Starting phenix.real_space_refine on Tue Aug 4 17:37:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t6l_55617/08_2026/9t6l_55617.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t6l_55617/08_2026/9t6l_55617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9t6l_55617/08_2026/9t6l_55617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t6l_55617/08_2026/9t6l_55617.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9t6l_55617/08_2026/9t6l_55617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t6l_55617/08_2026/9t6l_55617.map" } resolution = 2.9 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= 0.006 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 3478 2.51 5 N 913 2.21 5 O 972 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5400 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "C" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1824 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 217} Chain breaks: 2 Chain: "D" Number of atoms: 3091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3091 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 12, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 440 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 1.29, per 1000 atoms: 0.24 Number of scatterers: 5400 At special positions: 0 Unit cell: (62.9888, 93.632, 112.358, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 972 8.00 N 913 7.00 C 3478 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 584 " - pdb=" SG CYS C 588 " distance=2.05 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 83 " distance=2.04 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: 0.26 Conformation dependent library (CDL) restraints added in 137.9 milliseconds 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1300 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 2 sheets defined 73.3% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'C' and resid 575 through 591 Processing helix chain 'C' and resid 595 through 614 removed outlier: 3.957A pdb=" N GLN C 613 " --> pdb=" O ASP C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 635 removed outlier: 3.715A pdb=" N GLU C 633 " --> pdb=" O ARG C 629 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS C 634 " --> pdb=" O ILE C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 652 removed outlier: 3.959A pdb=" N GLN C 646 " --> pdb=" O GLN C 642 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA C 652 " --> pdb=" O LYS C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 673 Processing helix chain 'C' and resid 675 through 684 removed outlier: 4.095A pdb=" N ILE C 679 " --> pdb=" O ASN C 675 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR C 680 " --> pdb=" O SER C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 692 removed outlier: 3.582A pdb=" N ALA C 692 " --> pdb=" O ARG C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 709 Processing helix chain 'C' and resid 710 through 720 removed outlier: 3.743A pdb=" N CYS C 719 " --> pdb=" O PHE C 715 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS C 720 " --> pdb=" O ARG C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 730 removed outlier: 3.998A pdb=" N LEU C 728 " --> pdb=" O MET C 724 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP C 730 " --> pdb=" O GLY C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 748 removed outlier: 3.727A pdb=" N GLU C 736 " --> pdb=" O PHE C 732 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS C 738 " --> pdb=" O ASP C 734 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL C 739 " --> pdb=" O ARG C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 761 removed outlier: 3.549A pdb=" N LEU C 757 " --> pdb=" O PRO C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 765 through 774 Processing helix chain 'C' and resid 775 through 777 No H-bonds generated for 'chain 'C' and resid 775 through 777' Processing helix chain 'C' and resid 814 through 819 removed outlier: 3.549A pdb=" N PHE C 819 " --> pdb=" O MET C 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 19 removed outlier: 3.501A pdb=" N TYR D 9 " --> pdb=" O THR D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 30 Processing helix chain 'D' and resid 33 through 42 Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 45 through 49 removed outlier: 4.541A pdb=" N GLU D 48 " --> pdb=" O SER D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 74 removed outlier: 4.587A pdb=" N TYR D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL D 72 " --> pdb=" O CYS D 68 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY D 73 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 96 removed outlier: 3.786A pdb=" N GLN D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 127 Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 163 removed