Starting phenix.real_space_refine on Thu Jul 2 03:17:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ca1_45379/07_2026/9ca1_45379_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ca1_45379/07_2026/9ca1_45379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ca1_45379/07_2026/9ca1_45379_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ca1_45379/07_2026/9ca1_45379_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ca1_45379/07_2026/9ca1_45379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ca1_45379/07_2026/9ca1_45379.map" } resolution = 3.26 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= 0.020 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 Mn 2 7.51 5 P 10 5.49 5 S 40 5.16 5 C 3927 2.51 5 N 1080 2.21 5 O 1206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6265 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4844 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 30, 'TRANS': 581} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1219 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "D" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 143 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "E" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Classifications: {'DNA': 3} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Time building chain proxies: 1.40, per 1000 atoms: 0.22 Number of scatterers: 6265 At special positions: 0 Unit cell: (71.38, 87.98, 136.12, 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) Mn 2 24.99 S 40 16.00 P 10 15.00 O 1206 8.00 N 1080 7.00 C 3927 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 350.9 milliseconds 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1442 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 5 sheets defined 41.9% alpha, 16.3% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 119 through 134 removed outlier: 4.184A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 157 through 166 Processing helix chain 'A' and resid 171 through 204 removed outlier: 4.228A pdb=" N ALA A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG A 194 " --> pdb=" O CYS A 190 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR A 204 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.665A pdb=" N CYS A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 252 removed outlier: 3.775A pdb=" N ASP A 252 " --> pdb=" O THR A 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 252' Processing helix chain 'A' and resid 266 through 279 removed outlier: 4.639A pdb=" N LEU A 279 " --> pdb=" O ASN A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'A' and resid 349 through 357 removed outlier: 4.060A pdb=" N GLN A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 404 through 421 removed outlier: 4.249A pdb=" N LEU A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 removed outlier: 3.757A pdb=" N GLU A 454 " --> pdb=" O GLY A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 507 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 538 through 552 Processing helix chain 'A' and resid 553 through 556 Processing helix chain 'A' and resid 559 through 573 removed outlier: 3.764A pdb=" N LEU A 570 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE A 571 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 598 removed outlier: 3.845A pdb=" N ASP A 598 " --> pdb=" O HIS A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 611 removed outlier: 4.013A pdb=" N LEU A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 17 through 25 Processing helix chain 'B' and resid 32 through 42 removed outlier: 4.064A pdb=" N ASN B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 6.019A pdb=" N SER A 37 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER A 56 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 41 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL A 4 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N THR A 55 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N MET A 6 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR A 3 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VAL A 113 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU A 5 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N TRP A 115 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL A 7 " --> pdb=" O TRP A 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 66 Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 476 removed outlier: 5.580A pdb=" N VAL A 285 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ARG A 434 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA A 287 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR A 426 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LYS A 425 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 435 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU A 438 " --> pdb=" O ILE A 435 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER A 443 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N LEU A 256 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA A 245 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TRP A 259 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU A 243 " --> pdb=" O TRP A 259 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS A 246 " --> pdb=" O GLU A 480 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU A 480 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 527 through 530 removed outlier: 3.649A pdb=" N ARG A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 66 removed outlier: 4.400A pdb=" N ASP B 134 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N LEU B 140 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR B 107 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU B 142 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 109 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU B 95 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ARG B 96 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE B 76 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN B 98 " --> pdb=" O GLN B 74 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LYS B 126 " --> pdb=" O LEU B 150 " (cutoff:3.500A) 268 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1861 1.33 - 1.45: 1001 1.45 - 1.57: 3468 1.57 - 1.69: 17 1.69 - 1.81: 63 Bond restraints: 6410 Sorted by residual: bond pdb=" OH PTR A 336 " pdb=" P PTR A 336 " ideal model delta sigma weight residual 1.769 1.607 0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" O3' DA D 2 " pdb=" P DA D 3 " ideal model delta sigma weight residual 1.607 1.562 0.045 1.50e-02 4.44e+03 9.05e+00 bond pdb=" O1P PTR A 336 " pdb=" P PTR A 336 " ideal model delta sigma weight residual 1.522 1.480 0.042 2.00e-02 2.50e+03 4.48e+00 bond pdb=" N TRP A 73 " pdb=" CA TRP A 73 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.29e+00 bond pdb=" CZ PTR A 336 " pdb=" OH PTR A 336 " ideal model delta sigma weight residual 1.339 1.301 0.038 2.00e-02 2.50e+03 3.66e+00 ... (remaining 6405 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 8553 1.96 - 3.93: 139 3.93 - 5.89: 18 5.89 - 7.85: 2 7.85 - 9.82: 2 Bond angle restraints: 8714 Sorted by residual: angle pdb=" N3 DT D 1 " pdb=" C4 DT D 1 " pdb=" O4 DT D 1 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT E 7 " pdb=" C4 DT E 7 " pdb=" O4 DT E 7 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT E 6 " pdb=" C4 DT E 6 " pdb=" O4 DT E 6 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 angle pdb=" O4' DA D 3 " pdb=" C4' DA D 3 " pdb=" C3' DA D 3 " ideal model delta sigma weight residual 106.00 103.66 2.34 6.00e-01 2.78e+00 1.52e+01 angle pdb=" N VAL A 455 " pdb=" CA VAL A 455 " pdb=" C VAL A 455 " ideal model delta sigma weight residual 112.96 109.10 3.86 1.00e+00 1.00e+00 1.49e+01 ... (remaining 8709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 3398 17.90 - 35.80: 377 35.80 - 53.70: 80 53.70 - 71.60: 14 71.60 - 89.50: 8 Dihedral angle restraints: 3877 sinusoidal: 1643 harmonic: 2234 Sorted by residual: dihedral pdb=" CD ARG A 181 " pdb=" NE ARG A 181 " pdb=" CZ ARG A 181 " pdb=" NH1 ARG A 181 " ideal model delta sinusoidal sigma weight residual 0.00 41.83 -41.83 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" CB GLU A 340 " pdb=" CG GLU A 340 " pdb=" CD GLU A 340 " pdb=" OE1 GLU A 340 " ideal model delta sinusoidal sigma weight residual 0.00 -89.50 89.50 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU B 22 " pdb=" CG GLU B 22 " pdb=" CD GLU B 22 " pdb=" OE1 GLU B 22 " ideal model delta sinusoidal sigma weight residual 0.00 87.51 -87.51 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 3874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 566 0.027 - 0.054: 246 0.054 - 0.082: 107 0.082 - 0.109: 40 0.109 - 0.136: 18 Chirality restraints: 