Starting phenix.real_space_refine on Mon May 19 04:14:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pss_17861/05_2025/8pss_17861.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pss_17861/05_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_17861/05_2025/8pss_17861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pss_17861/05_2025/8pss_17861.map" model { file = "/net/cci-nas-00/data/ceres_data/8pss_17861/05_2025/8pss_17861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pss_17861/05_2025/8pss_17861.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.94, per 1000 atoms: 0.50 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: 5.28 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 9.10 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: 6.67 Time building geometry restraints manager: 6.25 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 0.330 Extract box with map and model: 0.770 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 55.540 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.070 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.004 0.001 TRP A 136 HIS 0.002 0.001 HIS A 371 PHE 0.006 0.001 PHE C 44 TYR 0.011 0.001 TYR C 95 ARG 0.007 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.13682 ( 407) hydrogen bonds : angle 5.52501 ( 1114) metal coordination : bond 0.00310 ( 4) metal coordination : angle 1.76563 ( 2) covalent geometry : bond 0.00211 ( 9268) covalent geometry : angle 0.43610 (12660) *********************** 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 : 1.512 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: 2.6906 time to fit residues: 287.7150 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 : 1.350 ------------------------------------------------------------------------------- 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 90 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3361 r_free = 0.3361 target = 0.111793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.075931 restraints weight = 34576.816| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 1.97 r_work: 0.2671 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9272 Z= 0.158 Angle : 0.475 4.232 12662 Z= 0.250 Chirality : 0.037 0.169 1445 Planarity : 0.004 0.049 1525 Dihedral : 11.448 73.683 1613 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.44 % Favored : 97.46 % Rotamer: Outliers : 1.94 % Allowed : 21.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.26), residues: 1065 helix: 1.85 (0.25), residues: 465 sheet: 0.84 (0.54), residues: 85 loop : 0.14 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.005 0.001 HIS A 367 PHE 0.012 0.001 PHE C 44 TYR 0.014 0.001 TYR A 403 ARG 0.004 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.05806 ( 407) hydrogen bonds : angle 4.53295 ( 1114) metal coordination : bond 0.00987 ( 4) metal coordination : angle 2.11435 ( 2) covalent geometry : bond 0.00368 ( 9268) covalent geometry : angle 0.47418 (12660) *********************** 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: 18 poor density : 89 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.7789 (mtt) REVERT: A 264 ARG cc_start: 0.8717 (mtt-85) cc_final: 0.8513 (tpp80) REVERT: B 151 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8699 (mttp) REVERT: C 54 LYS cc_start: 0.8529 (tppt) cc_final: 0.8219 (mmmt) REVERT: C 59 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9331 (mt) REVERT: C 66 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7665 (mp0) outliers start: 18 outliers final: 5 residues processed: 100 average time/residue: 2.6634 time to fit residues: 285.0435 Evaluate side-chains 93 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 23 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 C 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.111256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.075566 restraints weight = 34554.542| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 1.95 r_work: 0.2685 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9272 Z= 0.150 Angle : 0.460 4.151 12662 Z= 0.241 Chirality : 0.036 0.167 1445 Planarity : 0.003 0.049 1525 Dihedral : 11.281 73.559 1604 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.35 % Favored : 97.56 % Rotamer: Outliers : 2.47 % Allowed : 20.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1065 helix: 1.83 (0.25), residues: 465 sheet: 0.80 (0.55), residues: 85 loop : 0.08 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 PHE 0.013 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.006 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.05651 ( 407) hydrogen bonds : angle 4.31055 ( 1114) metal coordination : bond 0.00789 ( 4) metal coordination : angle 1.91846 ( 2) covalent geometry : bond 0.00350 ( 9268) covalent geometry : angle 0.45893 (12660) *********************** 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: 23 poor density : 88 time to evaluate : 1.906 Fit side-chains revert: symmetry clash REVERT: B 38 MET cc_start: 0.9245 (tpt) cc_final: 0.8786 (tpt) REVERT: B 151 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8687 (mttp) REVERT: C 54 LYS cc_start: 0.8553 (tppt) cc_final: 0.8262 (mmmt) REVERT: C 66 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7689 (mp0) outliers start: 