Starting phenix.real_space_refine on Sat Jul 4 03:15:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pt7_17869/07_2026/8pt7_17869.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pt7_17869/07_2026/8pt7_17869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pt7_17869/07_2026/8pt7_17869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pt7_17869/07_2026/8pt7_17869.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pt7_17869/07_2026/8pt7_17869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pt7_17869/07_2026/8pt7_17869.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8pt7_17869/07_2026/8pt7_17869.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pt7_17869/07_2026/8pt7_17869.cif" } resolution = 2.8 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= 0.002 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: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 29 5.49 5 Mg 1 5.21 5 S 51 5.16 5 C 5565 2.51 5 N 1601 2.21 5 O 1784 1.98 5 H 8690 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 17722 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6652 Classifications: {'peptide': 417} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 394} Chain: "B" Number of atoms: 7973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 7973 Classifications: {'peptide': 515} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 493} Chain: "C" Number of atoms: 2221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2221 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "V" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 408 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 4, 'rna3p_pyr': 6} Link IDs: {'rna2p': 4, 'rna3p': 9} Chain: "S" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 466 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 6, 'rna3p': 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2583 SG CYS A 161 46.948 44.799 105.483 1.00 56.25 S ATOM 4472 SG CYS A 282 45.858 47.622 107.959 1.00 69.01 S Time building chain proxies: 3.27, per 1000 atoms: 0.18 Number of scatterers: 17722 At special positions: 0 Unit cell: (87.36, 95.76, 124.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 51 16.00 P 29 15.00 Mg 1 11.99 O 1784 8.00 N 1601 7.00 C 5565 6.00 H 8690 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 595.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 284 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 296 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 161 " Number of angles added : 2 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 10 sheets defined 45.5% alpha, 13.4% beta 7 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.700A pdb=" N CYS A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 141 through 157 removed outlier: 3.575A pdb=" N ILE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 223 through 237 Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 312 through 323 removed outlier: 4.481A pdb=" N ASP A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.539A pdb=" N VAL A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.859A pdb=" N ALA A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 388 through 392 Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.780A pdb=" N GLN B 5 " --> pdb=" O TRP B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 40 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.896A pdb=" N LEU B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 104 Processing helix chain 'B' and resid 107 through 117 Processing helix chain 'B' and resid 130 through 137 Processing helix chain 'B' and resid 161 through 183 removed outlier: 3.729A pdb=" N VAL B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 187 removed outlier: 3.763A pdb=" N THR B 187 " --> pdb=" O ALA B 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 184 through 187' Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 235 through 248 removed outlier: 3.720A pdb=" N GLY B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 354 through 372 removed outlier: 3.965A pdb=" N LEU B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 396 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.692A pdb=" N GLY B 413 " --> pdb=" O THR B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.944A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 Processing helix chain 'B' and resid 479 through 498 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 16 through 23 Processing helix chain 'C' and resid 34 through 