977 Sorted by residual: chirality pdb=" CA ILE A 435 " pdb=" N ILE A 435 " pdb=" C ILE A 435 " pdb=" CB ILE A 435 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA PTR A 336 " pdb=" N PTR A 336 " pdb=" C PTR A 336 " pdb=" CB PTR A 336 " both_signs ideal model delta sigma weight residual False 2.35 2.48 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA PRO A 457 " pdb=" N PRO A 457 " pdb=" C PRO A 457 " pdb=" CB PRO A 457 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 974 not shown) Planarity restraints: 1092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 181 " -0.731 9.50e-02 1.11e+02 3.27e-01 6.53e+01 pdb=" NE ARG A 181 " 0.043 2.00e-02 2.50e+03 pdb=" CZ ARG A 181 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 181 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 181 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 476 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO A 477 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 477 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 477 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 77 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO A 78 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 78 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 78 " -0.023 5.00e-02 4.00e+02 ... (remaining 1089 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 103 2.68 - 3.23: 5725 3.23 - 3.79: 8978 3.79 - 4.34: 11810 4.34 - 4.90: 19824 Nonbonded interactions: 46440 Sorted by model distance: nonbonded pdb=" OD2 ASP A 511 " pdb="MN MN A 702 " model vdw 2.120 3.060 nonbonded pdb=" OE1 GLU A 340 " pdb="MN MN A 702 " model vdw 2.124 3.060 nonbonded pdb=" OD2 ASP A 117 " pdb="MN MN A 701 " model vdw 2.130 3.060 nonbonded pdb=" O3' DA D 4 " pdb="MN MN A 701 " model vdw 2.144 3.060 nonbonded pdb=" OE2 GLU A 9 " pdb="MN MN A 701 " model vdw 2.152 3.060 ... (remaining 46435 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: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.680 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: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 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 : 0.004 0.162 6411 Z= 0.244 Angle : 0.600 9.818 8714 Z= 0.341 Chirality : 0.040 0.136 977 Planarity : 0.011 0.327 1092 Dihedral : 15.560 89.505 2435 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.18 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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 (0.31), residues: 766 helix: 1.31 (0.31), residues: 299 sheet: 0.44 (0.49), residues: 121 loop : -0.90 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.010 0.001 TYR A 578 PHE 0.011 0.001 PHE A 127 TRP 0.014 0.001 TRP A 363 HIS 0.004 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.22 ( 6410) covalent geometry : angle 0.60050 / 0.34 ( 8714) hydrogen bonds : bond 0.09879 / 7.21 ( 268) hydrogen bonds : angle 4.98909 / 3.44 ( 768) Misc. bond : bond 0.09028 / 4.75 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 166 CYS cc_start: 0.7358 (t) cc_final: 0.7048 (t) REVERT: A 274 LEU cc_start: 0.8604 (tp) cc_final: 0.8385 (tt) REVERT: A 474 ASP cc_start: 0.7758 (m-30) cc_final: 0.7405 (m-30) REVERT: A 579 ARG cc_start: 0.6885 (mmp-170) cc_final: 0.6635 (mmp-170) REVERT: B 150 LEU cc_start: 0.8379 (mm) cc_final: 0.8173 (mp) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.0942 time to fit residues: 25.2254 Evaluate side-chains 197 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.112448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.100013 restraints weight = 9870.797| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.43 r_work: 0.3132 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6411 Z= 0.151 Angle : 0.544 7.438 8714 Z= 0.293 Chirality : 0.041 0.156 977 Planarity : 0.004 0.052 1092 Dihedral : 10.396 80.301 950 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.66 % Favored : 96.21 % Rotamer: Outliers : 1.20 % Allowed : 10.64 % Favored : 88.16 % 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: 0.27 (0.31), residues: 766 helix: 1.35 (0.31), residues: 301 sheet: 0.32 (0.48), residues: 121 loop : -0.92 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 369 TYR 0.015 0.001 TYR A 426 PHE 0.011 0.001 PHE A 214 TRP 0.007 0.001 TRP A 363 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 6410) covalent geometry : angle 