 402 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8099 (mttm) REVERT: E 442 GLU cc_start: 0.7351 (tt0) cc_final: 0.7102 (tt0) REVERT: E 464 ARG cc_start: 0.8219 (ptp90) cc_final: 0.7628 (ptp90) REVERT: E 577 LYS cc_start: 0.8126 (mttm) cc_final: 0.7708 (mttm) REVERT: E 642 GLU cc_start: 0.7443 (pt0) cc_final: 0.6884 (pt0) REVERT: E 645 ASP cc_start: 0.7569 (m-30) cc_final: 0.7104 (m-30) REVERT: E 682 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7072 (tm-30) REVERT: E 1116 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7637 (tttp) outliers start: 16 outliers final: 12 residues processed: 180 average time/residue: 0.6385 time to fit residues: 121.4288 Evaluate side-chains 191 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 402 LYS Chi-restraints excluded: chain E residue 443 LYS Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 545 GLU Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain E residue 899 MET Chi-restraints excluded: chain E residue 1008 LEU Chi-restraints excluded: chain E residue 1033 VAL Chi-restraints excluded: chain E residue 1116 LYS Chi-restraints excluded: chain E residue 1130 SER Chi-restraints excluded: chain E residue 1132 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 7 optimal weight: 0.0870 chunk 75 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 0.2980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 405 HIS E 454 ASN E 616 GLN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.155689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.128837 restraints weight = 11789.153| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.60 r_work: 0.3528 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9037 Z= 0.148 Angle : 0.581 7.915 12450 Z= 0.311 Chirality : 0.040 0.210 1391 Planarity : 0.005 0.046 1448 Dihedral : 17.168 170.847 1600 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.88 % Allowed : 17.39 % Favored : 80.73 % 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: 1.30 (0.27), residues: 971 helix: 1.69 (0.21), residues: 573 sheet: 0.01 (0.74), residues: 49 loop : -0.36 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E1224 TYR 0.037 0.002 TYR E 468 PHE 0.015 0.002 PHE E 465 TRP 0.011 0.001 TRP E1154 HIS 0.009 0.001 HIS E 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 9037) covalent geometry : angle 0.58092 / 0.31 (12450) hydrogen bonds : bond 0.04148 / 2.81 ( 406) hydrogen bonds : angle 3.42668 / 2.48 ( 1125) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.307 Fit side-chains REVERT: E 402 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8140 (mttm) REVERT: E 442 GLU cc_start: 0.7342 (tt0) cc_final: 0.7086 (tt0) REVERT: E 516 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7768 (tpt170) REVERT: E 577 LYS cc_start: 0.8111 (mttm) cc_final: 0.7677 (mttm) REVERT: E 642 GLU cc_start: 0.7414 (pt0) cc_final: 0.6851 (pt0) REVERT: E 645 ASP cc_start: 0.7556 (m-30) cc_final: 0.7095 (m-30) REVERT: E 682 GLU cc_start: 0.7378 (tm-30) cc_final: 0.7039 (tm-30) REVERT: E 1116 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7658 (tttp) outliers start: 16 outliers final: 10 residues processed: 182 average time/residue: 0.6541 time to fit residues: 125.6113 Evaluate side-chains 188 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 402 LYS Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 516 ARG Chi-restraints excluded: chain E residue 545 GLU Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain E residue 899 MET Chi-restraints excluded: chain E residue 1008 LEU Chi-restraints excluded: chain E residue 1033 VAL Chi-restraints excluded: chain E residue 1116 LYS Chi-restraints excluded: chain E residue 1130 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 16 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 95 optimal weight: 0.0980 chunk 91 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 43 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 405 HIS E 454 ASN E 616 GLN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.155015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.128033 restraints weight = 11776.244| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.59 r_work: 0.3526 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9037 Z= 0.165 Angle : 0.598 8.126 12450 Z= 0.320 Chirality : 0.041 0.212 1391 Planarity : 0.005 0.073 1448 Dihedral : 17.153 170.764 1600 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.53 % Allowed : 17.86 % Favored : 80.61 % 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: 1.24 (0.27), residues: 971 helix: 1.65 (0.21), residues: 573 sheet: -0.05 (0.73), residues: 49 loop : -0.37 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 550 TYR 0.042 0.002 TYR E 468 PHE 0.016 0.002 PHE E 465 TRP 0.012 0.002 TRP E1154 HIS 0.009 0.001 HIS E 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 ( 9037) covalent geometry : angle 0.59830 / 0.32 (12450) hydrogen bonds : bond 0.04229 / 2.88 ( 406) hydrogen bonds : angle 3.41450 / 2.48 ( 1125) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 0.325 Fit side-chains REVERT: E 402 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8127 (mttm) REVERT: E 442 GLU cc_start: 0.7348 (tt0) cc_final: 0.7090 (tt0) REVERT: E 516 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7795 (tpt170) REVERT: E 577 LYS cc_start: 0.8121 (mttm) cc_final: 0.7704 (mttm) REVERT: E 642 GLU cc_start: 0.7440 (pt0) cc_final: 0.6870 (pt0) REVERT: E 645 ASP cc_start: 0.7542 (m-30) cc_final: 0.7085 (m-30) REVERT: E 682 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7065 (tm-30) REVERT: E 1116 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7660 (tttp) outliers start: 13 outliers final: 10 residues processed: 176 average time/residue: 0.6919 time to fit residues: 128.5381 Evaluate side-chains 184 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 402 LYS Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 516 ARG Chi-restraints excluded: chain E residue 545 GLU Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain E residue 899 MET Chi-restraints excluded: chain E residue 1008 LEU Chi-restraints excluded: chain E residue 1033 VAL Chi-restraints excluded: chain E residue 1116 LYS Chi-restraints excluded: chain E residue 1130 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 75 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 405 HIS E 454 ASN E 616 GLN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.154473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.127538 restraints weight = 11776.847| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.60 r_work: 0.3518 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9037 Z= 0.180 Angle : 0.606 7.892 12450 Z= 0.324 Chirality : 0.042 0.214 1391 Planarity : 0.005 0.067 1448 Dihedral : 17.152 170.808 1600 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.76 % Allowed : 17.86 % Favored : 80.38 % 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: 1.19 (0.27), residues: 971 helix: 1.60 (0.21), residues: 573 sheet: -0.05 (0.74), residues: 49 loop : -0.39 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 550 TYR 0.037 0.002 TYR E 468 PHE 0.016 0.002 PHE E1186 TRP 0.012 0.002 TRP E1154 HIS 0.009 0.001 HIS E 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 9037) covalent geometry : angle 0.60565 / 0.32 (12450) hydrogen bonds : bond 0.04326 / 2.94 ( 406) hydrogen bonds : angle 3.46535 / 2.51 ( 1125) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3775.00 seconds wall clock time: 64 minutes 53.57 seconds (3893.57 seconds total)