outlier: 3.640A pdb=" N SER D 163 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 183 removed outlier: 3.513A pdb=" N LEU D 171 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS D 181 " --> pdb=" O LYS D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 198 removed outlier: 4.405A pdb=" N LEU D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 222 removed outlier: 3.702A pdb=" N PHE D 222 " --> pdb=" O ARG D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 239 Processing helix chain 'D' and resid 244 through 262 removed outlier: 3.633A pdb=" N TYR D 254 " --> pdb=" O MET D 250 " (cutoff:3.500A) Proline residue: D 257 - end of helix removed outlier: 3.595A pdb=" N LEU D 262 " --> pdb=" O VAL D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 274 removed outlier: 3.548A pdb=" N TYR D 274 " --> pdb=" O LEU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 278 No H-bonds generated for 'chain 'D' and resid 276 through 278' Processing helix chain 'D' and resid 279 through 289 Processing helix chain 'D' and resid 290 through 301 Processing helix chain 'D' and resid 301 through 309 Processing helix chain 'D' and resid 310 through 315 removed outlier: 3.592A pdb=" N GLU D 315 " --> pdb=" O PHE D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 334 Processing helix chain 'D' and resid 340 through 350 Processing helix chain 'D' and resid 356 through 370 Processing helix chain 'E' and resid 50 through 63 Processing sheet with id=AA1, first strand: chain 'D' and resid 265 through 266 Processing sheet with id=AA2, first strand: chain 'D' and resid 337 through 339 309 hydrogen bonds defined for protein. 897 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.51 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1743 1.35 - 1.48: 1371 1.48 - 1.61: 2353 1.61 - 1.74: 0 1.74 - 1.87: 55 Bond restraints: 5522 Sorted by residual: bond pdb=" CB CYS C 588 " pdb=" SG CYS C 588 " ideal model delta sigma weight residual 1.808 1.870 -0.062 3.30e-02 9.18e+02 3.51e+00 bond pdb=" CB CYS C 584 " pdb=" SG CYS C 584 " ideal model delta sigma weight residual 1.808 1.864 -0.056 3.30e-02 9.18e+02 2.93e+00 bond pdb=" C ARG C 749 " pdb=" N PRO C 750 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.06e+00 bond pdb=" C CYS C 584 " pdb=" O CYS C 584 " ideal model delta sigma weight residual 1.237 1.224 0.012 1.19e-02 7.06e+03 1.06e+00 bond pdb=" CA CYS C 588 " pdb=" CB CYS C 588 " ideal model delta sigma weight residual 1.530 1.547 -0.018 1.87e-02 2.86e+03 8.80e-01 ... (remaining 5517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 7278 1.23 - 2.46: 134 2.46 - 3.69: 33 3.69 - 4.92: 13 4.92 - 6.14: 4 Bond angle restraints: 7462 Sorted by residual: angle pdb=" N LEU D 185 " pdb=" CA LEU D 185 " pdb=" CB LEU D 185 " ideal model delta sigma weight residual 113.65 109.38 4.27 1.47e+00 4.63e-01 8.42e+00 angle pdb=" N LYS C 674 " pdb=" CA LYS C 674 " pdb=" C LYS C 674 " ideal model delta sigma weight residual 108.52 113.08 -4.56 1.74e+00 3.30e-01 6.87e+00 angle pdb=" C LYS C 587 " pdb=" N CYS C 588 " pdb=" CA CYS C 588 " ideal model delta sigma weight residual 120.99 125.68 -4.69 1.86e+00 2.89e-01 6.37e+00 angle pdb=" C PRO D 57 " pdb=" N TYR D 58 " pdb=" CA TYR D 58 " ideal model delta sigma weight residual 121.63 126.45 -4.82 1.91e+00 2.74e-01 6.36e+00 angle pdb=" N TYR D 58 " pdb=" CA TYR D 58 " pdb=" C TYR D 58 " ideal model delta sigma weight residual 114.62 112.26 2.36 1.14e+00 7.69e-01 4.28e+00 ... (remaining 7457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 3001 16.89 - 33.78: 256 33.78 - 50.67: 45 50.67 - 67.55: 14 67.55 - 84.44: 5 Dihedral angle restraints: 3321 sinusoidal: 1325 harmonic: 1996 Sorted by residual: dihedral pdb=" CB CYS D 68 " pdb=" SG CYS D 68 " pdb=" SG CYS D 83 " pdb=" CB CYS D 83 " ideal model delta sinusoidal sigma weight residual -86.00 -38.05 -47.95 1 1.00e+01 1.00e-02 3.17e+01 dihedral pdb=" CA PRO D 56 " pdb=" C PRO D 56 " pdb=" N PRO D 57 " pdb=" CA PRO D 57 " ideal model delta harmonic sigma weight residual -180.00 -153.85 -26.15 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CB CYS C 584 " pdb=" SG CYS C 584 " pdb=" SG CYS C 588 " pdb=" CB CYS C 588 " ideal model delta sinusoidal sigma weight residual -86.00 -129.69 43.69 1 1.00e+01 1.00e-02 2.66e+01 ... (remaining 3318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 442 0.022 - 0.044: 195 0.044 - 0.067: 132 0.067 - 0.089: 31 0.089 - 0.111: 22 Chirality restraints: 822 Sorted by residual: chirality pdb=" CA VAL D 373 " pdb=" N VAL D 373 " pdb=" C VAL D 373 " pdb=" CB VAL D 373 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.07e-01 chirality pdb=" CA PHE D 77 " pdb=" N PHE D 77 " pdb=" C PHE D 77 " pdb=" CB PHE D 77 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.02e-01 chirality pdb=" CA PRO C 694 " pdb=" N PRO