0.54413 / 0.29 ( 8714) hydrogen bonds : bond 0.04111 / 2.92 ( 268) hydrogen bonds : angle 4.33290 / 2.99 ( 768) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 197 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.8218 (tt) cc_final: 0.8015 (tp) REVERT: A 84 GLN cc_start: 0.8171 (tt0) cc_final: 0.7863 (tt0) REVERT: A 145 LYS cc_start: 0.8341 (ptmt) cc_final: 0.7923 (ptmt) REVERT: A 166 CYS cc_start: 0.8080 (t) cc_final: 0.7741 (t) REVERT: A 340 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7478 (mt-10) REVERT: A 425 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8205 (mttm) REVERT: A 474 ASP cc_start: 0.8298 (m-30) cc_final: 0.8081 (m-30) REVERT: A 510 THR cc_start: 0.8051 (m) cc_final: 0.7605 (p) REVERT: A 552 ASP cc_start: 0.7688 (t0) cc_final: 0.7443 (t0) REVERT: A 567 GLN cc_start: 0.7834 (tp40) cc_final: 0.7366 (tp40) REVERT: A 579 ARG cc_start: 0.7327 (mmp-170) cc_final: 0.7115 (mmp-170) REVERT: B 9 LEU cc_start: 0.8614 (mm) cc_final: 0.8239 (mm) outliers start: 8 outliers final: 4 residues processed: 199 average time/residue: 0.0913 time to fit residues: 22.9092 Evaluate side-chains 199 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 195 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 27 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 3 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 70 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 52 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.111970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.099488 restraints weight = 9799.288| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.44 r_work: 0.3122 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6411 Z= 0.154 Angle : 0.531 7.917 8714 Z= 0.283 Chirality : 0.041 0.136 977 Planarity : 0.004 0.053 1092 Dihedral : 10.421 78.832 950 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.39 % Favored : 96.48 % Rotamer: Outliers : 2.70 % Allowed : 12.44 % Favored : 84.86 % 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: 0.25 (0.31), residues: 766 helix: 1.36 (0.31), residues: 301 sheet: 0.09 (0.47), residues: 127 loop : -0.88 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 591 TYR 0.013 0.001 TYR A 426 PHE 0.012 0.002 PHE A 214 TRP 0.007 0.001 TRP A 115 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 6410) covalent geometry : angle 0.53148 / 0.28 ( 8714) hydrogen bonds : bond 0.04105 / 2.90 ( 268) hydrogen bonds : angle 4.25319 / 2.92 ( 768) Misc. bond : bond 0.00397 / 0.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 26 LEU cc_start: 0.8202 (tt) cc_final: 0.7967 (tp) REVERT: A 84 GLN cc_start: 0.7776 (tt0) cc_final: 0.7347 (tt0) REVERT: A 145 LYS cc_start: 0.8185 (ptmt) cc_final: 0.7752 (ptmt) REVERT: A 166 CYS cc_start: 0.7936 (t) cc_final: 0.7565 (t) REVERT: A 231 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8347 (tttp) REVERT: A 383 ASP cc_start: 0.8256 (t0) cc_final: 0.8030 (t70) REVERT: A 425 LYS cc_start: 0.8450 (mtmm) cc_final: 0.8088 (mttm) REVERT: A 474 ASP cc_start: 0.8124 (m-30) cc_final: 0.7902 (m-30) REVERT: A 510 THR cc_start: 0.8142 (OUTLIER) cc_final: 0.7728 (p) REVERT: A 552 ASP cc_start: 0.7573 (t0) cc_final: 0.7351 (t0) REVERT: A 579 ARG cc_start: 0.7167 (mmp-170) cc_final: 0.6940 (mmp-170) REVERT: B 9 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8135 (mm) REVERT: B 63 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7051 (mm-30) outliers start: 18 outliers final: 12 residues processed: 199 average time/residue: 0.0882 time to fit residues: 22.1545 Evaluate side-chains 207 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 118 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.110975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.098682 restraints weight = 9882.023| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.40 r_work: 0.3095 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6411 Z= 0.187 Angle : 0.541 8.192 8714 Z= 0.289 Chirality : 0.042 0.137 977 Planarity : 0.004 0.053 1092 Dihedral : 10.507 76.160 950 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.66 % Favored : 96.21 % Rotamer: Outliers : 2.85 % Allowed : 15.29 % Favored : 81.86 % 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: 0.24 (0.31), residues: 766 helix: 1.38 (0.31), residues: 301 sheet: 0.07 (0.47), residues: 127 loop : -0.91 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 