40 Processing helix chain 'C' and resid 42 through 55 Processing helix chain 'C' and resid 56 through 59 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 100 through 109 removed outlier: 3.996A pdb=" N GLN C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 removed outlier: 3.571A pdb=" N TYR A 45 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP A 52 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N CYS A 71 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA A 54 " --> pdb=" O CYS A 71 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU A 73 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLU A 56 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 194 removed outlier: 7.449A pdb=" N TRP A 198 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N MET A 255 " --> pdb=" O TRP A 198 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLN A 200 " --> pdb=" O MET A 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 194 removed outlier: 7.449A pdb=" N TRP A 198 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N MET A 255 " --> pdb=" O TRP A 198 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLN A 200 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 74 through 80 Processing sheet with id=AA6, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AA7, first strand: chain 'B' and resid 155 through 159 removed outlier: 3.879A pdb=" N ARG B 155 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N PHE B 140 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 327 through 329 Processing sheet with id=AA9, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AB1, first strand: chain 'C' and resid 71 through 83 removed outlier: 9.430A pdb=" N LYS C 73 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N SER C 121 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LYS C 75 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N TYR C 119 " --> pdb=" O LYS C 75 " (cutoff:3.500A) 395 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 3.86 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8662 1.03 - 1.23: 37 1.23 - 1.42: 3911 1.42 - 1.62: 5276 1.62 - 1.81: 72 Bond restraints: 17958 Sorted by residual: bond pdb=" C LEU C 56 " pdb=" N PRO C 57 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.35e-01 bond pdb=" CG PRO C 57 " pdb=" CD PRO C 57 " ideal model delta sigma weight residual 1.503 1.479 0.024 3.40e-02 8.65e+02 5.08e-01 bond pdb=" CB ASP B 467 " pdb=" CG ASP B 467 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 4.98e-01 bond pdb=" CA PRO C 57 " pdb=" C PRO C 57 " ideal model delta sigma weight residual 1.520 1.529 -0.009 1.42e-02 4.96e+03 4.28e-01 bond pdb=" N GLY B 262 " pdb=" CA GLY B 262 " ideal model delta sigma weight residual 1.444 1.451 -0.007 1.06e-02 8.90e+03 3.77e-01 ... (remaining 17953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.85: 29208 0.85 - 1.70: 2945 1.70 - 2.55: 164 2.55 - 3.41: 74 3.41 - 4.26: 12 Bond angle restraints: 32403 Sorted by residual: angle pdb=" CA GLU C 89 " pdb=" CB GLU C 89 " pdb=" CG GLU C 89 " ideal model delta sigma weight residual 114.10 117.48 -3.38 2.00e+00 2.50e-01 2.85e+00 angle pdb=" N ASP B 467 " pdb=" CA ASP B 467 " pdb=" C ASP B 467 " ideal model delta sigma weight residual 110.91 108.97 1.94 1.17e+00 7.31e-01 2.74e+00 angle pdb=" C ASP C 110 " pdb=" N ARG C 111 " pdb=" CA ARG C 111 " ideal model delta sigma weight residual 122.21 119.64 2.57 1.62e+00 3.81e-01 2.52e+00 angle pdb=" N VAL A 414 " pdb=" CA VAL A 414 " pdb=" C VAL A 414 " ideal model delta sigma weight residual 111.81 110.47 1.34 8.60e-01 1.35e+00 2.45e+00 angle pdb=" C ASP A 301 " pdb=" CA ASP A 301 " pdb=" CB ASP A 301 " ideal model delta sigma weight residual 109.45 112.21 -2.76 1.81e+00 3.05e-01 2.33e+00 ... (remaining 32398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 7423 17.86 - 35.72: 685 35.72 - 53.58: 240 53.58 - 71.45: 63 71.45 - 89.31: 22 Dihedral angle restraints: 8433 sinusoidal: 4828 harmonic: 3605 Sorted by residual: dihedral pdb=" CA LEU B 265 " pdb=" C LEU B 265 " pdb=" N MET B 266 " pdb=" CA MET B 266 " ideal model delta harmonic sigma weight residual 180.00 161.00 19.00 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CB GLU A 326 " pdb=" CG GLU A 326 " pdb=" CD GLU A 326 " pdb=" OE1 GLU A 326 " ideal model delta sinusoidal sigma weight residual 0.00 89.31 -89.31 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 381 " pdb=" CG GLU A 381 " pdb=" CD GLU A 381 " pdb=" OE1 GLU A 381 " ideal model delta sinusoidal