C 694 " pdb=" C PRO C 694 " pdb=" CB PRO C 694 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.97e-01 ... (remaining 819 not shown) Planarity restraints: 950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 585 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C MET C 585 " -0.037 2.00e-02 2.50e+03 pdb=" O MET C 585 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL C 586 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 693 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO C 694 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 694 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 694 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 45 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO D 46 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 46 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 46 " 0.022 5.00e-02 4.00e+02 ... (remaining 947 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 3335 3.05 - 3.51: 5510 3.51 - 3.98: 7671 3.98 - 4.44: 9698 4.44 - 4.90: 14780 Nonbonded interactions: 40994 Sorted by model distance: nonbonded pdb=" O ASP C 734 " pdb=" OD1 ASP C 734 " model vdw 2.590 3.040 nonbonded pdb=" N ALA C 751 " pdb=" O ALA C 751 " model vdw 2.634 2.496 nonbonded pdb=" N THR C 617 " pdb=" O THR C 617 " model vdw 2.642 2.496 nonbonded pdb=" N ASP D 356 " pdb=" O ASP D 356 " model vdw 2.643 2.496 nonbonded pdb=" N ASP D 59 " pdb=" OD1 ASP D 59 " model vdw 2.646 3.120 ... (remaining 40989 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.630 Find NCS groups from input model: 0.020 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:8.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 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 : 0.002 0.062 5524 Z= 0.109 Angle : 0.485 6.145 7466 Z= 0.261 Chirality : 0.036 0.111 822 Planarity : 0.003 0.044 950 Dihedral : 13.456 84.443 2015 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.34), residues: 657 helix: 1.46 (0.26), residues: 438 sheet: 0.43 (1.93), residues: 10 loop : -0.51 (0.45), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 716 TYR 0.013 0.001 TYR D 58 PHE 0.013 0.001 PHE D 62 TRP 0.006 0.001 TRP E 39 HIS 0.002 0.000 HIS C 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 ( 5522) covalent geometry : angle 0.47994 / 0.26 ( 7462) SS BOND : bond 0.01573 / 0.82 ( 2) SS BOND : angle 3.13995 / 1.60 ( 4) hydrogen bonds : bond 0.16648 / 10.99 ( 309) hydrogen bonds : angle 4.44245 / 3.12 ( 897) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: B 11 LEU cc_start: 0.8797 (mm) cc_final: 0.8432 (tp) REVERT: C 594 GLN cc_start: 0.9104 (mp10) cc_final: 0.8594 (mm-40) REVERT: C 602 GLN cc_start: 0.9354 (mm-40) cc_final: 0.9085 (mm110) REVERT: C 609 ASP cc_start: 0.8759 (m-30) cc_final: 0.8176 (m-30) REVERT: C 622 GLU cc_start: 0.8675 (tt0) cc_final: 0.8230 (tm-30) REVERT: C 636 ASP cc_start: 0.8756 (t0) cc_final: 0.8498 (t0) REVERT: C 654 ASN cc_start: 0.9174 (t0) cc_final: 0.8962 (t0) REVERT: C 789 ASP cc_start: 0.8950 (t70) cc_final: 0.8650 (t0) REVERT: C 817 ASP cc_start: 0.9103 (m-30) cc_final: 0.8884 (m-30) REVERT: E 47 ASN cc_start: 0.9277 (t0) cc_final: 0.8942 (t0) REVERT: E 50 ASP cc_start: 0.8266 (p0) cc_final: 0.7806 (p0) REVERT: E 53 SER cc_start: 0.9510 (m) cc_final: 0.9212 (p) REVERT: E 55 GLN cc_start: 0.9111 (mt0) cc_final: 0.8694 (mt0) outliers start: 0 outliers final: 1 residues processed: 79 average time/residue: 0.4246 time to fit residues: 35.3733 Evaluate side-chains 60 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 630 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 646 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.071568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.049522 restraints weight = 15375.126| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.74 r_work: 0.2623 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 5524 Z= 0.122 Angle : 0.498 9.253 7466 Z= 0.255 Chirality : 0.037 0.121 822 Planarity : 0.003 0.042 950 Dihedral : 3.637 24.412 729 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.23 % Allowed : 6.33 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.35), residues: 657 helix: 1.45 (0.26), residues: 456 sheet: -0.60 (1.62), residues: 12 loop : -0.40 (0.48), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 791 TYR 0.008 0.001 TYR C 711 PHE 0.015 0.001 PHE C 819 TRP 0.004 0.001 TRP D 103 HIS 0.002 0.000 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 5522) covalent geometry : angle 0.49428 / 0.25 ( 7462) SS BOND : bond 0.01371 / 0.72 ( 2) SS BOND : angle 2.54196 / 1.37 ( 4) hydrogen bonds : bond 0.04464 / 2.97 ( 309) hydrogen bonds : angle 3.66340 / 2.54 ( 897) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: B 11 LEU cc_start: 0.8568 (mm) cc_final: 0.8155 (tp) REVERT: C 595 ASP cc_start: 0.9068 (t0) cc_final: 