369 TYR 0.013 0.001 TYR A 426 PHE 0.013 0.002 PHE A 214 TRP 0.009 0.001 TRP A 115 HIS 0.003 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 ( 6410) covalent geometry : angle 0.54107 / 0.29 ( 8714) hydrogen bonds : bond 0.04355 / 3.07 ( 268) hydrogen bonds : angle 4.26886 / 2.93 ( 768) Misc. bond : bond 0.00172 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 26 LEU cc_start: 0.8297 (tt) cc_final: 0.8051 (tp) REVERT: A 84 GLN cc_start: 0.8028 (tt0) cc_final: 0.7639 (tt0) REVERT: A 145 LYS cc_start: 0.8367 (ptmt) cc_final: 0.8071 (ptmm) REVERT: A 166 CYS cc_start: 0.8145 (t) cc_final: 0.7804 (t) REVERT: A 231 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8550 (tttp) REVERT: A 425 LYS cc_start: 0.8568 (mtmm) cc_final: 0.8208 (mttm) REVERT: A 474 ASP cc_start: 0.8354 (m-30) cc_final: 0.8003 (m-30) REVERT: A 510 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.7853 (p) REVERT: A 552 ASP cc_start: 0.7778 (t0) cc_final: 0.7516 (t0) REVERT: A 579 ARG cc_start: 0.7393 (mmp-170) cc_final: 0.7148 (mmp-170) REVERT: B 9 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8206 (mm) REVERT: B 62 VAL cc_start: 0.8480 (p) cc_final: 0.7676 (p) REVERT: B 63 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7322 (mm-30) outliers start: 19 outliers final: 14 residues processed: 202 average time/residue: 0.0885 time to fit residues: 22.5308 Evaluate side-chains 215 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 115 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 53 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.110761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.098255 restraints weight = 9986.927| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.46 r_work: 0.3105 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6411 Z= 0.176 Angle : 0.533 8.640 8714 Z= 0.285 Chirality : 0.041 0.139 977 Planarity : 0.004 0.052 1092 Dihedral : 10.559 75.228 950 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.79 % Favored : 96.08 % Rotamer: Outliers : 3.75 % Allowed : 16.19 % Favored : 80.06 % 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: 0.22 (0.31), residues: 766 helix: 1.37 (0.31), residues: 301 sheet: 0.05 (0.48), residues: 127 loop : -0.93 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 591 TYR 0.013 0.001 TYR A 426 PHE 0.016 0.002 PHE A 214 TRP 0.010 0.001 TRP A 115 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 ( 6410) covalent geometry : angle 0.53290 / 0.29 ( 8714) hydrogen bonds : bond 0.04319 / 3.05 ( 268) hydrogen bonds : angle 4.22730 / 2.90 ( 768) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8182 (tt0) cc_final: 0.7939 (tt0) REVERT: A 84 GLN cc_start: 0.7782 (tt0) cc_final: 0.7342 (tt0) REVERT: A 145 LYS cc_start: 0.8319 (ptmt) cc_final: 0.7964 (ptmt) REVERT: A 166 CYS cc_start: 0.7994 (t) cc_final: 0.7640 (t) REVERT: A 231 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8381 (tttp) REVERT: A 340 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7286 (mt-10) REVERT: A 425 LYS cc_start: 0.8473 (mtmm) cc_final: 0.8124 (mttm) REVERT: A 474 ASP cc_start: 0.8127 (m-30) cc_final: 0.7781 (m-30) REVERT: A 510 THR cc_start: 0.8240 (OUTLIER) cc_final: 0.7860 (p) REVERT: A 579 ARG cc_start: 0.7210 (mmp-170) cc_final: 0.6965 (mmp-170) REVERT: B 9 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8092 (mm) REVERT: B 94 MET cc_start: 0.8381 (ttm) cc_final: 0.8147 (ttt) outliers start: 25 outliers final: 18 residues processed: 205 average time/residue: 0.0860 time to fit residues: 22.4395 Evaluate side-chains 217 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 158 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 1.9990 chunk 48 optimal weight: 0.0050 chunk 73 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.110733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.098284 restraints weight = 9795.466| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.41 r_work: 0.3101 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6411 Z= 0.174 Angle : 0.536 8.714 8714 Z= 0.287 Chirality : 0.041 0.136 977 Planarity : 0.004 0.051 1092 Dihedral : 10.565 72.861 950 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.45 % Allowed : 17.39 % Favored : 79.16 % 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: 0.20 (0.31), residues: 766 helix: 1.40 (0.31), residues: 300 sheet: -0.05 (0.47), residues: 132 loop : -0.94 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 591 TYR 0.013 0.001 TYR A 426 PHE 0.014 0.002 PHE A 214 TRP 0.009 0.001 TRP A 115 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 6410) covalent geometry : angle 0.53592 / 0.29 ( 8714) hydrogen bonds : bond 0.04303 / 3.04 ( 268) hydrogen bonds : angle 4.20313 / 2.88 ( 768) Misc. bond : bond 0.00090 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 0.156 Fit side-chains REVERT: A 9 GLU cc_start: 0.8366 (tt0) cc_final: 0.8129 (tt0) REVERT: A 84 GLN cc_start: 0.8069 (tt0) cc_final: 0.7662 (tt0) REVERT: A 145 LYS cc_start: 0.8442 (ptmt) cc_final: 0.8076 (ptmt) REVERT: A 166 CYS cc_start: 0.8187 (t) cc_final: 0.7860 (t) REVERT: A 231 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8561 (tttp) REVERT: A 232 ILE cc_start: 0.8653 (mt) cc_final: 0.8438 (tt) REVERT: A 340 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7602 (mt-10) REVERT: A 425 LYS cc_start: 0.8567 (mtmm) cc_final: 0.8210 (mttm) REVERT: A 474 ASP cc_start: 0.8339 (m-30) cc_final: 0.8026 (m-30) REVERT: A 510 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.7884 (p) REVERT: A 579 ARG cc_start: 0.7402 (mmp-170) cc_final: 0.7145 (mmp-170) REVERT: B 9 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8130 (mm) REVERT: B 11 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7700 (pm20) REVERT: B 63 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7309 (mm-30) REVERT: B 94 MET cc_start: 0.8461 (ttm) cc_final: 0.8241 (ttt) outliers start: 23 outliers final: 18 residues processed: 206 average time/residue: 0.0889 time to fit residues: 23.0742 Evaluate side-chains 220 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 118 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 58 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 75 optimal weight: 0.0570 chunk 32 optimal weight: 1.9990 chunk 55 optimal weight: 0.0770 chunk 0 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.111672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.099111 restraints weight = 9802.699| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.42 r_work: 0.3111 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6411 Z= 0.127 Angle : 0.516 9.042 8714 Z= 0.276 Chirality : 0.040 0.136 977 Planarity : 0.004 0.050 1092 Dihedral : 10.543 70.064 950 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.75 % Allowed : 18.89 % Favored : 77.36 % 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: 0.25 (0.31), residues: 766 helix: 1.45 (0.31), residues: 300 sheet: -0.06 (0.47), residues: 132 loop : -0.91 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 591 TYR 0.010 0.001 TYR A 426 PHE 0.016 0.001 PHE A 214 TRP 0.007 0.001 TRP A 115 HIS 0.004 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 6410) covalent geometry : angle 0.51571 / 0.28 ( 8714) hydrogen bonds : bond 0.03876 / 2.76 ( 268) hydrogen bonds : angle 4.13005 / 2.84 ( 768) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.223 Fit side-chains REVERT: A 9 GLU cc_start: 0.8340 (tt0) cc_final: 0.8013 (tt0) REVERT: A 84 GLN cc_start: 0.8048 (tt0) cc_final: 0.7616 (tt0) REVERT: A 88 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7200 (mm-30) REVERT: A 145 LYS cc_start: 0.8450 (ptmt) cc_final: 0.8119 (ptmt) REVERT: A 166 CYS cc_start: 0.8133 (t) cc_final: 0.7778 (t) REVERT: A 231 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8443 (ttmm) REVERT: A 340 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7578 (mt-10) REVERT: A 425 LYS cc_start: 0.8559 (mtmm) cc_final: 0.8188 (mttm) REVERT: A 474 ASP cc_start: 0.8353 (m-30) cc_final: 0.8017 (m-30) REVERT: A 510 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7844 (p) REVERT: A 579 ARG cc_start: 0.7383 (mmp-170) cc_final: 0.7124 (mmp-170) REVERT: B 9 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8115 (mm) REVERT: B 11 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7664 (pm20) REVERT: B 63 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7281 (mm-30) REVERT: B 94 MET cc_start: 0.8461 (ttm) cc_final: 0.8240 (ttt) outliers start: 25 outliers final: 17 residues processed: 206 average time/residue: 0.0942 time to fit residues: 24.5013 Evaluate side-chains 215 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 158 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 28 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 45 optimal