sigma weight residual 0.00 -89.27 89.27 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 8430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 918 0.026 - 0.053: 376 0.053 - 0.079: 76 0.079 - 0.105: 44 0.105 - 0.132: 31 Chirality restraints: 1445 Sorted by residual: chirality pdb=" CA VAL C 112 " pdb=" N VAL C 112 " pdb=" C VAL C 112 " pdb=" CB VAL C 112 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE B 125 " pdb=" N ILE B 125 " pdb=" C ILE B 125 " pdb=" CB ILE B 125 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA ILE B 253 " pdb=" N ILE B 253 " pdb=" C ILE B 253 " pdb=" CB ILE B 253 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1442 not shown) Planarity restraints: 2560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 469 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO B 470 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 133 " 0.126 9.50e-02 1.11e+02 4.21e-02 2.13e+00 pdb=" NE ARG A 133 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 133 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 133 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 133 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 133 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 133 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 133 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 133 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " -0.020 2.00e-02 2.50e+03 8.07e-03 2.12e+00 pdb=" N9 A V 4 " 0.019 2.00e-02 2.50e+03 pdb=" C8 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 4 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A V 4 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A V 4 " 0.004 2.00e-02 2.50e+03 pdb=" H8 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" H2 A V 4 " 0.001 2.00e-02 2.50e+03 ... (remaining 2557 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 831 2.18 - 2.78: 34123 2.78 - 3.39: 49388 3.39 - 3.99: 65796 3.99 - 4.60: 101554 Nonbonded interactions: 251692 Sorted by model distance: nonbonded pdb=" OE1 GLN B 57 " pdb=" HZ1 LYS B 181 " model vdw 1.569 2.450 nonbonded pdb=" OE1 GLU C 89 " pdb=" H GLU C 89 " model vdw 1.570 2.450 nonbonded pdb=" O2 C V 13 " pdb=" H21 G S 3 " model vdw 1.609 2.450 nonbonded pdb=" O PRO B 17 " pdb=" H GLN B 147 " model vdw 1.627 2.450 nonbonded pdb=" O ASN B 330 " pdb=" HG SER B 331 " model vdw 1.646 2.450 ... (remaining 251687 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: 2.080 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: 0.130 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 24.240 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 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 0.024 9272 Z= 0.096 Angle : 0.437 4.257 12662 Z= 0.232 Chirality : 0.035 0.132 1445 Planarity : 0.003 0.055 1525 Dihedral : 17.723 89.308 3617 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.44 % Favored : 97.46 % Rotamer: Outliers : 1.29 % Allowed : 23.44 % Favored : 75.27 % 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: 1.49 (0.26), residues: 1065 helix: 1.94 (0.25), residues: 462 sheet: 0.75 (0.52), residues: 87 loop : 0.23 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 133 TYR 0.011 0.001 TYR C 95 PHE 0.006 0.001 PHE C 44 TRP 0.004 0.001 TRP A 136 HIS 0.002 0.001 HIS A 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 ( 9268) covalent geometry : angle 0.43610 / 0.23 (12660) hydrogen bonds : bond 0.13682 / 9.07 ( 407) hydrogen bonds : angle 5.52501 / 3.88 ( 1114) metal coordination : bond 0.00310 / 0.15 ( 4) metal coordination : angle 1.76563 / 0.93 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: B 38 MET cc_start: 0.9239 (tpt) cc_final: 0.8756 (tpt) outliers start: 12 outliers final: 8 residues processed: 100 average time/residue: 1.2998 time to fit residues: 139.2762 Evaluate side-chains 95 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 125 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 195 ASN B 491 GLN C 109 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.112312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.076732 restraints weight = 34694.476| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 1.95 r_work: 0.2702 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.0641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9272 Z= 0.151 Angle : 0.469 4.192 12662 Z= 0.247 Chirality : 0.037 0.168 1445 Planarity : 0.004 0.049 1525 Dihedral : 10.203 73.675 1577 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.44 % Favored : 97.46 % Rotamer: Outliers : 1.83 % Allowed : 21.94 % Favored : 76.24 % 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: 1.42 (0.26), residues: 1065 helix: 1.89 (0.25), residues: 465 sheet: 0.84 (0.54), residues: 85 loop : 0.15 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 133 TYR 0.013 0.001 TYR A 403 PHE 0.011 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 9268) covalent geometry : angle 0.46861 / 0.25 (12660) hydrogen bonds : bond 0.05805 / 4.11 ( 407) hydrogen bonds : angle 4.54559 / 3.19 ( 1114) metal coordination : bond 0.00917 / 0.46 ( 4) metal coordination : angle 2.11987 / 1.