0.8767 (t0) REVERT: C 602 GLN cc_start: 0.9367 (mm-40) cc_final: 0.8965 (mm110) REVERT: C 608 GLN cc_start: 0.8916 (pp30) cc_final: 0.8713 (pp30) REVERT: C 609 ASP cc_start: 0.8744 (m-30) cc_final: 0.8290 (m-30) REVERT: C 622 GLU cc_start: 0.8717 (tt0) cc_final: 0.8107 (tm-30) REVERT: C 636 ASP cc_start: 0.8179 (t0) cc_final: 0.7482 (t0) REVERT: C 654 ASN cc_start: 0.9414 (t0) cc_final: 0.9203 (t0) REVERT: C 734 ASP cc_start: 0.8980 (t70) cc_final: 0.8655 (t0) REVERT: C 789 ASP cc_start: 0.8986 (t70) cc_final: 0.8705 (t0) REVERT: C 817 ASP cc_start: 0.8926 (m-30) cc_final: 0.8641 (m-30) REVERT: E 47 ASN cc_start: 0.9256 (t0) cc_final: 0.8941 (t0) REVERT: E 50 ASP cc_start: 0.7579 (p0) cc_final: 0.7117 (p0) REVERT: E 53 SER cc_start: 0.9452 (m) cc_final: 0.9098 (p) outliers start: 7 outliers final: 2 residues processed: 68 average time/residue: 0.3891 time to fit residues: 27.8871 Evaluate side-chains 55 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 615 ILE Chi-restraints excluded: chain C residue 644 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 62 optimal weight: 0.0040 chunk 65 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 646 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.069681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.047252 restraints weight = 15272.482| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.76 r_work: 0.2574 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5524 Z= 0.161 Angle : 0.504 6.433 7466 Z= 0.262 Chirality : 0.038 0.169 822 Planarity : 0.003 0.046 950 Dihedral : 3.546 24.811 727 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.05 % Allowed : 7.21 % Favored : 91.74 % 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: 1.35 (0.35), residues: 657 helix: 1.53 (0.26), residues: 458 sheet: -0.92 (1.68), residues: 12 loop : -0.47 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 791 TYR 0.015 0.001 TYR C 624 PHE 0.016 0.001 PHE C 819 TRP 0.004 0.001 TRP C 706 HIS 0.003 0.001 HIS C 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 5522) covalent geometry : angle 0.50036 / 0.26 ( 7462) SS BOND : bond 0.01404 / 0.74 ( 2) SS BOND : angle 2.59284 / 1.37 ( 4) hydrogen bonds : bond 0.04902 / 3.26 ( 309) hydrogen bonds : angle 3.62998 / 2.52 ( 897) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: B 11 LEU cc_start: 0.8638 (mm) cc_final: 0.8221 (tp) REVERT: C 595 ASP cc_start: 0.9135 (t0) cc_final: 0.8772 (t0) REVERT: C 602 GLN cc_start: 0.9349 (mm-40) cc_final: 0.8977 (mm110) REVERT: C 608 GLN cc_start: 0.9006 (pp30) cc_final: 0.8789 (pp30) REVERT: C 609 ASP cc_start: 0.8783 (m-30) cc_final: 0.8282 (m-30) REVERT: C 622 GLU cc_start: 0.8728 (tt0) cc_final: 0.8066 (tm-30) REVERT: C 636 ASP cc_start: 0.8333 (t0) cc_final: 0.7654 (t0) REVERT: C 654 ASN cc_start: 0.9443 (t0) cc_final: 0.9219 (t0) REVERT: C 789 ASP cc_start: 0.8964 (t70) cc_final: 0.8703 (t0) REVERT: C 817 ASP cc_start: 0.9025 (m-30) cc_final: 0.8732 (m-30) REVERT: D 70 TYR cc_start: 0.8006 (p90) cc_final: 0.7608 (p90) REVERT: E 47 ASN cc_start: 0.9256 (t0) cc_final: 0.8956 (t0) REVERT: E 50 ASP cc_start: 0.7643 (p0) cc_final: 0.7187 (p0) REVERT: E 53 SER cc_start: 0.9477 (m) cc_final: 0.9108 (p) REVERT: E 62 LYS cc_start: 0.9047 (tmmt) cc_final: 0.8793 (tmmt) REVERT: E 66 LYS cc_start: 0.8680 (tptp) cc_final: 0.8452 (tptp) REVERT: E 67 MET cc_start: 0.7961 (tmt) cc_final: 0.7734 (tmm) outliers start: 6 outliers final: 5 residues processed: 62 average time/residue: 0.5524 time to fit residues: 35.8782 Evaluate side-chains 61 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 615 ILE Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 185 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3322 r_free = 0.3322 target = 0.070179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.047962 restraints weight = 15224.953| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 3.70 r_work: 0.2586 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 5524 Z= 0.137 Angle : 0.489 7.138 7466 Z= 0.250 Chirality : 0.038 0.166 822 Planarity : 0.004 0.052 950 Dihedral : 3.517 24.039 727 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.23 % Allowed : 8.26 % Favored : 90.51 % 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: 1.37 (0.35), residues: 657 helix: 1.55 (0.25), residues: 458 sheet: -1.05 (1.68), residues: 12 loop : -0.46 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 791 TYR 0.011 0.001 TYR C 624 PHE 0.015 0.001 PHE C 819 TRP 0.003 0.001 TRP E 39 HIS 0.002 0.000 HIS C 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 5522) covalent geometry : angle 0.48525 / 0.25 ( 7462) SS BOND : bond 0.01406 / 0.74 ( 2) SS BOND : angle 2.58097 / 1.37 ( 4) hydrogen bonds : bond 0.04376 / 2.92 ( 309) hydrogen bonds : angle 3.51890 / 2.44 ( 897) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: B 11 LEU cc_start: 0.8663 (mm) cc_final: 0.8253 (tp) REVERT: C 595 ASP cc_start: 0.9157 (t0) cc_final: 0.8769 (t0) REVERT: C 602 GLN cc_start: 0.9329 (mm-40) cc_final: 0.8918 (mm110) REVERT: C 608 GLN cc_start: 0.9011 (pp30) cc_final: 0.8754 (pp30) REVERT: C 609 ASP cc_start: 0.8784 (m-30) cc_final: 0.8204 (m-30) REVERT: C 622 GLU cc_start: 0.8711 (tt0) cc_final: 0.8029 (tm-30) REVERT: C 636 ASP cc_start: 0.8169 (t0) cc_final: 0.7497 (t0) REVERT: C 654 ASN cc_start: 0.9428 (t0) cc_final: 0.9199 (t0) REVERT: C 758 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8296 (tp40) REVERT: C 789 ASP cc_start: 0.8948 (t70) cc_final: 0.8689 (t0) REVERT: C 817 ASP cc_start: 0.9020 (m-30) cc_final: 0.8727 (m-30) REVERT: D 70 TYR cc_start: 0.8029 (p90) cc_final: 0.7718 (p90) REVERT: E 47 ASN cc_start: 0.9273 (t0) cc_final: 0.8965 (t0) REVERT: E 50 ASP cc_start: 0.7658 (p0) cc_final: 0.7221 (p0) REVERT: E 51 ASP cc_start: 0.8834 (t0) cc_final: 0.8613 (t0) REVERT: E 53 SER cc_start: 0.9463 (m) cc_final: 0.9069 (p) REVERT: E 55 GLN cc_start: 0.9155 (mt0) cc_final: 0.8930 (mt0) REVERT: E 62 LYS cc_start: 0.9068 (tmmt) cc_final: 0.8665 (tmmt) REVERT: E 66 LYS cc_start: 0.8716 (tptp) cc_final: 0.8422 (tptp) outliers start: 7 outliers final: 5 residues processed: 66 average time/residue: 0.4155 time to fit residues: 29.0241 Evaluate side-chains 64 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 615 ILE Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 758 GLN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 185 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.070507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.048314 restraints weight = 15593.135| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.73 r_work: 0.2596 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 5524 Z= 0.126 Angle : 0.475 7.167 7466 Z= 0.243 Chirality : 0.037 0.110 822 Planarity : 0.003 0.048 950 Dihedral : 3.469 23.479 727 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.05 % Allowed : 9.31 % Favored : 89.63 % 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: 1.46 (0.35), residues: 657 helix: 1.63 (0.25), residues: 458 sheet: -1.17 (1.67), residues: 12 loop : -0.44 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 791 TYR 0.010 0.001 TYR C 624 PHE 0.014 0.001 PHE C 819 TRP 0.003 0.000 TRP C 706 HIS 0.002 0.000 HIS C 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 5522) covalent geometry : angle 0.47124 / 0.24 ( 7462) SS BOND : bond 0.01389 / 0.73 ( 2) SS BOND : angle 2.56789 / 1.35 ( 4) hydrogen bonds : bond 0.04156 / 2.77 ( 309) hydrogen bonds : angle 3.41784 / 2.37 ( 897) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: B 11 LEU cc_start: 0.8665 (mm) cc_final: 0.8260 (tp) REVERT: C 595 ASP cc_start: 0.9172 (t0) cc_final: 0.8783 (t0) REVERT: C 602 GLN cc_start: 0.9302 (mm-40) cc_final: 0.8885 (mm110) REVERT: C 608 GLN cc_start: 0.9017 (pp30) cc_final: 0.8765 (pp30) REVERT: C 609 ASP cc_start: 0.8793 (m-30) cc_final: 0.8261 (m-30) REVERT: C 622 GLU cc_start: 0.8705 (tt0) cc_final: 0.8019 (tm-30) REVERT: C 636 ASP cc_start: 0.8120 (t0) cc_final: 0.7401 (t0) REVERT: C 654 ASN cc_start: 0.9422 (t0) cc_final: 0.9194 (t0) REVERT: C 758 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8331 (tp40) REVERT: C 789 ASP cc_start: 0.8954 (t70) cc_final: 0.8423 (t0) REVERT: C 817 ASP cc_start: 0.9005 (m-30) cc_final: 0.8707 (m-30) REVERT: D 70 TYR cc_start: 0.7984 (p90) cc_final: 0.7663 (p90) REVERT: E 47 ASN cc_start: 0.9256 (t0) cc_final: 0.8966 (t0) REVERT: E 50 ASP cc_start: 0.7613 (p0) cc_final: 0.7201 (p0) REVERT: E 51 ASP cc_start: 0.8819 (t0) cc_final: 0.8466 (t0) REVERT: E 53 SER cc_start: 0.9471 (m) cc_final: 0.9086 (p) REVERT: E 55 GLN cc_start: 0.9126 (mt0) cc_final: 0.8916 (mt0) REVERT: E 62 LYS cc_start: 0.9148 (tmmt) cc_final: 0.8847 (tmmt) REVERT: E 66 LYS cc_start: 0.8739 (tptp) cc_final: 0.8415 (tptp) outliers start: 6 outliers final: 5 residues processed: 67 average time/residue: 0.4816 time to fit residues: 33.8517 Evaluate side-chains 63 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 615 ILE Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 758 GLN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 185 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 28 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 646 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.070784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.048600 restraints weight = 15385.345| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 3.72 r_work: 0.2600 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5524 Z= 0.115 Angle : 0.477 7.499 7466 Z= 0.243 Chirality : 0.037 0.111 822 Planarity : 0.004 0.059 950 Dihedral : 3.436 23.358 727 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.05 % Allowed : 9.67 % Favored : 89.28 % 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: 1.47 (0.35), residues: 657 helix: 1.63 (0.25), residues: 458 sheet: -1.20 (1.67), residues: 12 loop : -0.43 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 791 TYR 0.007 0.001 TYR C 711 PHE 0.014 0.001 PHE C 819 TRP 0.003 0.000 TRP C 706 HIS 0.002 0.000 HIS C 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 ( 5522) covalent geometry : angle 0.47382 / 0.24 ( 7462) SS BOND : bond 0.01373 / 0.72 ( 2) SS BOND : angle 2.51551 / 1.32 ( 4) hydrogen bonds : bond 0.03983 / 2.64 ( 309) hydrogen bonds : angle 3.37468 / 2.34 ( 897) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LEU cc_start: 0.8670 (mm) cc_final: 0.8265 (tp) REVERT: C 595 ASP cc_start: 0.9174 (t0) cc_final: 0.8784 (t0) REVERT: C 602 GLN cc_start: 0.9274 (mm-40) cc_final: 0.8859 (mm110) REVERT: C 608 GLN cc_start: 0.9013 (pp30) cc_final: 0.8771 (pp30) REVERT: C 609 ASP cc_start: 0.8788 (m-30) cc_final: 0.8277 (m-30) REVERT: C 622 GLU cc_start: 0.8701 (tt0) cc_final: 0.8036 (tm-30) REVERT: C 636 ASP cc_start: 0.8074 (t0) cc_final: 0.7357 (t0) REVERT: C 758 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8354 (tp40) REVERT: C 789 ASP cc_start: 0.8983 (t70) cc_final: 0.8472 (t0) REVERT: C 817 ASP cc_start: 0.9028 (m-30) cc_final: 0.8733 (m-30) REVERT: D 70 TYR cc_start: 0.7983 (p90) cc_final: 0.7720 (p90) REVERT: E 47 ASN cc_start: 0.9258 (t0) cc_final: 0.8967 (t0) REVERT: E 50 ASP cc_start: 0.7597 (p0) cc_final: 0.7188 (p0) REVERT: E 53 SER cc_start: 0.9473 (m) cc_final: 0.9066 (p) REVERT: E 55 GLN cc_start: 0.9106 (mt0) cc_final: 0.8883 (mt0) outliers start: 6 outliers final: 5 residues processed: 66 average time/residue: 0.4226 time to fit residues: 29.3840 Evaluate side-chains 64 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 615 ILE Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 758 GLN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 185 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 30 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 58 optimal weight: 0.0170 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 8 GLN ** 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 = 0.3330 r_free = 0.3330 target = 0.070646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.048562 restraints weight = 15438.088| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.69 r_work: 0.2601 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 5524 Z= 0.126 Angle : 0.501 8.073 7466 Z= 0.251 Chirality : 0.037 0.111 822 Planarity : 0.004 0.064 950 Dihedral : 3.446 24.186 727 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.05 % Allowed : 10.37 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.35), residues: 657 helix: 1.67 (0.25), residues: 458 sheet: -1.17 (1.68), residues: 12 loop : -0.45 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 791 TYR 0.009 0.001 TYR C 624 PHE 0.013 0.001 PHE C 819 TRP 0.003 0.001 TRP C 706 HIS 0.002 0.000 HIS C 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 5522) covalent geometry : angle 0.49805 / 0.25 ( 7462) SS BOND : bond 0.01375 / 0.72 ( 2) SS BOND : angle 2.55985 / 1.34 ( 4) hydrogen bonds : bond 0.04069 / 2.71 ( 309) hydrogen bonds : angle 3.37393 / 2.34 ( 897) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 LEU cc_start: 0.8679 (mm) cc_final: 0.8273 (tp) REVERT: C 595 ASP cc_start: 0.9175 (t0) cc_final: 0.8784 (t0) REVERT: C 602 GLN cc_start: 0.9248 (mm-40) cc_final: 0.8838 (mm110) REVERT: C 608 GLN cc_start: 0.9019 (pp30) cc_final: 0.8774 (pp30) REVERT: C 609 ASP cc_start: 0.8799 (m-30) cc_final: 0.8281 (m-30) REVERT: C 622 GLU cc_start: 0.8704 (tt0) cc_final: 0.8012 (tm-30) REVERT: C 636 ASP cc_start: 0.8097 (t0) cc_final: 0.7368 (t0) REVERT: C 758 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8341 (tp40) REVERT: C 789 ASP cc_start: 0.8957 (t70) cc_final: 0.8454 (t0) REVERT: C 817 ASP cc_start: 0.9044 (m-30) cc_final: 0.8757 (m-30) REVERT: D 70 TYR cc_start: 0.7978 (p90) cc_final: 0.7713 (p90) REVERT: E 47 ASN cc_start: 0.9247 (t0) cc_final: 0.8968 (t0) REVERT: E 50 ASP cc_start: 0.7530 (p0) cc_final: 0.7119 (p0) REVERT: E 51 ASP cc_start: 0.8822 (t0) cc_final: 0.8567 (t0) REVERT: E 53 SER cc_start: 0.9471 (m) cc_final: 0.9058 (p) REVERT: E 55 GLN cc_start: 0.9094 (mt0) cc_final: 0.8860 (mt0) outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.4555 time to fit residues: 30.1868 Evaluate side-chains 62 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 615 ILE Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 758 GLN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 185 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 16 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 35 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 50 optimal weight: 0.0470 