Starting phenix.real_space_refine on Sun Mar 10 22:37:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzr_29638/03_2024/8fzr_29638.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzr_29638/03_2024/8fzr_29638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzr_29638/03_2024/8fzr_29638.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzr_29638/03_2024/8fzr_29638.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzr_29638/03_2024/8fzr_29638.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzr_29638/03_2024/8fzr_29638.pdb" } resolution = 3.6 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= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 76 5.49 5 S 32 5.16 5 C 3342 2.51 5 N 966 2.21 5 O 1294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 490": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5711 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4071 Classifications: {'peptide': 503} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 477} Chain: "R" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1639 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 34, 'rna3p_pyr': 33} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 158 SG CYS A 20 22.510 31.353 95.799 1.00 0.00 S ATOM 180 SG CYS A 23 23.297 28.877 95.832 1.00 0.00 S ATOM 754 SG CYS A 94 24.926 28.690 98.909 1.00 0.00 S ATOM 760 SG CYS A 95 25.270 30.234 95.400 1.00 0.00 S Time building chain proxies: 3.97, per 1000 atoms: 0.70 Number of scatterers: 5711 At special positions: 0 Unit cell: (66.3176, 78.534, 136.126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 32 16.00 P 76 15.00 O 1294 8.00 N 966 7.00 C 3342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 2.33 Conformation dependent library (CDL) restraints added in 950.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 23 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 95 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 20 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 94 " Number of angles added : 6 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 3 sheets defined 40.4% alpha, 10.1% beta 4 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 Processing helix chain 'A' and resid 30 through 35 removed outlier: 3.651A pdb=" N LEU A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 45 removed outlier: 3.988A pdb=" N ARG A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 77 removed outlier: 4.139A pdb=" N ARG A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 125 removed outlier: 3.807A pdb=" N ILE A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 120 " --> pdb=" O CYS A 116 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 113 through 125' Processing helix chain 'A' and resid 140 through 145 removed outlier: 3.992A pdb=" N ASN A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 178 removed outlier: 3.503A pdb=" N LYS A 172 " --> pdb=" O HIS A 168 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 194 removed outlier: 3.610A pdb=" N LYS A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 214 removed outlier: 3.773A pdb=" N TRP A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 removed outlier: 3.930A pdb=" N LEU A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ALA A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 removed outlier: 3.590A pdb=" N ARG A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 removed outlier: 4.039A pdb=" N TYR A 303 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 329 through 333 removed outlier: 3.845A pdb=" N GLY A 332 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 333 " --> pdb=" O SER A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 333' Processing helix chain 'A' and resid 372 through 376 Processing helix chain 'A' and resid 382 through 396 removed outlier: 3.836A pdb=" N SER A 386 " --> pdb=" O CYS A 382 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A 392 " --> pdb=" O ASN A 388 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.509A pdb=" N THR A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE A 410 " --> pdb=" O LEU A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 413 through 418 removed outlier: 3.671A pdb=" N ASN A 417 " --> pdb=" O LYS A 414 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY A 418 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 444 removed outlier: 3.709A pdb=" N LEU A 437 " --> pdb=" O PRO A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 450 removed