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.7731 (mtt) REVERT: B 151 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8714 (mttp) REVERT: C 54 LYS cc_start: 0.8517 (tppt) cc_final: 0.8217 (mmmt) REVERT: C 59 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9324 (mt) REVERT: C 66 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7631 (mp0) outliers start: 17 outliers final: 5 residues processed: 100 average time/residue: 1.3083 time to fit residues: 140.1872 Evaluate side-chains 91 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 75 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN B 491 GLN C 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.112995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.077625 restraints weight = 34714.724| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 1.95 r_work: 0.2720 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9272 Z= 0.111 Angle : 0.443 4.036 12662 Z= 0.231 Chirality : 0.036 0.165 1445 Planarity : 0.003 0.047 1525 Dihedral : 9.970 73.522 1568 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.15 % Allowed : 21.51 % Favored : 76.34 % 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 (0.26), residues: 1065 helix: 2.17 (0.25), residues: 452 sheet: 0.99 (0.55), residues: 83 loop : 0.16 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 133 TYR 0.012 0.001 TYR A 403 PHE 0.009 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 9268) covalent geometry : angle 0.44214 / 0.23 (12660) hydrogen bonds : bond 0.05326 / 3.82 ( 407) hydrogen bonds : angle 4.28343 / 3.00 ( 1114) metal coordination : bond 0.00407 / 0.20 ( 4) metal coordination : angle 2.07540 / 1.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: B 38 MET cc_start: 0.9180 (tpt) cc_final: 0.8715 (tpt) REVERT: B 151 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8692 (mttp) REVERT: C 54 LYS cc_start: 0.8524 (tppt) cc_final: 0.8236 (mmmt) REVERT: C 66 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7656 (mp0) outliers start: 20 outliers final: 5 residues processed: 105 average time/residue: 1.3359 time to fit residues: 149.9212 Evaluate side-chains 96 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 75 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 103 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN B 491 GLN C 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.112665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.077259 restraints weight = 34771.800| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 1.95 r_work: 0.2694 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9272 Z= 0.146 Angle : 0.453 4.171 12662 Z= 0.238 Chirality : 0.036 0.161 1445 Planarity : 0.004 0.048 1525 Dihedral : 10.000 73.558 1568 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.26 % Allowed : 21.51 % Favored : 76.24 % 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: 1.52 (0.26), residues: 1065 helix: 2.09 (0.25), residues: 452 sheet: 0.86 (0.55), residues: 85 loop : 0.15 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 133 TYR 0.013 0.001 TYR A 403 PHE 0.012 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 9268) covalent geometry : angle 0.45208 / 0.24 (12660) hydrogen bonds : bond 0.05523 / 3.95 ( 407) hydrogen bonds : angle 4.23744 / 2.97 ( 1114) metal coordination : bond 0.00767 / 0.38 ( 4) metal coordination : angle 1.74252 / 0.92 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.491 Fit side-chains REVERT: A 409 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8508 (ttm110) REVERT: B 38 MET cc_start: 0.9236 (tpt) cc_final: 0.8761 (tpt) REVERT: B 151 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8676 (mttp) REVERT: C 54 LYS cc_start: 0.8540 (tppt) cc_final: 0.8250 (mmmt) REVERT: C 66 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7666 (mp0) outliers start: 21 outliers final: 8 residues