chunk 38 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 627 HIS ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.072780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.050551 restraints weight = 15768.499| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.80 r_work: 0.2659 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 5524 Z= 0.100 Angle : 0.497 7.944 7466 Z= 0.247 Chirality : 0.036 0.115 822 Planarity : 0.003 0.046 950 Dihedral : 3.306 22.601 727 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.88 % Allowed : 11.07 % Favored : 88.05 % 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: 1.58 (0.35), residues: 657 helix: 1.70 (0.25), residues: 458 sheet: -1.19 (1.98), residues: 10 loop : -0.36 (0.49), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 791 TYR 0.007 0.001 TYR D 376 PHE 0.013 0.001 PHE C 819 TRP 0.002 0.000 TRP C 706 HIS 0.001 0.000 HIS C 627 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 5522) covalent geometry : angle 0.49452 / 0.25 ( 7462) SS BOND : bond 0.01322 / 0.70 ( 2) SS BOND : angle 2.36512 / 1.25 ( 4) hydrogen bonds : bond 0.03349 / 2.24 ( 309) hydrogen bonds : angle 3.24803 / 2.25 ( 897) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 LEU cc_start: 0.8641 (mm) cc_final: 0.8238 (tp) REVERT: C 595 ASP cc_start: 0.9170 (t0) cc_final: 0.8774 (t0) REVERT: C 602 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8919 (mm110) REVERT: C 608 GLN cc_start: 0.8989 (pp30) cc_final: 0.8739 (pp30) REVERT: C 609 ASP cc_start: 0.8790 (m-30) cc_final: 0.8282 (m-30) REVERT: C 622 GLU cc_start: 0.8658 (tt0) cc_final: 0.7956 (tm-30) REVERT: C 636 ASP cc_start: 0.7840 (t0) cc_final: 0.7124 (t0) REVERT: C 758 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8329 (tp40) REVERT: C 778 LEU cc_start: 0.9264 (mt) cc_final: 0.8827 (pp) REVERT: C 789 ASP cc_start: 0.8934 (t70) cc_final: 0.8506 (t0) REVERT: C 817 ASP cc_start: 0.9038 (m-30) cc_final: 0.8756 (m-30) REVERT: D 70 TYR cc_start: 0.7909 (p90) cc_final: 0.7548 (p90) REVERT: E 47 ASN cc_start: 0.9219 (t0) cc_final: 0.8942 (t0) REVERT: E 50 ASP cc_start: 0.7391 (p0) cc_final: 0.7024 (p0) REVERT: E 51 ASP cc_start: 0.8808 (t0) cc_final: 0.8364 (t0) REVERT: E 53 SER cc_start: 0.9476 (m) cc_final: 0.9041 (p) REVERT: E 55 GLN cc_start: 0.9081 (mt0) cc_final: 0.8841 (mt0) REVERT: E 62 LYS cc_start: 0.8815 (ttpp) cc_final: 0.8431 (tmmt) REVERT: E 66 LYS cc_start: 0.8882 (tppp) cc_final: 0.8490 (tppt) outliers start: 5 outliers final: 2 residues processed: 64 average time/residue: 0.4244 time to fit residues: 28.6889 Evaluate side-chains 63 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 615 ILE Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 758 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 5 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 8 GLN ** 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 = 0.3309 r_free = 0.3309 target = 0.069839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.047741 restraints weight = 15856.374| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.74 r_work: 0.2580 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 5524 Z= 0.171 Angle : 0.549 8.441 7466 Z= 0.272 Chirality : 0.038 0.143 822 Planarity : 0.004 0.083 950 Dihedral : 3.439 22.466 727 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.53 % Allowed : 11.60 % Favored : 87.87 % 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: 1.60 (0.35), residues: 657 helix: 1.74 (0.25), residues: 458 sheet: -1.08 (1.71), residues: 12 loop : -0.43 (0.49), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 791 TYR 0.011 0.001 TYR C 624 PHE 0.015 0.001 PHE C 662 TRP 0.004 0.001 TRP C 706 HIS 0.003 0.001 HIS C 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 ( 5522) covalent geometry : angle 0.54528 / 0.27 ( 7462) SS BOND : bond 0.01436 / 0.75 ( 2) SS BOND : angle 2.76760 / 1.44 ( 4) hydrogen bonds : bond 0.04681 / 3.10 ( 309) hydrogen bonds : angle 3.44334 / 2.40 ( 897) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 LEU cc_start: 0.8693 (mm) cc_final: 0.8282 (tp) REVERT: C 595 ASP cc_start: 0.9178 (t0) cc_final: 0.8774 (t0) REVERT: C 602 GLN cc_start: 0.9228 (mm-40) cc_final: 0.8827 (mm110) REVERT: C 608 GLN cc_start: 0.9017 (pp30) cc_final: 0.8789 (pp30) REVERT: C 609 ASP cc_start: 0.8818 (m-30) cc_final: 0.8339 (m-30) REVERT: C 622 GLU cc_start: 0.8689 (tt0) cc_final: 0.8020 (tm-30) REVERT: C 636 ASP cc_start: 0.8190 (t0) cc_final: 0.7484 (t0) REVERT: C 688 ARG cc_start: 0.9043 (mtp-110) cc_final: 0.8728 (ttp80) REVERT: C 758 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8311 (tp40) REVERT: C 789 ASP cc_start: 0.8946 (t70) cc_final: 0.8490 (t0) REVERT: C 817 ASP cc_start: 0.9053 (m-30) cc_final: 0.8768 (m-30) REVERT: D 70 TYR cc_start: 0.7966 (p90) cc_final: 0.7707 (p90) REVERT: E 47 ASN