outlier: 4.245A pdb=" N ASP A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 removed outlier: 3.838A pdb=" N GLU A 472 " --> pdb=" O PHE A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 485 removed outlier: 3.715A pdb=" N VAL A 483 " --> pdb=" O ARG A 479 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 6.313A pdb=" N PHE A 5 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU A 498 " --> pdb=" O PHE A 5 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 7 " --> pdb=" O LEU A 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 102 removed outlier: 6.474A pdb=" N TYR A 98 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N TYR A 293 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE A 100 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ILE A 253 " --> pdb=" O TYR A 290 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY A 292 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER A 255 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N TYR A 294 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 13.408A pdb=" N TYR A 257 " --> pdb=" O TYR A 294 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL A 245 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N PHE A 258 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE A 243 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TRP A 260 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE A 241 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LEU A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N TYR A 236 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A 242 " --> pdb=" O TYR A 234 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 156 " --> pdb=" O CYS A 233 " (cutoff:3.500A) 93 hydrogen bonds defined for protein. 219 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 9 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1507 1.34 - 1.46: 1549 1.46 - 1.57: 2749 1.57 - 1.69: 152 1.69 - 1.81: 49 Bond restraints: 6006 Sorted by residual: bond pdb=" N GLU A 490 " pdb=" CA GLU A 490 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.73e+00 bond pdb=" N THR A 491 " pdb=" CA THR A 491 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.73e+00 bond pdb=" N PHE A 487 " pdb=" CA PHE A 487 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.61e-02 3.86e+03 4.05e+00 bond pdb=" N GLY A 488 " pdb=" CA GLY A 488 " ideal model delta sigma weight residual 1.449 1.475 -0.026 1.45e-02 4.76e+03 3.24e+00 bond pdb=" N PHE A 489 " pdb=" CA PHE A 489 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.76e+00 ... (remaining 6001 not shown) Histogram of bond angle deviations from ideal: 100.73 - 107.38: 604 107.38 - 114.02: 3435 114.02 - 120.67: 2363 120.67 - 127.32: 1914 127.32 - 133.97: 181 Bond angle restraints: 8497 Sorted by residual: angle pdb=" N PHE A 487 " pdb=" CA PHE A 487 " pdb=" C PHE A 487 " ideal model delta sigma weight residual 109.11 115.29 -6.18 1.42e+00 4.96e-01 1.89e+01 angle pdb=" C3' C R 49 " pdb=" O3' C R 49 " pdb=" P G R 50 " ideal model delta sigma weight residual 120.20 125.42 -5.22 1.50e+00 4.44e-01 1.21e+01 angle pdb=" N VAL A 177 " pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 113.53 110.45 3.08 9.80e-01 1.04e+00 9.86e+00 angle pdb=" O3' C R 49 " pdb=" C3' C R 49 " pdb=" C2' C R 49 " ideal model delta sigma weight residual 109.50 113.86 -4.36 1.50e+00 4.44e-01 8.47e+00 angle pdb=" CA PHE A 487 " pdb=" C PHE A 487 " pdb=" O PHE A 487 " ideal model delta sigma weight residual 121.86 117.92 3.94 1.39e+00 5.18e-01 8.03e+00 ... (remaining 8492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 3447 34.82 - 69.63: 239 69.63 - 104.45: 34 104.45 - 139.26: 0 139.26 - 174.08: 1 Dihedral angle restraints: 3721 sinusoidal: 2247 harmonic: 1474 Sorted by residual: dihedral pdb=" C4' C R 49 " pdb=" C3' C R 49 " pdb=" O3' C R 49 " pdb=" P G R 50 " ideal model delta sinusoidal sigma weight residual 250.00 75.92 174.08 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA TRP A 260 " pdb=" C TRP A 260 " pdb=" N ASP A 261 " pdb=" CA ASP A 261 " ideal model delta harmonic sigma weight residual 180.00 160.26 19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" O4' C R 49 " pdb=" C1' C R 49 " pdb=" N1 C R 49 " pdb=" C2 C R 49 " ideal model delta sinusoidal sigma weight residual -128.00 -74.93 -53.07 1 1.70e+01 3.46e-03 1.33e+01 ... (remaining 3718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 787 0.039 - 0.077: 137 0.077 - 0.116: 48 0.116 - 0.154: 4 0.154 - 0.193: 