Starting phenix.real_space_refine on Thu Dec 7 23:25:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzr_29638/12_2023/8fzr_29638.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzr_29638/12_2023/8fzr_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_29638/12_2023/8fzr_29638.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzr_29638/12_2023/8fzr_29638.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzr_29638/12_2023/8fzr_29638.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzr_29638/12_2023/8fzr_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-1.21rc1-5172/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: 3.87, per 1000 atoms: 0.68 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: 2.70 Conformation dependent library (CDL) restraints added in 890.7 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: 1.66 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: 1.48 Time building geometry restraints manager: 2.48 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: 3408 34.82 - 69.63: 218 69.63 - 104.45: 34 104.45 - 139.26: 0 139.26 - 174.08: 1 Dihedral angle restraints: 3661 sinusoidal: 2187 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 3658 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: 0.890 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: 3.580 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.700 Find NCS groups from input model: 0.130 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.290 ------------------------------------------------------------------------------- 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 : 19.692 174.077 2721 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 : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 8 residues processed: 108 average time/residue: 0.2096 time to fit residues: 28.3210 Evaluate side-chains 51 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0528 time to fit residues: 1.3606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 316 HIS 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: 0.2690 moved from start: 0.3791 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= 0.324 Angle : 0.768 9.175 8497 Z= 0.395 Chirality : 0.043 0.207 977 Planarity : 0.005 0.038 803 Dihedral : 22.608 172.337 1710 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 30.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 7.42 % Allowed : 19.55 % Favored : 73.03 % 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: -1.80 (0.37), residues: 501 helix: -0.90 (0.51), residues: 91 sheet: -2.29 (0.76), residues: 40 loop : -1.20 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 215 HIS 0.007 0.002 HIS A 64 PHE 0.017 0.003 PHE A 78 TYR 0.022 0.003 TYR A 293 ARG 0.009 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 77 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 44 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 22 residues processed: 74 average time/residue: 0.2009 time to fit residues: 19.3416 Evaluate side-chains 59 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 37 time to evaluate : 0.530 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.0630 time to fit residues: 3.1008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 46 optimal weight: 30.0000 chunk 17 optimal weight: 8.9990 chunk 41 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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: 0.2552 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6006 Z= 0.179 Angle : 0.605 6.682 8497 Z= 0.313 Chirality : 0.039 0.196 977 Planarity : 0.004 0.033 803 Dihedral : 22.456 171.906 1710 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.80 % Allowed : 23.82 % Favored : 74.38 % 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: -1.61 (0.38), residues: 501 helix: -0.50 (0.50), residues: 109 sheet: -2.37 (0.75), residues: 40 loop : -1.13 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 209 HIS 0.005 0.001 HIS A 64 PHE 0.017 0.002 PHE A 456 TYR 0.019 0.002 TYR A 293 ARG 0.002 0.000 ARG A 357 *********************** 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 58 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 55 average time/residue: 0.2434 time to fit residues: 16.8999 Evaluate side-chains 43 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.520 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1506 time to fit residues: 1.2636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 34 optimal weight: 0.0020 chunk 52 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 14 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 31 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 overall best weight: 4.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2865 moved from start: 0.6103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 6006 Z= 0.388 Angle : 0.841 9.842 8497 Z= 0.437 Chirality : 0.044 0.212 977 Planarity : 0.006 0.056 803 Dihedral : 23.280 171.285 1710 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 42.25 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.98 % Favored : 90.62 % Rotamer: Outliers : 4.49 % Allowed : 25.39 % Favored : 70.11 % 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: -1.95 (0.37), residues: 501 helix: -0.24 (0.56), residues: 75 sheet: -2.59 (0.72), residues: 40 loop : -1.47 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 215 HIS 0.008 0.002 HIS A 64 PHE 0.026 0.003 PHE A 78 TYR 0.026 0.003 TYR A 289 ARG 0.007 0.001 ARG A 43 *********************** 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 61 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 41 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 56 average time/residue: 0.1630 time to fit residues: 12.4544 Evaluate side-chains 46 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 34 time to evaluate : 0.467 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0838 time to fit residues: 2.1867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 13 optimal weight: 0.0050 chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 HIS ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 HIS ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2652 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6006 Z= 0.182 Angle : 0.620 7.467 8497 Z= 0.324 Chirality : 0.039 0.209 977 Planarity : 0.004 0.030 803 Dihedral : 23.113 172.750 1710 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 22.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.39 % Favored : 94.41 % Rotamer: Outliers : 3.60 % Allowed : 24.72 % Favored : 71.69 % 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: -1.70 (0.38), residues: 501 helix: -0.48 (0.53), residues: 94 sheet: -2.61 (0.73), residues: 39 loop : -1.19 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 209 HIS 0.005 0.001 HIS A 64 PHE 0.016 0.002 PHE A 78 TYR 0.018 0.002 TYR A 293 ARG 0.002 0.001 ARG A 119 *********************** 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 55 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 39 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 54 average time/residue: 0.1753 time to fit residues: 12.8197 Evaluate side-chains 44 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.562 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0711 time to fit residues: 1.2966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2782 moved from start: 0.6736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6006 Z= 0.265 Angle : 0.695 8.595 8497 Z= 0.361 Chirality : 0.041 0.222 977 Planarity : 0.004 0.030 803 Dihedral : 23.342 173.743 1710 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 33.