Starting phenix.real_space_refine on Sun Aug 24 07:15:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pss_17861/08_2025/8pss_17861.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pss_17861/08_2025/8pss_17861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pss_17861/08_2025/8pss_17861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pss_17861/08_2025/8pss_17861.map" model { file = "/net/cci-nas-00/data/ceres_data/8pss_17861/08_2025/8pss_17861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pss_17861/08_2025/8pss_17861.cif" } resolution = 2.83 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-2.0-5787/lib/python3.9/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: 2.97, per 1000 atoms: 0.17 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: 4.33 Conformation dependent library (CDL) restraints added in 695.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 2.86 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: 3.93 Time building geometry restraints manager: 2.07 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: 7435 17.86 - 35.72: 695 35.72 - 53.58: 251 53.58 - 71.45: 74 71.45 - 89.31: 22 Dihedral angle restraints: 8477 sinusoidal: 4872 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 8474 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 22.150 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:7.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 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 : 18.022 89.308 3653 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 aren 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 covalent geometry : bond 0.00211 ( 9268) covalent geometry : angle 0.43610 (12660) hydrogen bonds : bond 0.13682 ( 407) hydrogen bonds : angle 5.52501 ( 1114) metal coordination : bond 0.00310 ( 4) metal coordination : angle 1.76563 ( 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 : 0.434 Fit side-chains revert: symmetry clash REVERT: B 38 MET cc_start: 0.9257 (tpt) cc_final: 0.8778 (tpt) outliers start: 12 outliers final: 8 residues processed: 100 average time/residue: 1.2093 time to fit residues: 128.4533 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 : 0.427 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3363 r_free = 0.3363 target = 0.112009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.076165 restraints weight = 34659.014| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 1.96 r_work: 0.2675 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.0645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9272 Z= 0.151 Angle : 0.471 4.219 12662 Z= 0.248 Chirality : 0.037 0.171 1445 Planarity : 0.004 0.049 1525 Dihedral : 11.439 73.673 1613 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.54 % Favored : 97.37 % Rotamer: Outliers : 1.83 % Allowed : 21.83 % 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 aren not related in a simple way. whole: 1.41 (0.26), residues: 1065 helix: 1.88 (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 0.003 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 covalent geometry : bond 0.00348 ( 9268) covalent geometry : angle 0.47010 (12660) hydrogen bonds : bond 0.05771 ( 407) hydrogen bonds : angle 4.54609 ( 1114) metal coordination : bond 0.00905 ( 4) metal coordination : angle 2.10680 ( 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 : 0.296 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.7726 (mtt) REVERT: A 264 ARG cc_start: 0.8704 (mtt-85) cc_final: 0.8504 (tpp80) REVERT: B 151 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8699 (mttp) REVERT: C 54 LYS cc_start: 0.8518 (tppt) cc_final: 0.8208 (mmmt) REVERT: C 59 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9320 (mt) REVERT: C 66 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7648 (mp0) outliers start: 17 outliers final: 5 residues processed: 100 average time/residue: 1.1770 time to fit residues: 125.0207 Evaluate side-chains 94 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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: 0.9990 chunk 26 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3363 r_free = 0.3363 target = 0.112089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.076353 restraints weight = 34651.503| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 1.96 r_work: 0.2684 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.0841 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= 0.127 Angle : 0.450 4.085 12662 Z= 0.235 Chirality : 0.036 0.166 1445 Planarity : 0.003 0.048 1525 Dihedral : 11.235 73.533 1604 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.16 % Favored : 97.75 % Rotamer: Outliers : 2.37 % Allowed : 21.29 % 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 aren not related in a simple way. whole: 1.47 (0.26), residues: 1065 helix: 1.99 (0.25), residues: 459 sheet: 0.84 (0.55), residues: 85 loop : 0.14 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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 0.004 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9268) covalent geometry : angle 0.44936 (12660) hydrogen bonds : bond 0.05465 ( 407) hydrogen bonds : angle 4.26875 ( 1114) metal coordination : bond 0.00545 ( 4) metal coordination : angle 2.01944 ( 