23 outliers final: 8 residues processed: 105 average time/residue: 2.7340 time to fit residues: 306.3150 Evaluate side-chains 97 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 1.384 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3352 r_free = 0.3352 target = 0.111296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.075713 restraints weight = 34536.236| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 1.94 r_work: 0.2669 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1027 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= 0.141 Angle : 0.453 4.139 12662 Z= 0.238 Chirality : 0.036 0.162 1445 Planarity : 0.003 0.048 1525 Dihedral : 11.265 73.532 1604 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.94 % Allowed : 22.15 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1065 helix: 1.95 (0.24), residues: 458 sheet: 0.80 (0.55), residues: 85 loop : 0.12 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 PHE 0.012 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.005 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.05535 ( 407) hydrogen bonds : angle 4.23161 ( 1114) metal coordination : bond 0.00700 ( 4) metal coordination : angle 1.83136 ( 2) covalent geometry : bond 0.00327 ( 9268) covalent geometry : angle 0.45260 (12660) *********************** 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 107 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 1.395 Fit side-chains revert: symmetry clash REVERT: A 409 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8508 (ttm110) REVERT: B 38 MET cc_start: 0.9239 (tpt) cc_final: 0.8762 (tpt) REVERT: B 151 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8657 (mttp) REVERT: C 54 LYS cc_start: 0.8557 (tppt) cc_final: 0.8250 (mmmt) REVERT: C 66 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7696 (mp0) outliers start: 18 outliers final: 9 residues processed: 100 average time/residue: 2.7497 time to fit residues: 293.4298 Evaluate side-chains 98 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 1.423 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 33 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.111363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.075690 restraints weight = 34839.631| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 1.95 r_work: 0.2664 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1109 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= 0.131 Angle : 0.445 4.112 12662 Z= 0.234 Chirality : 0.036 0.157 1445 Planarity : 0.003 0.048 1525 Dihedral : 11.230 73.502 1604 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.37 % Allowed : 21.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.26), residues: 1065 helix: 2.09 (0.24), residues: 452 sheet: 0.80 (0.55), residues: 85 loop : 0.17 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 PHE 0.012 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.006 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.05415 ( 407) hydrogen bonds : angle 4.14956 ( 1114) metal coordination : bond 0.00626 ( 4) metal coordination : angle 1.90950 ( 2) covalent geometry : bond 0.00303 ( 9268) covalent geometry : angle 0.44466 (12660) *********************** 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: 22 poor density : 89 time to evaluate : 1.372 Fit side-chains REVERT: A 119 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8855 (mtp180) REVERT: A 409 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8487 (ttm110) REVERT: B 38 MET cc_start: 0.9212 (tpt) cc_final: 0.8743 (tpt) REVERT: B 151 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8634 (mttp) REVERT: C 54 LYS cc_start: 0.8557 (tppt) cc_final: 0.8334 (mmtm) REVERT: C 66 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7740 (mp0) outliers start: 22 outliers final: 8 residues processed: 105 average time/residue: 2.9522 time to fit residues: 330.4425 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 : 1.563 ------------------------------------------------------------------------------- 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 409 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 3 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.111665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.076077 restraints weight = 34808.068| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 1.95 r_work: 0.2671 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9272 Z= 0.115 Angle : 0.436 4.071 12662 Z= 0.229 Chirality : 0.035 0.154 1445 Planarity : 0.003 0.047 1525 Dihedral : 11.187 73.470 1604 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.83 % Allowed : 21.61 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.26), residues: 1065 helix: 2.18 (0.25), residues: 452 sheet: 0.79 (0.54), residues: 87 loop : 0.19 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 PHE 0.011 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.007 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.05280 ( 407) hydrogen bonds : angle 4.09521 ( 1114) metal coordination : bond 0.00503 ( 4) metal coordination : angle 1.95401 ( 2) covalent geometry : bond 0.00266 ( 9268) covalent geometry : angle 0.43554 (12660) *********************** 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 107 