1 Chirality restraints: 977 Sorted by residual: chirality pdb=" C3' C R 49 " pdb=" C4' C R 49 " pdb=" O3' C R 49 " pdb=" C2' C R 49 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" CA ILE A 259 " pdb=" N ILE A 259 " pdb=" C ILE A 259 " pdb=" CB ILE A 259 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE A 253 " pdb=" N ILE A 253 " pdb=" C ILE A 253 " pdb=" CB ILE A 253 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 974 not shown) Planarity restraints: 803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 486 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C LEU A 486 " -0.038 2.00e-02 2.50e+03 pdb=" O LEU A 486 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE A 487 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 487 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C PHE A 487 " 0.029 2.00e-02 2.50e+03 pdb=" O PHE A 487 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY A 488 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 249 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO A 250 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 250 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 250 " 0.017 5.00e-02 4.00e+02 ... (remaining 800 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1065 2.77 - 3.30: 5148 3.30 - 3.83: 9289 3.83 - 4.37: 10496 4.37 - 4.90: 16735 Nonbonded interactions: 42733 Sorted by model distance: nonbonded pdb=" N ASP A 89 " pdb=" OD1 ASP A 89 " model vdw 2.234 2.520 nonbonded pdb=" O ILE A 253 " pdb=" N TYR A 290 " model vdw 2.252 2.520 nonbonded pdb=" O2' G R 15 " pdb=" OP1 G R 19 " model vdw 2.254 2.440 nonbonded pdb=" O GLY A 77 " pdb=" OH TYR A 293 " model vdw 2.278 2.440 nonbonded pdb=" O ASP A 71 " pdb=" ND2 ASN A 75 " model vdw 2.290 2.520 ... (remaining 42728 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 group one per residue 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: 0.870 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: 0.000 Extract box with map and model: 3.630 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.890 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2377 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 0.034 6006 Z= 0.130 Angle : 0.477 7.751 8497 Z= 0.270 Chirality : 0.034 0.193 977 Planarity : 0.004 0.031 803 Dihedral : 20.143 174.077 2781 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 1.00 % Allowed : 4.59 % Favored : 94.41 % Rotamer: Outliers : 6.97 % Allowed : 10.56 % Favored : 82.47 % 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: -1.87 (0.37), residues: 501 helix: -0.88 (0.55), residues: 93 sheet: -2.68 (0.69), residues: 45 loop : -1.19 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 267 HIS 0.002 0.001 HIS A 226 PHE 0.008 0.001 PHE A 139 TYR 0.007 0.001 TYR A 173 ARG 0.001 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 81 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 PHE cc_start: 0.5898 (OUTLIER) cc_final: 0.5225 (p90) REVERT: A 293 TYR cc_start: 0.4648 (OUTLIER) cc_final: 0.3981 (m-80) REVERT: A 310 GLU cc_start: 0.3034 (OUTLIER) cc_final: 0.2770 (tp30) REVERT: A 361 PHE cc_start: 0.4508 (OUTLIER) cc_final: 0.4079 (m-80) outliers start: 31 outliers final: 8 residues processed: 108 average time/residue: 0.2232 time to fit residues: 30.1242 Evaluate side-chains 55 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 43 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 168 HIS ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN A 326 GLN A 416 HIS A 442 GLN A 475 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2684 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6006 Z= 0.304 Angle : 0.760 9.124 8497 Z= 0.390 Chirality : 0.043 0.207 977 Planarity : 0.005 0.038 803 Dihedral : 23.311 172.542 1794 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 29.