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: 22 poor density : 89 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.7941 (mtt) REVERT: B 38 MET cc_start: 0.9211 (tpt) cc_final: 0.8749 (tpt) REVERT: B 151 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8677 (mttp) REVERT: C 54 LYS cc_start: 0.8548 (tppt) cc_final: 0.8258 (mmmt) REVERT: C 66 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7686 (mp0) outliers start: 22 outliers final: 7 residues processed: 106 average time/residue: 1.2163 time to fit residues: 136.9727 Evaluate side-chains 98 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 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 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: 7.9990 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3332 r_free = 0.3332 target = 0.110035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.074135 restraints weight = 34609.953| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 1.96 r_work: 0.2640 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9272 Z= 0.197 Angle : 0.481 4.295 12662 Z= 0.254 Chirality : 0.037 0.163 1445 Planarity : 0.004 0.050 1525 Dihedral : 11.333 73.629 1604 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.82 % Favored : 97.09 % Rotamer: Outliers : 2.26 % Allowed : 21.61 % Favored : 76.13 % 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 aren not related in a simple way. whole: 1.29 (0.25), residues: 1065 helix: 1.79 (0.24), residues: 459 sheet: 0.72 (0.54), residues: 85 loop : 0.11 (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 0.017 0.001 PHE C 44 TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 9268) covalent geometry : angle 0.48063 (12660) hydrogen bonds : bond 0.05960 ( 407) hydrogen bonds : angle 4.31116 ( 1114) metal coordination : bond 0.01182 ( 4) metal coordination : angle 1.63807 ( 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 109 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.356 Fit side-chains REVERT: A 119 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.8892 (mtp180) REVERT: A 409 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8516 (ttm110) REVERT: B 38 MET cc_start: 0.9261 (tpt) cc_final: 0.8763 (tpt) REVERT: B 151 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8660 (mttp) REVERT: C 54 LYS cc_start: 0.8566 (tppt) cc_final: 0.8259 (mmmt) REVERT: C 66 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7718 (mp0) outliers start: 21 outliers final: 9 residues processed: 102 average time/residue: 1.3098 time to fit residues: 142.0050 Evaluate side-chains 99 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 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=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: 0.6980 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 211 ASN B 491 GLN C 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.074675 restraints weight = 34558.207| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 1.95 r_work: 0.2647 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9272 Z= 0.165 Angle : 0.464 4.218 12662 Z= 0.245 Chirality : 0.037 0.158 1445 Planarity : 0.004 0.050 1525 Dihedral : 11.324 73.556 1604 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.37 % Allowed : 21.29 % 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 aren not related in a simple way. whole: 1.24 (0.25), residues: 1065 helix: 1.77 (0.24), residues: 459 sheet: 0.63 (0.54), residues: 85 loop : 0.07 (0.26), residues: 521 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 0.014 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 covalent geometry : bond 0.00385 ( 9268) covalent geometry : angle 0.46304 (12660) hydrogen bonds : bond 0.05713 ( 407) hydrogen bonds : angle 4.26838 ( 1114) metal coordination : bond 0.00894 ( 4) metal coordination : angle 1.86165 ( 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 110 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.299 Fit side-chains REVERT: A 409 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8507 (ttm110) REVERT: B 38 MET cc_start: 0.9255 (tpt) cc_final: 0.8769 (tpt) REVERT: B 151 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8655 (mttp) REVERT: C 54 LYS cc_start: 0.8564 (tppt) cc_final: 0.8250 (mmmt) REVERT: C 66 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7742 (mp0) outliers start: 22 outliers final: 10 residues processed: 103 average time/residue: 1.1985 time to fit residues: 131.2685 Evaluate side-chains 99 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 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 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 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: 0.2980 chunk 95 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 211 ASN B 491 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.111372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.075795 restraints weight = 34471.348| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 1.95 r_work: 0.2670 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1220 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= 0.113 Angle : 0.438 4.084 12662 Z= 0.230 Chirality : 0.035 0.154 1445 Planarity : 0.004 0.049 1525 Dihedral : 11.229 73.475 1604 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.04 % Allowed : 21.29 % 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 aren not related in a simple way. whole: 1.50 (0.26), residues: 1065 helix: 2.08 (0.24), residues: 452 sheet: 0.69 (0.54), residues: 85 loop : 0.15 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 133 TYR 0.012 0.001 TYR A 403 PHE 0.010 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 covalent geometry : bond 0.00260 ( 9268) covalent geometry : angle 0.43741 (12660) hydrogen bonds : bond 0.05298 ( 407) hydrogen bonds : angle 4.12903 ( 1114) metal coordination : bond 0.00463 ( 4) metal coordination : angle 1.96969 ( 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 109 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.484 Fit side-chains REVERT: A 409 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8473 (ttm110) REVERT: B 151 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8644 (mttp) REVERT: B 235 MET cc_start: 0.9234 (mmp) cc_final: 0.8915 (mmp) REVERT: C 54 LYS cc_start: 0.8553 (tppt) cc_final: 0.8334 (mmtm) REVERT: C 66 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7756 (mp0) outliers start: 19 outliers final: 8 residues processed: 103 average time/residue: 1.1914 time to fit residues: 130.7232 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 : 0.464 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 88 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 211 ASN B 491 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.110571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.074708 restraints weight = 34902.806| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 1.97 r_work: 0.2651 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9272 Z= 0.150 Angle : 0.453 4.167 12662 Z= 0.239 Chirality : 0.036 0.155 1445 Planarity : 0.004 0.049 1525 Dihedral : 11.263 73.553 1604 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.26 % Allowed : 20.97 % 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 aren not related in a simple way. whole: 1.40 (0.25), residues: 1065 helix: 1.98 (0.24), residues: 452 sheet: 0.64 (0.54), residues: 87 loop : 0.11 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 133 TYR 0.013 0.001 TYR A 403 PHE 0.014 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 covalent geometry : bond 0.00350 ( 9268) covalent geometry : angle 0.45254 (12660) hydrogen bonds : bond 0.05559 ( 407) hydrogen bonds : angle 4.16865 ( 1114) metal coordination : bond 0.00807 ( 4) metal coordination : angle 1.75977 ( 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 109 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.370 Fit side-chains REVERT: A 409 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8489 (ttm110) REVERT: B 151 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8629 (mttp) REVERT: C 54 LYS cc_start: 0.8560 (tppt) cc_final: 0.8245 (mmmt) REVERT: C 66 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: C 100 ASP cc_start: 0.8821 (t0) cc_final: 0.8555 (t0) outliers start: 21 outliers final: 10 residues processed: 102 average time/residue: 1.1855 time to fit residues: 128.7554 Evaluate side-chains 103 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 75 CYS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 17 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3360 r_free = 0.3360 target = 0.112095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.076542 restraints weight = 34637.138| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.96 r_work: 0.2681 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9272 Z= 0.101 Angle : 0.433 4.058 12662 Z= 0.227 Chirality : 0.035 0.151 1445 Planarity : 0.004 0.050 1525 Dihedral : 11.173 73.457 1604 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.61 % Allowed : 21.94 % 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 aren not related in a simple way. whole: 1.59 (0.26), residues: 1065 helix: 2.17 (0.25), residues: 452 sheet: 0.90 (0.55), residues: 85 loop : 0.16 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 0.004 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 9268) covalent geometry : angle 0.43238 (12660) hydrogen bonds : bond 0.05149 ( 407) hydrogen bonds : angle 4.03591 ( 1114) metal coordination : bond 0.00384 ( 4) metal coordination : angle 1.97347 ( 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: 15 poor density : 91 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 409 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8470 (ttm110) REVERT: B 127 ASP cc_start: 0.8735 (m-30) cc_final: 0.8494 (m-30) REVERT: B 151 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8616 (mttp) REVERT: B 302 ARG cc_start: 0.8493 (mmm-85) cc_final: 0.8176 (mmm160) REVERT: C 54 LYS cc_start: 0.8551 (tppt) cc_final: 0.8273 (mmtp) REVERT: C 66 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7741 (mp0) REVERT: C 100 ASP cc_start: 0.8815 (t0) cc_final: 0.8463 (t0) outliers start: 15 outliers final: 10 residues processed: 100 average time/residue: 1.2967 time to fit residues: 137.8766 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 : 0.314 ------------------------------------------------------------------------------- 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 401 THR Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 