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 1.435 Fit side-chains REVERT: A 409 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8487 (ttm110) REVERT: B 127 ASP cc_start: 0.8777 (m-30) cc_final: 0.8492 (m-30) REVERT: B 151 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8647 (mttp) REVERT: B 475 ARG cc_start: 0.8724 (mtp180) cc_final: 0.8463 (mtt90) REVERT: C 54 LYS cc_start: 0.8555 (tppt) cc_final: 0.8265 (mmtp) REVERT: C 66 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: C 96 ASN cc_start: 0.9092 (m-40) cc_final: 0.8888 (m-40) outliers start: 17 outliers final: 8 residues processed: 102 average time/residue: 2.7648 time to fit residues: 300.7491 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 : 1.398 ------------------------------------------------------------------------------- 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 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 57 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3347 r_free = 0.3347 target = 0.111206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.075403 restraints weight = 34682.198| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 1.97 r_work: 0.2664 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1287 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= 0.129 Angle : 0.441 4.284 12662 Z= 0.232 Chirality : 0.036 0.153 1445 Planarity : 0.004 0.048 1525 Dihedral : 11.192 73.505 1604 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.15 % Allowed : 21.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.26), residues: 1065 helix: 2.13 (0.24), residues: 452 sheet: 0.72 (0.54), residues: 89 loop : 0.19 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 PHE 0.012 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.007 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.05365 ( 407) hydrogen bonds : angle 4.09481 ( 1114) metal coordination : bond 0.00631 ( 4) metal coordination : angle 1.84123 ( 2) covalent geometry : bond 0.00300 ( 9268) covalent geometry : angle 0.44079 (12660) *********************** 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 104 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 1.343 Fit side-chains REVERT: A 119 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8881 (mtp180) REVERT: A 409 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8483 (ttm110) REVERT: B 151 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8640 (mttp) REVERT: C 54 LYS cc_start: 0.8556 (tppt) cc_final: 0.8247 (mmmt) REVERT: C 66 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: C 96 ASN cc_start: 0.9103 (m-40) cc_final: 0.8882 (m-40) outliers start: 20 outliers final: 10 residues processed: 98 average time/residue: 2.8533 time to fit residues: 297.2858 Evaluate side-chains 99 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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 409 ARG 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 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 39 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3346 r_free = 0.3346 target = 0.111165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.075454 restraints weight = 34626.587| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 1.96 r_work: 0.2659 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1339 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= 0.132 Angle : 0.443 4.350 12662 Z= 0.233 Chirality : 0.036 0.153 1445 Planarity : 0.004 0.049 1525 Dihedral : 11.195 73.524 1604 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.04 % Allowed : 21.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.26), residues: 1065 helix: 2.14 (0.24), residues: 452 sheet: 0.72 (0.54), residues: 89 loop : 0.20 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 PHE 0.012 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.007 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.05376 ( 407) hydrogen bonds : angle 4.07800 ( 1114) metal coordination : bond 0.00634 ( 4) metal coordination : angle 1.88332 ( 2) covalent geometry : bond 0.00308 ( 9268) covalent geometry : angle 0.44215 (12660) *********************** 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 110 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 1.410 Fit side-chains REVERT: A 119 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8879 (mtp180) REVERT: A 409 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8492 (ttm110) REVERT: B 127 ASP cc_start: 0.8749 (m-30) cc_final: 0.8486 (m-30) REVERT: B 151 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8630 (mttp) REVERT: B 487 ARG cc_start: 0.7877 (tpm-80) cc_final: 0.7550 (tpm170) REVERT: C 54 LYS cc_start: 0.8562 (tppt) cc_final: 0.8293 (mmtp) REVERT: C 66 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: C 100 ASP cc_start: 0.8789 (t0) cc_final: 0.8437 (t0) outliers start: 19 outliers final: 10 residues processed: 104 average time/residue: 2.9393 time to fit residues: 325.3479 Evaluate side-chains 99 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 1.517 ------------------------------------------------------------------------------- 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 409 ARG 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.108812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.073124 restraints weight = 35094.863| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 1.96 r_work: 0.2624 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.1513 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= 0.234 Angle : 0.499 4.502 12662 Z= 0.266 Chirality : 0.039 0.156 1445 Planarity : 0.004 0.051 1525 Dihedral : 11.405 73.797 1604 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 1.94 % Allowed : 21.