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.98 % Favored : 90.82 % Rotamer: Outliers : 2.92 % Allowed : 26.97 % Favored : 70.11 % 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: -1.97 (0.37), residues: 501 helix: -0.82 (0.53), residues: 95 sheet: -2.59 (0.73), residues: 40 loop : -1.36 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 215 HIS 0.006 0.001 HIS A 64 PHE 0.021 0.002 PHE A 78 TYR 0.017 0.002 TYR A 293 ARG 0.004 0.001 ARG A 156 *********************** 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 55 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 50 average time/residue: 0.2040 time to fit residues: 13.4402 Evaluate side-chains 48 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.506 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0866 time to fit residues: 2.0633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 31 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** 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: 0.2759 moved from start: 0.7161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6006 Z= 0.234 Angle : 0.653 7.303 8497 Z= 0.342 Chirality : 0.040 0.243 977 Planarity : 0.004 0.033 803 Dihedral : 23.507 175.086 1710 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 28.58 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.19 % Favored : 92.61 % Rotamer: Outliers : 2.47 % Allowed : 26.29 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.01 (0.38), residues: 501 helix: -0.89 (0.50), residues: 113 sheet: -2.71 (0.71), residues: 39 loop : -1.37 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 215 HIS 0.005 0.001 HIS A 64 PHE 0.016 0.002 PHE A 78 TYR 0.019 0.002 TYR A 293 ARG 0.005 0.001 ARG A 79 *********************** 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 49 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 46 average time/residue: 0.2388 time to fit residues: 14.0611 Evaluate side-chains 43 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.523 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0609 time to fit residues: 1.1328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 43 optimal weight: 0.0870 chunk 49 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 48 optimal weight: 0.3980 chunk 51 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A 417 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2683 moved from start: 0.7287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6006 Z= 0.200 Angle : 0.643 8.200 8497 Z= 0.334 Chirality : 0.040 0.237 977 Planarity : 0.005 0.063 803 Dihedral : 23.431 176.502 1710 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 25.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.99 % Favored : 92.81 % Rotamer: Outliers : 0.67 % Allowed : 27.64 % Favored : 71.69 % 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: -1.75 (0.37), residues: 501 helix: -0.40 (0.55), residues: 93 sheet: -2.47 (0.73), residues: 39 loop : -1.29 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 435 HIS 0.003 0.001 HIS A 64 PHE 0.016 0.001 PHE A 78 TYR 0.020 0.002 TYR A 293 ARG 0.012 0.001 ARG A 276 *********************** 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 46 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 46 average time/residue: 0.1969 time to fit residues: 12.1060 Evaluate side-chains 39 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.570 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 22 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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: 0.2842 moved from start: 0.7972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6006 Z= 0.306 Angle : 0.750 10.726 8497 Z= 0.388 Chirality : 0.041 0.244 977 Planarity : 0.005 0.035 803 Dihedral : 23.818 176.169 1710 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 35.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.98 % Favored : 89.82 % Rotamer: Outliers : 1.12 % Allowed : 27.64 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.05 (0.37), residues: 501 helix: -1.15 (0.53), residues: 95 sheet: -2.65 (0.89), residues: 29 loop : -1.39 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 215 HIS 0.011 0.002 HIS A 13 PHE 0.022 0.002 PHE A 78 TYR 0.026 0.002 TYR A 398 ARG 0.012 0.001 ARG A 276 *********************** 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 47 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 46 average time/residue: 0.2043 time to fit residues: 12.3014 Evaluate side-chains 42 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.455 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0547 time to fit residues: 0.9520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A 422 ASN A 426 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2877 moved from start: 0.8498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6006 Z= 0.328 Angle : 0.764 8.508 8497 Z= 0.396 Chirality : 0.043 0.244 977 Planarity : 0.005 0.044 803 Dihedral : 24.131 176.913 1710 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 39.49 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.78 % Favored : 90.02 % Rotamer: Outliers : 0.45 % Allowed : 26.74 % Favored : 72.81 % 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: -2.38 (0.36), residues: 501 helix: -1.66 (0.49), residues: 103 sheet: -2.65 (0.70), residues: 38 loop : -1.50 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 215 HIS 0.006 0.002 HIS A 231 PHE 0.025 0.002 PHE A 78 TYR 0.027 0.002 TYR A 293 ARG 0.007 0.001 ARG A 276 ********************** 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 41 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 0.2213 time to fit residues: 11.8784 Evaluate side-chains 40 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.652 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0563 time to fit residues: 0.8331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 45 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 0.0270 chunk 51 optimal weight: 10.0000 chunk 30 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.134413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.118240 restraints weight = 37836.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.120017 restraints weight = 28500.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.121288 restraints weight = 23286.200| |-----------------------------------------------------------------------------| r_work (final): 0.4480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.8265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6006 Z= 0.184 Angle : 0.666 8.682 8497 Z= 0.338 Chirality : 0.040 0.243 977 Planarity : 0.004 0.040 803 Dihedral : 23.717 179.765 1710 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.19 % Favored : 94.61 % Rotamer: Outliers : 0.22 % Allowed : 26.97 % Favored : 72.81 % 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: -1.90 (0.38), residues: 501 helix: -0.94 (0.51), residues: 103 sheet: -2.36 (0.70), residues: 40 loop : -1.28 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 260 HIS 0.006 0.001 HIS A 13 PHE 0.014 0.001 PHE A 139 TYR 0.015 0.001 TYR A 293 ARG 0.004 0.001 ARG A 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1256.89 seconds wall clock time: 23 minutes 49.28 seconds (1429.28 seconds total)