processed: 104 average time/residue: 1.2658 time to fit residues: 140.9559 Evaluate side-chains 98 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 123 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN B 211 ASN B 491 GLN C 3 GLN C 96 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.109945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.074493 restraints weight = 34703.738| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 1.93 r_work: 0.2666 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9272 Z= 0.216 Angle : 0.484 4.326 12662 Z= 0.256 Chirality : 0.038 0.159 1445 Planarity : 0.004 0.050 1525 Dihedral : 10.139 73.653 1568 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.72 % Favored : 97.18 % Rotamer: Outliers : 2.58 % Allowed : 21.18 % Favored : 76.24 % 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: 1.22 (0.25), residues: 1065 helix: 1.74 (0.24), residues: 459 sheet: 0.73 (0.54), residues: 85 loop : 0.05 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 133 TYR 0.015 0.001 TYR A 403 PHE 0.018 0.001 PHE C 44 TRP 0.006 0.001 TRP A 136 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 ( 9268) covalent geometry : angle 0.48352 / 0.26 (12660) hydrogen bonds : bond 0.06014 / 4.27 ( 407) hydrogen bonds : angle 4.33153 / 3.04 ( 1114) metal coordination : bond 0.01303 / 0.65 ( 4) metal coordination : angle 1.62030 / 0.85 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 119 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8876 (mtp180) REVERT: A 255 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.7959 (mtt) REVERT: A 409 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8544 (ttm110) REVERT: B 38 MET cc_start: 0.9245 (tpt) cc_final: 0.8742 (tpt) REVERT: B 151 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8666 (mttp) REVERT: C 54 LYS cc_start: 0.8555 (tppt) cc_final: 0.8251 (mmmt) REVERT: C 66 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7713 (mp0) outliers start: 24 outliers final: 10 residues processed: 102 average time/residue: 1.3811 time to fit residues: 150.3691 Evaluate side-chains 101 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 125 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 89 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN B 491 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.112420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.076943 restraints weight = 34499.530| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 1.95 r_work: 0.2706 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9272 Z= 0.106 Angle : 0.437 4.059 12662 Z= 0.229 Chirality : 0.036 0.153 1445 Planarity : 0.004 0.049 1525 Dihedral : 9.990 73.475 1568 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.61 % Allowed : 21.72 % Favored : 76.67 % 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: 1.52 (0.26), residues: 1065 helix: 2.09 (0.25), residues: 452 sheet: 0.85 (0.55), residues: 85 loop : 0.15 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 133 TYR 0.011 0.001 TYR A 403 PHE 0.009 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 9268) covalent geometry : angle 0.43606 / 0.23 (12660) hydrogen bonds : bond 0.05205 / 3.77 ( 407) hydrogen bonds : angle 4.14013 / 2.90 ( 1114) metal coordination : bond 0.00360 / 0.18 ( 4) metal coordination : angle 1.98215 / 1.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.481 Fit side-chains REVERT: A 255 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.7436 (mmt) REVERT: A 409 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8478 (ttm110) REVERT: B 38 MET cc_start: 0.9190 (tpt) cc_final: 0.8640 (tpt) REVERT: B 127 ASP cc_start: 0.8757 (m-30) cc_final: 0.8496 (m-30) REVERT: B 151 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8651 (mttp) REVERT: B 235 MET cc_start: 0.9250 (mmp) cc_final: 0.8889 (mmt) REVERT: C 54 LYS cc_start: 0.8539 (tppt) cc_final: 0.8328 (mmtm) REVERT: C 66 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7731 (mp0) outliers start: 15 outliers final: 9 residues processed: 101 average time/residue: 1.2328 time to fit residues: 133.4253 Evaluate side-chains 101 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 125 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 83 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 88 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 0.0970 chunk 77 optimal weight: 0.