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1065 helix: 1.70 (0.24), residues: 459 sheet: 0.55 (0.53), residues: 89 loop : 0.03 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 136 HIS 0.004 0.001 HIS A 367 PHE 0.021 0.001 PHE C 44 TYR 0.016 0.002 TYR A 403 ARG 0.007 0.001 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.06184 ( 407) hydrogen bonds : angle 4.29645 ( 1114) metal coordination : bond 0.01432 ( 4) metal coordination : angle 1.50087 ( 2) covalent geometry : bond 0.00548 ( 9268) covalent geometry : angle 0.49891 (12660) *********************** 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 105 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 1.461 Fit side-chains REVERT: A 119 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8912 (mtp180) REVERT: A 409 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8523 (ttm110) REVERT: B 151 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8668 (mttp) REVERT: C 54 LYS cc_start: 0.8572 (tppt) cc_final: 0.8292 (mmtp) REVERT: C 66 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: C 100 ASP cc_start: 0.8885 (t0) cc_final: 0.8654 (t0) outliers start: 18 outliers final: 8 residues processed: 99 average time/residue: 2.9114 time to fit residues: 306.8381 Evaluate side-chains 98 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 409 ARG 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 125 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 81 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.110685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.075283 restraints weight = 34608.667| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 1.95 r_work: 0.2661 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1500 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= 0.124 Angle : 0.451 4.327 12662 Z= 0.237 Chirality : 0.036 0.154 1445 Planarity : 0.004 0.054 1525 Dihedral : 11.279 73.589 1604 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.61 % Allowed : 22.69 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.26), residues: 1065 helix: 2.03 (0.24), residues: 452 sheet: 0.64 (0.54), residues: 89 loop : 0.12 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.005 0.001 HIS A 367 PHE 0.010 0.001 PHE C 44 TYR 0.012 0.001 TYR C 95 ARG 0.007 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.05412 ( 407) hydrogen bonds : angle 4.11761 ( 1114) metal coordination : bond 0.00580 ( 4) metal coordination : angle 1.87822 ( 2) covalent geometry : bond 0.00287 ( 9268) covalent geometry : angle 0.44995 (12660) ********************** 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 : 1.281 Fit side-chains revert: symmetry clash REVERT: A 119 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8876 (mtp180) REVERT: A 409 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8496 (ttm110) REVERT: B 151 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8635 (mttp) REVERT: B 471 LEU cc_start: 0.8812 (mm) cc_final: 0.8556 (mp) REVERT: B 487 ARG cc_start: 0.7838 (tpm-80) cc_final: 0.7560 (tpp80) REVERT: C 54 LYS cc_start: 0.8570 (tppt) cc_final: 0.8297 (mmtp) REVERT: C 66 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7772 (mp0) outliers start: 15 outliers final: 7 residues processed: 98 average time/residue: 2.9377 time to fit residues: 305.9315 Evaluate side-chains 97 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 409 ARG 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 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 56 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 91 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.0370 chunk 57 optimal weight: 0.2980 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 = 0.3365 r_free = 0.3365 target = 0.112431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.077191 restraints weight = 34935.184| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.96 r_work: 0.2700 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9272 Z= 0.095 Angle : 0.431 4.832 12662 Z= 0.225 Chirality : 0.035 0.149 1445 Planarity : 0.004 0.054 1525 Dihedral : 11.117 73.447 1604 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.29 % Allowed : 22.90 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.26), residues: 1065 helix: 2.29 (0.25), residues: 452 sheet: 0.89 (0.54), residues: 87 loop : 0.17 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 PHE 0.007 0.001 PHE C 44 TYR 0.010 0.001 TYR A 403 ARG 0.007 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.05039 ( 407) hydrogen bonds : angle 3.97239 ( 1114) metal coordination : bond 0.00306 ( 4) metal coordination : angle 1.96302 ( 2) covalent geometry : bond 0.00219 ( 9268) covalent geometry : angle 0.43043 (12660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12223.25 seconds wall clock time: 209 minutes 39.15 seconds (12579.15 seconds total)