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 8.54 % Allowed : 19.33 % Favored : 72.13 % 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: -1.72 (0.37), residues: 501 helix: -0.74 (0.54), residues: 85 sheet: -2.27 (0.76), residues: 40 loop : -1.17 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 215 HIS 0.006 0.002 HIS A 226 PHE 0.021 0.003 PHE A 454 TYR 0.019 0.002 TYR A 162 ARG 0.007 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 43 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 TYR cc_start: 0.6273 (OUTLIER) cc_final: 0.4717 (p90) REVERT: A 258 PHE cc_start: -0.0385 (OUTLIER) cc_final: -0.0925 (t80) REVERT: A 260 TRP cc_start: 0.4404 (OUTLIER) cc_final: 0.3190 (m-10) outliers start: 38 outliers final: 24 residues processed: 77 average time/residue: 0.1996 time to fit residues: 19.8779 Evaluate side-chains 64 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 37 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 260 TRP Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 16 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN A 316 HIS ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2888 moved from start: 0.5775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 6006 Z= 0.402 Angle : 0.841 13.299 8497 Z= 0.438 Chirality : 0.045 0.208 977 Planarity : 0.006 0.040 803 Dihedral : 24.102 170.336 1787 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 40.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 9.66 % Allowed : 20.00 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.24 (0.36), residues: 501 helix: -0.97 (0.53), residues: 83 sheet: -2.52 (0.76), residues: 38 loop : -1.60 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 215 HIS 0.006 0.001 HIS A 231 PHE 0.023 0.003 PHE A 78 TYR 0.018 0.003 TYR A 257 ARG 0.017 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 44 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 TYR cc_start: 0.0383 (OUTLIER) cc_final: -0.2840 (m-80) REVERT: A 45 MET cc_start: 0.3866 (ppp) cc_final: 0.3581 (ppp) REVERT: A 258 PHE cc_start: 0.0060 (OUTLIER) cc_final: -0.0362 (t80) REVERT: A 260 TRP cc_start: 0.4583 (OUTLIER) cc_final: 0.3432 (m-10) REVERT: A 276 ARG cc_start: 0.6366 (OUTLIER) cc_final: 0.5760 (ttp-110) outliers start: 43 outliers final: 28 residues processed: 81 average time/residue: 0.2002 time to fit residues: 20.9515 Evaluate side-chains 69 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 37 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 44 TYR Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 260 TRP Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 307 TYR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2910 moved from start: 0.6928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6006 Z= 0.352 Angle : 0.772 8.202 8497 Z= 0.404 Chirality : 0.044 0.218 977 Planarity : 0.005 0.034 803 Dihedral : 24.504 172.281 1785 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 42.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.78 % Favored : 91.02 % Rotamer: Outliers : 9.66 % Allowed : 21.57 % Favored : 68.76 % 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: -2.20 (0.37), residues: 501 helix: -0.80 (0.55), residues: 89 sheet: -2.91 (0.67), residues: 39 loop : -1.56 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 215 HIS 0.008 0.002 HIS A 64 PHE 0.023 0.003 PHE A 78 TYR 0.022 0.002 TYR A 289 ARG 0.017 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 43 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 PHE cc_start: -0.0015 (OUTLIER) cc_final: -0.0388 (t80) REVERT: A 260 TRP cc_start: 0.4798 (OUTLIER) cc_final: 0.3726 (m-10) outliers start: 43 outliers final: 30 residues processed: 79 average time/residue: 0.1888 time to fit residues: 19.5376 Evaluate side-chains 71 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 39 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 260 TRP Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 307 TYR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2830 moved from start: 0.7078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6006 Z= 0.237 Angle : 0.691 8.610 8497 Z= 0.361 Chirality : 0.041 0.235 977 Planarity : 0.005 0.030 803 Dihedral : 24.343 173.576 1785 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 32.85 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.19 % Favored : 92.61 % Rotamer: Outliers : 8.99 % Allowed : 22.02 % Favored : 68.99 % 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: -1.91 (0.38), residues: 501 helix: -0.60 (0.55), residues: 91 sheet: -2.86 (0.65), residues: 39 loop : -1.33 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 40 HIS 0.008 0.001 HIS A 64 PHE 0.020 0.002 PHE A 78 TYR 0.023 0.002 TYR A 44 ARG 0.004 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 41 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 PHE cc_start: -0.0095 (OUTLIER) cc_final: -0.0652 (t80) outliers start: 40 outliers final: 31 residues processed: 72 average time/residue: 0.2049 time to fit residues: 19.0607 Evaluate side-chains 70 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 38 