weight: 0.0030 chunk 69 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.111270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.098637 restraints weight = 9903.058| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.44 r_work: 0.3103 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6411 Z= 0.152 Angle : 0.534 9.155 8714 Z= 0.287 Chirality : 0.041 0.168 977 Planarity : 0.004 0.050 1092 Dihedral : 10.523 66.091 950 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.45 % Allowed : 18.59 % Favored : 77.96 % 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: 0.18 (0.31), residues: 766 helix: 1.39 (0.31), residues: 300 sheet: -0.09 (0.47), residues: 132 loop : -0.95 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 369 TYR 0.011 0.001 TYR A 426 PHE 0.014 0.002 PHE A 214 TRP 0.007 0.001 TRP A 115 HIS 0.003 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 6410) covalent geometry : angle 0.53429 / 0.29 ( 8714) hydrogen bonds : bond 0.04040 / 2.86 ( 268) hydrogen bonds : angle 4.15758 / 2.85 ( 768) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.156 Fit side-chains REVERT: A 22 SER cc_start: 0.6541 (m) cc_final: 0.5697 (p) REVERT: A 84 GLN cc_start: 0.8053 (tt0) cc_final: 0.7596 (tt0) REVERT: A 145 LYS cc_start: 0.8500 (ptmt) cc_final: 0.8159 (ptmt) REVERT: A 166 CYS cc_start: 0.8155 (t) cc_final: 0.7796 (t) REVERT: A 207 LEU cc_start: 0.8762 (pt) cc_final: 0.8537 (pp) REVERT: A 231 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8394 (ttmm) REVERT: A 340 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7453 (mt-10) REVERT: A 386 ASP cc_start: 0.7643 (m-30) cc_final: 0.7313 (m-30) REVERT: A 425 LYS cc_start: 0.8584 (mtmm) cc_final: 0.8222 (mttm) REVERT: A 474 ASP cc_start: 0.8339 (m-30) cc_final: 0.8004 (m-30) REVERT: A 510 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7845 (p) REVERT: A 579 ARG cc_start: 0.7394 (mmp-170) cc_final: 0.7134 (mmp-170) REVERT: B 9 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8126 (mm) REVERT: B 11 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7684 (pm20) REVERT: B 63 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7279 (mm-30) REVERT: B 94 MET cc_start: 0.8476 (ttm) cc_final: 0.8252 (ttt) outliers start: 23 outliers final: 18 residues processed: 207 average time/residue: 0.0826 time to fit residues: 21.6511 Evaluate side-chains 219 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 158 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 50 optimal weight: 0.0980 chunk 53 optimal weight: 0.3980 chunk 56 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.111382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.098817 restraints weight = 9871.233| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.44 r_work: 0.3114 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6411 Z= 0.156 Angle : 0.549 9.362 8714 Z= 0.294 Chirality : 0.041 0.151 977 Planarity : 0.004 0.050 1092 Dihedral : 10.488 65.648 950 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.30 % Allowed : 19.64 % Favored : 77.06 % 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: 0.18 (0.31), residues: 766 helix: 1.40 (0.31), residues: 300 sheet: -0.06 (0.47), residues: 132 loop : -0.97 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 369 TYR 0.012 0.001 TYR A 426 PHE 0.013 0.002 PHE A 214 TRP 0.008 0.001 TRP A 115 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 6410) covalent geometry : angle 0.54920 / 0.29 ( 8714) hydrogen bonds : bond 0.04076 / 2.88 ( 268) hydrogen bonds : angle 4.17327 / 2.86 ( 768) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.228 Fit side-chains REVERT: A 22 SER cc_start: 0.6430 (m) cc_final: 0.5577 (p) REVERT: A 84 GLN cc_start: 0.7821 (tt0) cc_final: 0.7351 (tt0) REVERT: A 88 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6831 (mm-30) REVERT: A 145 LYS cc_start: 0.8327 (ptmt) cc_final: 0.7982 (ptmt) REVERT: A 166 CYS cc_start: 0.8005 (t) cc_final: 0.7641 (t) REVERT: A 207 LEU cc_start: 0.8758 (pt) cc_final: 0.8491 (pp) REVERT: A 231 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8215 (ttmm) REVERT: A 340 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7136 (mt-10) REVERT: A 386 ASP cc_start: 0.7422 (m-30) cc_final: 0.7051 (m-30) REVERT: A 425 LYS cc_start: 0.8494 (mtmm) cc_final: 0.8138 (mttm) REVERT: A 474 ASP cc_start: 0.8104 (m-30) cc_final: 0.7807 (m-30) REVERT: A 