Starting phenix.real_space_refine on Sun Mar 17 11:55:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pss_17861/03_2024/8pss_17861.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pss_17861/03_2024/8pss_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pss_17861/03_2024/8pss_17861.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pss_17861/03_2024/8pss_17861.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pss_17861/03_2024/8pss_17861.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pss_17861/03_2024/8pss_17861.pdb" } 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 Residue "A GLU 58": "OE1" <-> "OE2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "B GLU 390": "OE1" <-> "OE2" Residue "B GLU 463": "OE1" <-> "OE2" Residue "C GLU 115": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 8.46, per 1000 atoms: 0.48 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 - 3.50 Amino acid : False - 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: 14.34 Conformation dependent library (CDL) restraints added in 1.8 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: 7.92 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.700A pdb=" N CYS A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 141 through 157 removed outlier: 3.575A pdb=" N ILE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 223 through 237 Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 312 through 323 removed outlier: 4.481A pdb=" N ASP A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.539A pdb=" N VAL A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.859A pdb=" N ALA A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 388 through 392 Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.780A pdb=" N GLN B 5 " --> pdb=" O TRP B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 40 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.896A pdb=" N LEU B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 104 Processing helix chain 'B' and resid 107 through 117 Processing helix chain 'B' and resid 130 through 137 Processing helix chain 'B' and resid 161 through 183 removed outlier: 3.729A pdb=" N VAL B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 187 removed outlier: 3.763A pdb=" N THR B 187 " --> pdb=" O ALA B 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 184 through 187' Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 235 through 248 removed outlier: 3.720A pdb=" N GLY B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 354 through 372 removed outlier: 3.965A pdb=" N LEU B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 396 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.692A pdb=" N GLY B 413 " --> pdb=" O THR B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.944A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 Processing helix chain 'B' and resid 479 through 498 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 16 through 23 Processing helix chain 'C' and resid 34 through 40 Processing helix chain 'C' and resid 42 through 55 Processing helix chain 'C' and resid 56 through 59 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 100 through 109 removed outlier: 3.996A pdb=" N GLN C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 removed outlier: 3.571A pdb=" N TYR A 45 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP A 52 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N CYS A 71 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA A 54 " --> pdb=" O CYS A 71 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU A 73 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLU A 56 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 194 removed outlier: 7.449A pdb=" N TRP A 198 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N MET A 255 " --> pdb=" O TRP A 198 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLN A 200 " --> pdb=" O MET A 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 194 removed outlier: 7.449A pdb=" N TRP A 198 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N MET A 255 " --> pdb=" O TRP A 198 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLN A 200 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 74 through 80 Processing sheet with id=AA6, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AA7, first strand: chain 'B' and resid 155 through 159 removed outlier: 3.879A pdb=" N ARG B 155 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N PHE B 140 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 327 through 329 Processing sheet with id=AA9, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AB1, first strand: chain 'C' and resid 71 through 83 removed outlier: 9.430A pdb=" N LYS C 73 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N SER C 121 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LYS C 75 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N TYR C 119 " --> pdb=" O LYS C 75 " (cutoff:3.500A) 395 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 6.47 Time building geometry restraints manager: 14.89 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: 100.26 - 107.00: 461 107.00 - 113.73: 21216 113.73 - 120.47: 5867 120.47 - 127.21: 4712 127.21 - 133.95: 147 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 1.850 nonbonded pdb=" OE1 GLU C 89 " pdb=" H GLU C 89 " model vdw 1.570 1.850 nonbonded pdb=" O2 C V 13 " pdb=" H21 G S 3 " model vdw 1.609 1.850 nonbonded pdb=" O PRO B 17 " pdb=" H GLN B 147 " model vdw 1.627 1.850 nonbonded pdb=" O ASN B 330 " pdb=" HG SER B 331 " model vdw 1.646 1.850 ... (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 ========== 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.350 Extract box with map and model: 6.240 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 67.700 Find NCS groups from input model: 0.280 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:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.150 ------------------------------------------------------------------------------- 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 9268 Z= 0.140 Angle : 0.436 4.257 12660 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 *********************** 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 fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 1.428 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: 2.6358 time to fit residues: 282.1114 Evaluate side-chains 95 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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: 4.9990 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: 2.9990 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9268 Z= 0.291 Angle : 0.476 4.430 12660 Z= 0.251 Chirality : 0.037 0.171 1445 Planarity : 0.004 0.047 1525 Dihedral : 11.385 73.722 1613 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.00 % Favored : 96.90 % Rotamer: Outliers : 2.15 % Allowed : 21.94 % 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: 1.31 (0.25), residues: 1065 helix: 1.78 (0.25), residues: 465 sheet: 0.68 (0.52), residues: 87 loop : 0.13 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS A 371 PHE 0.014 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.004 0.000 ARG A 133 *********************** 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 110 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 1.496 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.7952 (mtt) REVERT: A 264 ARG cc_start: 0.8252 (mtt-85) cc_final: 0.8029 (tpp80) REVERT: B 151 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8687 (mttp) REVERT: C 59 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9335 (mt) REVERT: C 66 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7497 (mp0) outliers start: 20 outliers final: 11 residues processed: 102 average time/residue: 2.5985 time to fit residues: 284.0032 Evaluate side-chains 98 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 234 SER Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 180 SER 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 Chi-restraints excluded: chain C residue 125 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9268 Z= 0.214 Angle : 0.445 4.173 12660 Z= 0.233 Chirality : 0.036 0.166 1445 Planarity : 0.003 0.047 1525 Dihedral : 11.268 73.538 1610 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.44 % Favored : 97.46 % Rotamer: Outliers : 2.58 % Allowed : 21.61 % 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: 1.35 (0.25), residues: 1065 helix: 1.85 (0.25), residues: 465 sheet: 0.63 (0.53), residues: 87 loop : 0.13 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.003 0.001 HIS A 371 PHE 0.012 0.001 PHE C 44 TYR 0.011 0.001 TYR A 403 ARG 0.006 0.000 ARG A 133 *********************** 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 112 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: B 38 MET cc_start: 0.9255 (tpt) cc_final: 0.8819 (tpt) REVERT: B 151 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8659 (mttp) REVERT: C 54 LYS cc_start: 0.8429 (tppt) cc_final: 0.8194 (mmmt) REVERT: C 66 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7504 (mp0) outliers start: 24 outliers final: 8 residues processed: 102 average time/residue: 2.7715 time to fit residues: 301.2926 Evaluate side-chains 95 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 1.460 ------------------------------------------------------------------------------- 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 234 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 71 SER 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 96 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9268 Z= 0.289 Angle : 0.469 4.343 12660 Z= 0.247 Chirality : 0.037 0.164 1445 Planarity : 0.004 0.047 1525 Dihedral : 11.274 73.621 1605 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.82 % Favored : 97.09 % Rotamer: Outliers : 2.90 % Allowed : 21.83 % 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: 1.21 (0.25), residues: 1065 helix: 1.72 (0.24), residues: 465 sheet: 0.52 (0.52), residues: 87 loop : 0.08 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS A 371 PHE 0.016 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.006 0.000 ARG A 133 *********************** 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 111 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 84 time to evaluate : 1.383 Fit side-chains REVERT: A 119 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8884 (mtp180) REVERT: A 255 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.7907 (mtt) REVERT: B 38 MET cc_start: 0.9285 (tpt) cc_final: 0.8841 (tpt) REVERT: B 151 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8633 (mttp) REVERT: C 54 LYS cc_start: 0.8445 (tppt) cc_final: 0.8220 (mmmt) REVERT: C 66 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7515 (mp0) outliers start: 27 outliers final: 10 residues processed: 100 average time/residue: 2.7592 time to fit residues: 294.6357 Evaluate side-chains 98 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 1.423 ------------------------------------------------------------------------------- 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 234 SER Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 71 SER 