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 307 TYR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 13 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 45 optimal weight: 30.0000 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 6 optimal weight: 0.0050 chunk 31 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2843 moved from start: 0.7471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6006 Z= 0.249 Angle : 0.687 8.006 8497 Z= 0.359 Chirality : 0.042 0.240 977 Planarity : 0.005 0.060 803 Dihedral : 24.411 175.257 1785 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 32.75 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.58 % Favored : 92.22 % Rotamer: Outliers : 7.64 % Allowed : 24.27 % Favored : 68.09 % 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: -2.10 (0.38), residues: 501 helix: -0.93 (0.52), residues: 97 sheet: -2.77 (0.65), residues: 39 loop : -1.44 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 40 HIS 0.006 0.001 HIS A 64 PHE 0.022 0.002 PHE A 78 TYR 0.020 0.002 TYR A 44 ARG 0.004 0.001 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 41 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 PHE cc_start: -0.0163 (OUTLIER) cc_final: -0.0778 (t80) REVERT: A 361 PHE cc_start: 0.5099 (OUTLIER) cc_final: 0.4517 (m-80) outliers start: 34 outliers final: 28 residues processed: 69 average time/residue: 0.1905 time to fit residues: 17.2403 Evaluate side-chains 67 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 37 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 31 optimal weight: 9.9990 chunk 46 optimal weight: 40.0000 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 34 optimal weight: 0.1980 chunk 33 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 0.1980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 GLN A 417 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2684 moved from start: 0.7466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6006 Z= 0.170 Angle : 0.628 8.109 8497 Z= 0.324 Chirality : 0.039 0.242 977 Planarity : 0.005 0.056 803 Dihedral : 24.157 177.711 1784 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.59 % Favored : 94.21 % Rotamer: Outliers : 5.39 % Allowed : 26.97 % Favored : 67.64 % 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: -1.86 (0.38), residues: 501 helix: -0.67 (0.50), residues: 103 sheet: -2.56 (0.69), residues: 40 loop : -1.30 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 40 HIS 0.005 0.001 HIS A 226 PHE 0.012 0.001 PHE A 456 TYR 0.018 0.002 TYR A 44 ARG 0.004 0.001 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 40 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 PHE cc_start: -0.0347 (OUTLIER) cc_final: -0.1045 (t80) outliers start: 24 outliers final: 15 residues processed: 58 average time/residue: 0.1896 time to fit residues: 14.3879 Evaluate side-chains 56 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 40 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2929 moved from start: 0.8296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6006 Z= 0.352 Angle : 0.775 8.175 8497 Z= 0.402 Chirality : 0.044 0.255 977 Planarity : 0.005 0.042 803 Dihedral : 24.701 176.598 1782 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 40.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.58 % Favored : 90.22 % Rotamer: Outliers : 6.97 % Allowed : 24.94 % Favored : 68.09 % 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: -2.34 (0.37), residues: 501 helix: -1.05 (0.51), residues: 107 sheet: -2.50 (0.77), residues: 40 loop : -1.69 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 215 HIS 0.008 0.002 HIS A 13 PHE 0.025 0.002 PHE A 78 TYR 0.020 0.002 TYR A 44 ARG 0.005 0.001 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 37 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.2121 (tpt) cc_final: 0.1890 (tpt) REVERT: A 65 MET cc_start: 0.5039 (pmm) cc_final: 0.4745 (pmm) REVERT: A 257 TYR cc_start: 0.1305 (OUTLIER) cc_final: -0.0231 (t80) REVERT: A 258 PHE cc_start: 0.0077 (OUTLIER) cc_final: -0.0342 (t80) REVERT: A 316 HIS cc_start: 0.4466 (OUTLIER) cc_final: 0.3500 (p-80) REVERT: A 361 PHE cc_start: 0.5296 (OUTLIER) cc_final: 0.4709 (m-80) REVERT: A 484 ILE cc_start: 0.6653 (OUTLIER) cc_final: 0.6384 (mm) outliers start: 31 outliers final: 20 residues processed: 63 average time/residue: 0.1905 time to fit residues: 15.8219 Evaluate side-chains 61 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 36 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 22 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 30.0000 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2941 moved from start: 0.8842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6006 Z= 0.328 Angle : 0.772 10.016 8497 Z= 0.400 Chirality : 0.044 0.261 977 Planarity : 0.005 0.048 803 Dihedral : 24.905 177.754 1782 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 39.