457 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 211 ASN B 491 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.110075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.074446 restraints weight = 34538.093| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 1.94 r_work: 0.2641 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9272 Z= 0.178 Angle : 0.465 4.674 12662 Z= 0.246 Chirality : 0.037 0.153 1445 Planarity : 0.004 0.050 1525 Dihedral : 11.278 73.622 1604 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.72 % Allowed : 22.04 % 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 aren not related in a simple way. whole: 1.31 (0.25), residues: 1065 helix: 1.87 (0.24), residues: 459 sheet: 0.71 (0.54), residues: 87 loop : 0.06 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 133 TYR 0.014 0.001 TYR A 403 PHE 0.017 0.001 PHE C 44 TRP 0.005 0.001 TRP A 136 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 9268) covalent geometry : angle 0.46494 (12660) hydrogen bonds : bond 0.05719 ( 407) hydrogen bonds : angle 4.16662 ( 1114) metal coordination : bond 0.01042 ( 4) metal coordination : angle 1.49783 ( 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 104 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.328 Fit side-chains REVERT: A 409 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8502 (ttm110) REVERT: B 151 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8612 (mttp) REVERT: C 54 LYS cc_start: 0.8569 (tppt) cc_final: 0.8300 (mmtp) REVERT: C 66 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: C 100 ASP cc_start: 0.8864 (t0) cc_final: 0.8636 (t0) outliers start: 16 outliers final: 9 residues processed: 98 average time/residue: 1.1129 time to fit residues: 116.0922 Evaluate side-chains 101 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 13 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 0.0270 chunk 45 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 57 optimal weight: 0.1980 chunk 33 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 211 ASN B 491 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.111724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.076298 restraints weight = 34360.080| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 1.95 r_work: 0.2674 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9272 Z= 0.096 Angle : 0.437 4.628 12662 Z= 0.230 Chirality : 0.035 0.152 1445 Planarity : 0.004 0.053 1525 Dihedral : 11.199 73.495 1604 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.61 % Allowed : 22.26 % Favored : 76.13 % 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 aren not related in a simple way. whole: 1.57 (0.26), residues: 1065 helix: 2.15 (0.25), residues: 452 sheet: 0.89 (0.55), residues: 85 loop : 0.15 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 133 TYR 0.012 0.001 TYR C 95 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 covalent geometry : bond 0.00219 ( 9268) covalent geometry : angle 0.43648 (12660) hydrogen bonds : bond 0.05216 ( 407) hydrogen bonds : angle 4.05442 ( 1114) metal coordination : bond 0.00347 ( 4) metal coordination : angle 1.85844 ( 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 103 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 409 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8464 (ttm110) REVERT: B 151 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8638 (mttp) REVERT: B 487 ARG cc_start: 0.7874 (tpm-80) cc_final: 0.7657 (tpm170) REVERT: C 54 LYS cc_start: 0.8563 (tppt) cc_final: 0.8268 (mmmt) REVERT: C 66 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: C 100 ASP cc_start: 0.8853 (t0) cc_final: 0.8497 (t0) outliers start: 15 outliers final: 8 residues processed: 97 average time/residue: 1.2327 time to fit residues: 126.9313 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 : 0.390 ------------------------------------------------------------------------------- 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 151 LYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 457 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 100 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3348 r_free = 0.3348 target = 0.111231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.075797 restraints weight = 34755.240| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 1.94 r_work: 0.2666 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9272 Z= 0.122 Angle : 0.441 4.981 12662 Z= 0.232 Chirality : 0.036 0.153 1445 Planarity : 0.004 0.053 1525 Dihedral : 11.189 73.535 1604 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.72 % Allowed : 22.15 % Favored : 76.13 % 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 aren not related in a simple way. whole: 1.57 (0.26), residues: 1065 helix: 2.16 (0.25), residues: 452 sheet: 0.90 (0.55), residues: 85 loop : 0.14 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 covalent geometry : bond 0.00285 ( 9268) covalent geometry : angle 0.44090 (12660) hydrogen bonds : bond 0.05314 ( 407) hydrogen bonds : angle 4.05172 ( 1114) metal coordination : bond 0.00574 ( 4) metal coordination : angle 1.72483 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5304.42 seconds wall clock time: 90 minutes 32.55 seconds (5432.55 seconds total)