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN B 491 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.076519 restraints weight = 34935.277| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 1.95 r_work: 0.2694 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9272 Z= 0.118 Angle : 0.438 4.094 12662 Z= 0.230 Chirality : 0.036 0.152 1445 Planarity : 0.004 0.048 1525 Dihedral : 9.982 73.490 1568 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.61 % Allowed : 21.72 % Favored : 76.67 % 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: 1.54 (0.26), residues: 1065 helix: 2.12 (0.24), residues: 452 sheet: 0.86 (0.55), residues: 85 loop : 0.15 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 133 TYR 0.012 0.001 TYR A 403 PHE 0.011 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 9268) covalent geometry : angle 0.43787 / 0.23 (12660) hydrogen bonds : bond 0.05281 / 3.81 ( 407) hydrogen bonds : angle 4.12405 / 2.89 ( 1114) metal coordination : bond 0.00538 / 0.27 ( 4) metal coordination : angle 1.80487 / 0.95 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.634 Fit side-chains REVERT: A 255 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.7844 (mtt) REVERT: A 409 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8495 (ttm110) REVERT: B 38 MET cc_start: 0.9179 (tpt) cc_final: 0.8626 (tpt) REVERT: B 151 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8643 (mttp) REVERT: B 235 MET cc_start: 0.9247 (mmp) cc_final: 0.8913 (mmp) REVERT: C 54 LYS cc_start: 0.8539 (tppt) cc_final: 0.8235 (mmmt) REVERT: C 66 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7717 (mp0) outliers start: 15 outliers final: 8 residues processed: 98 average time/residue: 1.2886 time to fit residues: 134.8015 Evaluate side-chains 100 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 125 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 17 optimal weight: 0.0370 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 0.0170 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 0.0170 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN B 491 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.114313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.079131 restraints weight = 34636.912| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.95 r_work: 0.2742 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9272 Z= 0.081 Angle : 0.420 4.175 12662 Z= 0.219 Chirality : 0.035 0.148 1445 Planarity : 0.003 0.053 1525 Dihedral : 9.840 73.387 1568 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.29 % Allowed : 21.94 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.26), residues: 1065 helix: 2.40 (0.25), residues: 452 sheet: 0.71 (0.55), residues: 89 loop : 0.24 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 133 TYR 0.009 0.001 TYR A 403 PHE 0.005 0.001 PHE B 158 TRP 0.005 0.001 TRP A 346 HIS 0.003 0.000 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.08 ( 9268) covalent geometry : angle 0.41883 / 0.22 (12660) hydrogen bonds : bond 0.04823 / 3.53 ( 407) hydrogen bonds : angle 3.95331 / 2.78 ( 1114) metal coordination : bond 0.00210 / 0.10 ( 4) metal coordination : angle 2.25709 / 1.21 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.484 Fit side-chains REVERT: A 409 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8464 (ttm110) REVERT: B 38 MET cc_start: 0.9155 (tpt) cc_final: 0.8598 (tpt) REVERT: B 127 ASP cc_start: 0.8670 (m-30) cc_final: 0.8452 (m-30) REVERT: B 487 ARG cc_start: 0.7871 (tpm-80) cc_final: 0.7555 (tpm170) REVERT: C 54 LYS cc_start: 0.8535 (tppt) cc_final: 0.8274 (mmtp) REVERT: C 66 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7698 (mp0) outliers start: 12 outliers final: 8 residues processed: 101 average time/residue: 1.2086 time to fit residues: 130.7348 Evaluate side-chains 99 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 75 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.0000 chunk 3 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN B 491 GLN B 501 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.112211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.076937 restraints weight = 34607.013| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.95 r_work: 0.2708 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9272 Z= 0.128 Angle : 0.440 4.714 12662 Z= 0.230 Chirality : 0.036 0.150 1445 Planarity : 0.004 0.050 1525 Dihedral : 9.898 73.501 1568 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.72 % Allowed : 21.83 % Favored : 76.45 % 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: 1.66 (0.26), residues: 