cc_start: 0.9220 (t0) cc_final: 0.8958 (t0) REVERT: E 50 ASP cc_start: 0.7542 (p0) cc_final: 0.7137 (p0) REVERT: E 51 ASP cc_start: 0.8832 (t0) cc_final: 0.8525 (t0) REVERT: E 53 SER cc_start: 0.9464 (m) cc_final: 0.9037 (p) REVERT: E 55 GLN cc_start: 0.9086 (mt0) cc_final: 0.8829 (mt0) REVERT: E 66 LYS cc_start: 0.8958 (tppp) cc_final: 0.8464 (tptp) outliers start: 3 outliers final: 1 residues processed: 61 average time/residue: 0.4088 time to fit residues: 26.2111 Evaluate side-chains 60 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 615 ILE Chi-restraints excluded: chain C residue 758 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 48 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 8 GLN ** 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 = 0.3323 r_free = 0.3323 target = 0.070815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.048685 restraints weight = 15829.199| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.77 r_work: 0.2604 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 5524 Z= 0.131 Angle : 0.537 8.639 7466 Z= 0.264 Chirality : 0.037 0.155 822 Planarity : 0.004 0.084 950 Dihedral : 3.422 22.324 727 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.53 % Allowed : 11.25 % Favored : 88.22 % 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: 1.60 (0.35), residues: 657 helix: 1.73 (0.25), residues: 458 sheet: -1.07 (1.69), residues: 12 loop : -0.41 (0.49), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 791 TYR 0.009 0.001 TYR C 624 PHE 0.013 0.001 PHE C 819 TRP 0.003 0.001 TRP C 706 HIS 0.002 0.000 HIS C 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 5522) covalent geometry : angle 0.53397 / 0.26 ( 7462) SS BOND : bond 0.01367 / 0.72 ( 2) SS BOND : angle 2.63793 / 1.37 ( 4) hydrogen bonds : bond 0.04116 / 2.74 ( 309) hydrogen bonds : angle 3.35849 / 2.34 ( 897) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 LEU cc_start: 0.8680 (mm) cc_final: 0.8263 (tp) REVERT: C 595 ASP cc_start: 0.9178 (t0) cc_final: 0.8778 (t0) REVERT: C 602 GLN cc_start: 0.9210 (mm-40) cc_final: 0.8822 (mm110) REVERT: C 608 GLN cc_start: 0.9006 (pp30) cc_final: 0.8781 (pp30) REVERT: C 609 ASP cc_start: 0.8810 (m-30) cc_final: 0.8282 (m-30) REVERT: C 622 GLU cc_start: 0.8674 (tt0) cc_final: 0.7991 (tm-30) REVERT: C 636 ASP cc_start: 0.8056 (t0) cc_final: 0.7335 (t0) REVERT: C 688 ARG cc_start: 0.9048 (mtp-110) cc_final: 0.8728 (ttp80) REVERT: C 758 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8309 (tp40) REVERT: C 789 ASP cc_start: 0.8941 (t70) cc_final: 0.8487 (t0) REVERT: C 791 ARG cc_start: 0.9143 (mmm160) cc_final: 0.8459 (mmt-90) REVERT: C 817 ASP cc_start: 0.9018 (m-30) cc_final: 0.8722 (m-30) REVERT: D 70 TYR cc_start: 0.7943 (p90) cc_final: 0.7677 (p90) REVERT: E 47 ASN cc_start: 0.9221 (t0) cc_final: 0.8944 (t0) REVERT: E 50 ASP cc_start: 0.7492 (p0) cc_final: 0.7088 (p0) REVERT: E 51 ASP cc_start: 0.8846 (t0) cc_final: 0.8407 (t0) REVERT: E 53 SER cc_start: 0.9459 (m) cc_final: 0.9051 (p) REVERT: E 55 GLN cc_start: 0.9096 (mt0) cc_final: 0.8850 (mt0) REVERT: E 66 LYS cc_start: 0.8962 (tppp) cc_final: 0.8478 (tptp) outliers start: 3 outliers final: 2 residues processed: 61 average time/residue: 0.3862 time to fit residues: 24.7502 Evaluate side-chains 61 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 615 ILE Chi-restraints excluded: chain C residue 758 GLN Chi-restraints excluded: chain D residue 66 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 43 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 8 GLN ** 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 = 0.3324 r_free = 0.3324 target = 0.071046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.048886 restraints weight = 15958.740| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.78 r_work: 0.2611 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5524 Z= 0.127 Angle : 0.540 8.806 7466 Z= 0.265 Chirality : 0.037 0.161 822 Planarity : 0.004 0.080 950 Dihedral : 3.375 21.268 727 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.35 % Allowed : 11.60 % Favored : 88.05 % 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: 1.63 (0.35), residues: 657 helix: 1.75 (0.25), residues: 458 sheet: -0.96 (2.04), residues: 10 loop : -0.41 (0.49), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 791 TYR 0.009 0.001 TYR C 624 PHE 0.012 0.001 PHE C 819 TRP 0.003 0.001 TRP C 706 HIS 0.002 0.000 HIS C 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 5522) covalent geometry : angle 0.53675 / 0.26 ( 7462) SS BOND : bond 0.01394 / 0.73 ( 2) SS BOND : angle 2.57872 / 1.34 ( 4) hydrogen bonds : bond 0.03989 / 2.66 ( 309) hydrogen bonds : angle 3.31819 / 2.31 ( 897) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1470.48 seconds wall clock time: 25 minutes 41.85 seconds (1541.85 seconds total)