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 86 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 0.4980 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9268 Z= 0.179 Angle : 0.434 4.182 12660 Z= 0.227 Chirality : 0.035 0.156 1445 Planarity : 0.003 0.047 1525 Dihedral : 11.168 73.485 1605 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.26 % Allowed : 22.58 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.43 (0.25), residues: 1065 helix: 1.98 (0.24), residues: 458 sheet: 0.50 (0.52), residues: 87 loop : 0.16 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.003 0.001 HIS A 371 PHE 0.011 0.001 PHE C 44 TYR 0.010 0.001 TYR A 403 ARG 0.005 0.000 ARG A 133 *********************** 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 fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 1.335 Fit side-chains revert: symmetry clash REVERT: A 409 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8464 (ttm110) REVERT: B 38 MET cc_start: 0.9257 (tpt) cc_final: 0.8822 (tpt) REVERT: B 151 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8628 (mttp) REVERT: B 302 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.8009 (mmm160) REVERT: C 54 LYS cc_start: 0.8451 (tppt) cc_final: 0.8219 (mmmt) REVERT: C 66 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7517 (mp0) outliers start: 21 outliers final: 11 residues processed: 101 average time/residue: 2.8107 time to fit residues: 302.3941 Evaluate side-chains 98 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain B residue 24 ASP 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 Chi-restraints excluded: chain C residue 114 ASN 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 34 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 8 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 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 75 ASN A 195 ASN B 211 ASN B 491 GLN C 96 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9268 Z= 0.204 Angle : 0.437 4.222 12660 Z= 0.230 Chirality : 0.036 0.155 1445 Planarity : 0.003 0.047 1525 Dihedral : 11.138 73.501 1604 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.47 % Allowed : 22.15 % Favored : 75.38 % 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: 1.98 (0.24), residues: 458 sheet: 0.53 (0.52), residues: 87 loop : 0.14 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.003 0.001 HIS A 371 PHE 0.013 0.001 PHE C 44 TYR 0.011 0.001 TYR A 403 ARG 0.006 0.000 ARG A 133 *********************** 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 108 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 1.405 Fit side-chains revert: symmetry clash REVERT: A 119 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8878 (mtp180) REVERT: A 409 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8467 (ttm110) REVERT: B 38 MET cc_start: 0.9266 (tpt) cc_final: 0.8814 (tpt) REVERT: B 151 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8621 (mttp) REVERT: B 302 ARG cc_start: 0.8314 (mmm-85) cc_final: 0.8062 (mmm160) REVERT: C 54 LYS cc_start: 0.8482 (tppt) cc_final: 0.8228 (mmmt) REVERT: C 66 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7529 (mp0) outliers start: 23 outliers final: 10 residues processed: 100 average time/residue: 2.9463 time to fit residues: 313.0518 Evaluate side-chains 99 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain B residue 24 ASP 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 Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 125 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9268 Z= 0.181 Angle : 0.430 4.189 12660 Z= 0.225 Chirality : 0.035 0.152 1445 Planarity : 0.003 0.048 1525 Dihedral : 11.094 73.496 1603 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.26 % Allowed : 22.26 % Favored : 75.48 % 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: 1.48 (0.25), residues: 1065 helix: 2.05 (0.24), residues: 458 sheet: 0.58 (0.52), residues: 87 loop : 0.16 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.003 0.001 HIS A 371 PHE 0.012 0.001 PHE C 44 TYR 0.010 0.001 TYR A 403 ARG 0.007 0.000 ARG A 133 *********************** 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 fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 1.404 Fit side-chains revert: symmetry clash REVERT: A 119 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8881 (mtp180) REVERT: A 255 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.7225 (mmt) REVERT: A 409 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8455 (ttm110) REVERT: B 38 MET cc_start: 0.9260 (tpt) cc_final: 0.8725 (tpt) REVERT: B 151 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8604 (mttp) REVERT: B 302 ARG cc_start: 0.8330 (mmm-85) cc_final: 0.8067 (mmm160) REVERT: B 467 ASP cc_start: 0.8076 (t0) cc_final: 0.7874 (t0) REVERT: C 54 LYS cc_start: 0.8497 (tppt) cc_final: 0.8207 (mmtp) REVERT: C 66 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7506 (mp0) outliers start: 21 outliers final: 10 residues processed: 100 average time/residue: 2.9396 time to fit residues: 312.1080 Evaluate side-chains 101 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain B residue 24 ASP 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 Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 125 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 0.0270 overall best weight: 0.8642 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9268 Z= 0.185 Angle : 0.430 4.198 12660 Z= 0.225 Chirality : 0.035 0.152 1445 Planarity : 0.003 0.050 1525 Dihedral : 11.081 73.508 1603 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.15 % Allowed : 21.94 % 