1065 helix: 2.28 (0.25), residues: 452 sheet: 0.48 (0.52), residues: 93 loop : 0.23 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 133 TYR 0.013 0.001 TYR A 403 PHE 0.012 0.001 PHE C 44 TRP 0.004 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 9268) covalent geometry : angle 0.43929 / 0.23 (12660) hydrogen bonds : bond 0.05244 / 3.79 ( 407) hydrogen bonds : angle 4.03363 / 2.83 ( 1114) metal coordination : bond 0.00643 / 0.32 ( 4) metal coordination : angle 1.52143 / 0.80 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.458 Fit side-chains REVERT: A 409 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8498 (ttm110) REVERT: B 38 MET cc_start: 0.9185 (tpt) cc_final: 0.8621 (tpt) REVERT: B 151 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8684 (mttp) REVERT: B 487 ARG cc_start: 0.7862 (tpm-80) cc_final: 0.7547 (tpm170) REVERT: C 54 LYS cc_start: 0.8553 (tppt) cc_final: 0.8267 (mmmt) REVERT: C 66 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7709 (mp0) outliers start: 16 outliers final: 10 residues processed: 97 average time/residue: 1.2774 time to fit residues: 132.6907 Evaluate side-chains 98 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 125 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 13 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 6 optimal weight: 0.0270 chunk 14 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 57 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN B 491 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.113027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.077899 restraints weight = 34459.354| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.95 r_work: 0.2726 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9272 Z= 0.093 Angle : 0.431 4.752 12662 Z= 0.225 Chirality : 0.035 0.152 1445 Planarity : 0.004 0.053 1525 Dihedral : 9.866 73.445 1568 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.18 % Allowed : 22.15 % Favored : 76.67 % 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: 1.72 (0.26), residues: 1065 helix: 2.35 (0.25), residues: 452 sheet: 0.58 (0.53), residues: 91 loop : 0.24 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 133 TYR 0.011 0.001 TYR C 95 PHE 0.009 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.09 ( 9268) covalent geometry : angle 0.43050 / 0.22 (12660) hydrogen bonds : bond 0.05029 / 3.65 ( 407) hydrogen bonds : angle 3.98780 / 2.80 ( 1114) metal coordination : bond 0.00359 / 0.18 ( 4) metal coordination : angle 1.73246 / 0.91 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.497 Fit side-chains REVERT: A 409 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8481 (ttm110) REVERT: B 38 MET cc_start: 0.9181 (tpt) cc_final: 0.8615 (tpt) REVERT: B 235 MET cc_start: 0.9241 (mmp) cc_final: 0.8897 (mmp) REVERT: C 54 LYS cc_start: 0.8549 (tppt) cc_final: 0.8265 (mmmt) outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 1.3677 time to fit residues: 131.5213 Evaluate side-chains 92 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain C residue 75 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 100 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 54 optimal weight: 0.0970 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN B 491 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.113583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.078511 restraints weight = 34817.708| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.95 r_work: 0.2735 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9272 Z= 0.091 Angle : 0.428 5.054 12662 Z= 0.223 Chirality : 0.035 0.149 1445 Planarity : 0.004 0.053 1525 Dihedral : 9.828 73.427 1568 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.08 % Allowed : 22.47 % Favored : 76.45 % 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: 1.79 (0.26), residues: 1065 helix: 2.43 (0.25), residues: 452 sheet: 0.59 (0.53), residues: 91 loop : 0.24 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 133 TYR 0.010 0.001 TYR A 403 PHE 0.007 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.003 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 ( 9268) covalent geometry : angle 0.42739 / 0.22 (12660) hydrogen bonds : bond 0.04935 / 3.60 ( 407) hydrogen bonds : angle 3.93339 / 2.76 ( 1114) metal coordination : bond 0.00303 / 0.15 ( 4) metal coordination : angle 1.84314 / 0.98 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6089.94 seconds wall clock time: 104 minutes 0.65 seconds (6240.65 seconds total)