510 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7870 (p) REVERT: A 579 ARG cc_start: 0.7194 (mmp-170) cc_final: 0.6924 (mmp-170) REVERT: B 9 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8027 (mm) REVERT: B 11 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7569 (pm20) REVERT: B 63 GLU cc_start: 0.7519 (mm-30) cc_final: 0.6968 (mm-30) outliers start: 22 outliers final: 18 residues processed: 200 average time/residue: 0.0945 time to fit residues: 23.8501 Evaluate side-chains 213 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 158 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.111293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.098935 restraints weight = 9671.660| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.37 r_work: 0.3115 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6411 Z= 0.167 Angle : 0.557 9.508 8714 Z= 0.298 Chirality : 0.041 0.151 977 Planarity : 0.004 0.050 1092 Dihedral : 10.481 66.350 950 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.45 % Allowed : 19.19 % Favored : 77.36 % 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: 0.17 (0.31), residues: 766 helix: 1.44 (0.31), residues: 301 sheet: -0.14 (0.46), residues: 134 loop : -0.99 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 369 TYR 0.013 0.001 TYR A 426 PHE 0.014 0.002 PHE A 214 TRP 0.008 0.001 TRP A 115 HIS 0.003 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 6410) covalent geometry : angle 0.55749 / 0.30 ( 8714) hydrogen bonds : bond 0.04185 / 2.95 ( 268) hydrogen bonds : angle 4.19752 / 2.88 ( 768) Misc. bond : bond 0.00060 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 195 time to evaluate : 0.283 Fit side-chains REVERT: A 22 SER cc_start: 0.6665 (m) cc_final: 0.5859 (p) REVERT: A 84 GLN cc_start: 0.8085 (tt0) cc_final: 0.7618 (tt0) REVERT: A 145 LYS cc_start: 0.8446 (ptmt) cc_final: 0.8084 (ptmt) REVERT: A 166 CYS cc_start: 0.8181 (t) cc_final: 0.7849 (t) REVERT: A 207 LEU cc_start: 0.8779 (pt) cc_final: 0.8551 (pp) REVERT: A 231 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8403 (ttmm) REVERT: A 340 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7452 (mt-10) REVERT: A 386 ASP cc_start: 0.7629 (m-30) cc_final: 0.7275 (m-30) REVERT: A 425 LYS cc_start: 0.8597 (mtmm) cc_final: 0.8242 (mttm) REVERT: A 474 ASP cc_start: 0.8329 (m-30) cc_final: 0.8022 (m-30) REVERT: A 510 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7889 (p) REVERT: A 579 ARG cc_start: 0.7410 (mmp-170) cc_final: 0.7145 (mmp-170) REVERT: B 9 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8116 (mm) REVERT: B 11 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: B 63 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7218 (mm-30) outliers start: 23 outliers final: 18 residues processed: 204 average time/residue: 0.0930 time to fit residues: 23.9343 Evaluate side-chains 218 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 158 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 0.0020 chunk 6 optimal weight: 0.0030 chunk 19 optimal weight: 0.6980 chunk 47 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 69 optimal weight: 0.0270 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 overall best weight: 0.1856 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.113222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.100595 restraints weight = 9667.083| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.39 r_work: 0.3140 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6411 Z= 0.106 Angle : 0.531 9.506 8714 Z= 0.283 Chirality : 0.040 0.154 977 Planarity : 0.004 0.049 1092 Dihedral : 10.386 64.601 950 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.25 % Allowed : 20.69 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.31), residues: 766 helix: 1.51 (0.31), residues: 300 sheet: 0.01 (0.47), residues: 132 loop : -0.95 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 369 TYR 0.011 0.001 TYR A 411 PHE 0.016 0.001 PHE A 214 TRP 0.007 0.001 TRP A 115 HIS 0.003 0.000 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 ( 6410) covalent geometry : angle 0.53059 / 0.28 ( 8714) hydrogen bonds : bond 0.03445 / 2.46 ( 268) hydrogen bonds : angle 4.10508 / 2.81 ( 768) Misc. bond : bond 0.00008 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1562.42 seconds wall clock time: 27 minutes 32.31 seconds (1652.31 seconds total)