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: 1.53 (0.25), residues: 1065 helix: 2.08 (0.25), residues: 458 sheet: 0.59 (0.51), residues: 89 loop : 0.20 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.003 0.001 HIS A 371 PHE 0.012 0.001 PHE C 44 TYR 0.010 0.001 TYR A 403 ARG 0.007 0.000 ARG A 133 *********************** 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 fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: A 119 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8884 (mtp180) REVERT: A 255 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.7384 (mmt) REVERT: A 409 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8458 (ttm110) REVERT: B 38 MET cc_start: 0.9256 (tpt) cc_final: 0.8725 (tpt) REVERT: B 151 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8634 (mttp) REVERT: B 302 ARG cc_start: 0.8320 (mmm-85) cc_final: 0.8062 (mmm160) REVERT: C 54 LYS cc_start: 0.8487 (tppt) cc_final: 0.8239 (mmmt) REVERT: C 66 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7526 (mp0) outliers start: 20 outliers final: 10 residues processed: 99 average time/residue: 2.9438 time to fit residues: 309.7968 Evaluate side-chains 100 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain B residue 24 ASP 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 Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 125 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9268 Z= 0.254 Angle : 0.454 4.276 12660 Z= 0.240 Chirality : 0.036 0.154 1445 Planarity : 0.004 0.051 1525 Dihedral : 11.189 73.669 1603 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.37 % Allowed : 22.04 % Favored : 75.59 % 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: 1.28 (0.25), residues: 1065 helix: 1.81 (0.24), residues: 465 sheet: 0.53 (0.52), residues: 87 loop : 0.09 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 136 HIS 0.003 0.001 HIS A 371 PHE 0.017 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.007 0.000 ARG A 133 *********************** 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 108 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 86 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.9212 (OUTLIER) cc_final: 0.8902 (mtp180) REVERT: A 409 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8469 (ttm110) REVERT: B 38 MET cc_start: 0.9286 (tpt) cc_final: 0.8820 (tpt) REVERT: B 151 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8637 (mttp) REVERT: C 54 LYS cc_start: 0.8470 (tppt) cc_final: 0.8227 (mmmt) REVERT: C 66 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7525 (mp0) outliers start: 22 outliers final: 12 residues processed: 101 average time/residue: 3.0507 time to fit residues: 326.4095 Evaluate side-chains 98 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 234 SER Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain B residue 24 ASP 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 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 62 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9268 Z= 0.190 Angle : 0.437 4.219 12660 Z= 0.230 Chirality : 0.036 0.152 1445 Planarity : 0.004 0.053 1525 Dihedral : 11.130 73.601 1603 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.04 % Allowed : 22.37 % Favored : 75.59 % 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 (0.25), residues: 1065 helix: 2.01 (0.24), residues: 458 sheet: 0.55 (0.52), residues: 87 loop : 0.14 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.003 0.001 HIS A 371 PHE 0.012 0.001 PHE C 44 TYR 0.012 0.001 TYR C 95 ARG 0.007 0.000 ARG A 133 ********************** 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 101 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8887 (mtp180) REVERT: A 409 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8465 (ttm110) REVERT: B 38 MET cc_start: 0.9263 (tpt) cc_final: 0.8730 (tpt) REVERT: B 151 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8613 (mttp) REVERT: B 471 LEU cc_start: 0.8763 (mm) cc_final: 0.8493 (mp) REVERT: C 54 LYS cc_start: 0.8467 (tppt) cc_final: 0.8228 (mmmt) outliers start: 19 outliers final: 13 residues processed: 95 average time/residue: 2.9735 time to fit residues: 300.4050 Evaluate side-chains 98 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 1.476 ------------------------------------------------------------------------------- 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 234 SER Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain B residue 24 ASP 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 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 26 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3341 r_free = 0.3341 target = 0.110834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.075236 restraints weight = 34658.806| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 1.97 r_work: 0.2659 rms_B_bonded: 2.26 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: 0.8943 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9268 Z= 0.217 Angle : 0.442 4.248 12660 Z= 0.233 Chirality : 0.036 0.153 1445 Planarity : 0.004 0.052 1525 Dihedral : 11.139 73.640 1603 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.15 % Allowed : 22.58 % 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: 1.38 (0.25), residues: 1065 helix: 1.94 (0.24), residues: 459 sheet: 0.52 (0.52), residues: 87 loop : 0.13 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.003 0.001 HIS A 371 PHE 0.014 0.001 PHE C 44 TYR 0.012 0.001 TYR C 95 ARG 0.007 0.000 ARG A 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6520.61 seconds wall clock time: 114 minutes 31.13 seconds (6871.13 seconds total)