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.98 % Favored : 90.82 % Rotamer: Outliers : 6.74 % Allowed : 24.72 % Favored : 68.54 % 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: -2.88 (0.35), residues: 501 helix: -1.67 (0.44), residues: 120 sheet: -2.69 (0.73), residues: 40 loop : -2.01 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 40 HIS 0.008 0.002 HIS A 64 PHE 0.031 0.002 PHE A 78 TYR 0.016 0.002 TYR A 289 ARG 0.005 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 39 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.4997 (pmm) cc_final: 0.4709 (pmm) REVERT: A 257 TYR cc_start: 0.1283 (OUTLIER) cc_final: -0.0091 (t80) REVERT: A 258 PHE cc_start: 0.0222 (OUTLIER) cc_final: -0.0190 (t80) REVERT: A 316 HIS cc_start: 0.4024 (OUTLIER) cc_final: 0.3323 (p-80) REVERT: A 361 PHE cc_start: 0.5373 (OUTLIER) cc_final: 0.4789 (m-80) outliers start: 30 outliers final: 22 residues processed: 63 average time/residue: 0.1888 time to fit residues: 15.5606 Evaluate side-chains 62 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 36 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 9.9990 chunk 45 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2992 moved from start: 0.9545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6006 Z= 0.333 Angle : 0.795 10.806 8497 Z= 0.409 Chirality : 0.044 0.283 977 Planarity : 0.005 0.047 803 Dihedral : 25.180 178.441 1782 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 41.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.98 % Favored : 88.82 % Rotamer: Outliers : 6.29 % Allowed : 24.27 % Favored : 69.44 % 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: -3.17 (0.35), residues: 501 helix: -1.74 (0.43), residues: 131 sheet: -3.24 (0.64), residues: 45 loop : -2.19 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 215 HIS 0.010 0.002 HIS A 64 PHE 0.034 0.002 PHE A 78 TYR 0.016 0.002 TYR A 289 ARG 0.009 0.001 ARG A 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 36 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 TYR cc_start: 0.1395 (OUTLIER) cc_final: -0.0046 (t80) REVERT: A 258 PHE cc_start: 0.0234 (OUTLIER) cc_final: -0.0175 (t80) REVERT: A 316 HIS cc_start: 0.3996 (OUTLIER) cc_final: 0.3477 (p-80) REVERT: A 361 PHE cc_start: 0.5283 (OUTLIER) cc_final: 0.4725 (m-80) outliers start: 28 outliers final: 21 residues processed: 59 average time/residue: 0.1777 time to fit residues: 13.9038 Evaluate side-chains 61 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 36 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 45 optimal weight: 30.0000 chunk 18 optimal weight: 7.9990 chunk 46 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 2 optimal weight: 0.3980 chunk 32 optimal weight: 0.0770 chunk 51 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.128011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.112367 restraints weight = 38518.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.114171 restraints weight = 28369.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.115551 restraints weight = 22710.737| |-----------------------------------------------------------------------------| r_work (final): 0.4367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.9295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6006 Z= 0.188 Angle : 0.679 9.437 8497 Z= 0.348 Chirality : 0.041 0.297 977 Planarity : 0.005 0.052 803 Dihedral : 24.880 177.970 1782 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 23.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.59 % Favored : 93.21 % Rotamer: Outliers : 4.72 % Allowed : 25.62 % Favored : 69.66 % 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: -2.50 (0.36), residues: 501 helix: -1.32 (0.45), residues: 122 sheet: -2.50 (0.72), residues: 40 loop : -1.76 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 40 HIS 0.007 0.001 HIS A 64 PHE 0.025 0.002 PHE A 78 TYR 0.015 0.002 TYR A 162 ARG 0.004 0.001 ARG A 276 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1345.15 seconds wall clock time: 25 minutes 19.69 seconds (1519.69 seconds total)