Starting phenix.real_space_refine on Wed Sep 25 06:33:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn5_3240/09_2024/5fn5_3240.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn5_3240/09_2024/5fn5_3240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn5_3240/09_2024/5fn5_3240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn5_3240/09_2024/5fn5_3240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn5_3240/09_2024/5fn5_3240.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn5_3240/09_2024/5fn5_3240.cif" } resolution = 4.3 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= 0.007 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 6313 2.51 5 N 1572 2.21 5 O 1724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9645 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5222 Classifications: {'peptide': 665} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 627} Chain: "B" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1735 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 215} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1868 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 233} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 820 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 5.53, per 1000 atoms: 0.57 Number of scatterers: 9645 At special positions: 0 Unit cell: (93.8, 142.8, 96.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1724 8.00 N 1572 7.00 C 6313 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.02 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.04 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 213 " distance=2.07 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.1 seconds 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 7 sheets defined 59.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 34 through 41 removed outlier: 3.842A pdb=" N ARG A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 88 Processing helix chain 'A' and resid 105 through 113 Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.892A pdb=" N GLY A 146 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 4.198A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 337 through 350 Processing helix chain 'A' and resid 381 through 387 Processing helix chain 'A' and resid 387 through 407 removed outlier: 3.666A pdb=" N GLY A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 431 removed outlier: 4.025A pdb=" N ARG A 429 " --> pdb=" O SER A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 474 through 479 removed outlier: 4.065A pdb=" N ASN A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 504 removed outlier: 3.570A pdb=" N GLY A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.733A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 561 through 575 removed outlier: 3.541A pdb=" N VAL A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 633 through 638 Processing helix chain 'A' and resid 665 through 698 removed outlier: 5.173A pdb=" N ASP A 695 " --> pdb=" O ASN A 691 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 102 Proline residue: B 88 - end of helix removed outlier: 3.509A pdb=" N LEU B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 190 removed outlier: 3.676A pdb=" N PHE B 179 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 180 " --> pdb=" O PHE B 176 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 214 Processing helix chain 'B' and resid 218 through 240 Processing helix chain 'B' and resid 244 through 263 Processing helix chain 'B' and resid 382 through 398 Processing helix chain 'B' and resid 403 through 429 removed outlier: 3.699A pdb=" N THR B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 464 removed outlier: 3.675A pdb=" N VAL B 444 " --> pdb=" O THR B 440 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) Proline residue: B 455 - end of helix Processing helix chain 'C' and resid 2 through 24 Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 28 through 60 removed outlier: 3.557A pdb=" N VAL C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 102 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 114 through 142 removed outlier: 3.654A pdb=" N SER C 129 " --> pdb=" O PHE C 125 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 185 removed outlier: 3.510A pdb=" N PHE C 179 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASP C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 206 removed outlier: 3.939A pdb=" N LEU C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 233 removed outlier: 3.759A pdb=" N ILE C 217 " --> pdb=" O SER C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 243 removed outlier: 3.590A pdb=" N LEU C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 20 removed outlier: 3.801A pdb=" N ASN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 42 removed outlier: 3.782A pdb=" N TRP D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP D 36 " --> pdb=" O VAL D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 54 Processing helix chain 'D' and resid 55 through 82 Processing helix chain 'D' and resid 86 through 92 Processing sheet with id=AA, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.559A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AC, first strand: chain 'A' and resid 413 through 414 removed outlier: 3.543A pdb=" N VAL A 440 " --> pdb=" O HIS A 379 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER A 437 " --> pdb=" O PHE A 362 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'A' and resid 413 through 414 removed outlier: 3.543A pdb=" N VAL A 440 " --> pdb=" O HIS A 379 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 361 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP A 257 " --> pdb=" O ARG A 626 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'A' and resid 437 through 438 removed outlier: 6.800A pdb=" N SER A 437 " --> pdb=" O PHE A 362 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'A' and resid 603 through 604 Processing sheet with id=BA, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.969A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1671 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1599 1.32 - 1.45: 2853 1.45 - 1.58: 5376 1.58 - 1.71: 12 1.71 - 1.83: 54 Bond restraints: 9894 Sorted by residual: bond pdb=" CA SER B 401 " pdb=" C SER B 401 " ideal model delta sigma weight residual 1.523 1.608 -0.084 1.34e-02 5.57e+03 3.97e+01 bond pdb=" N LEU C 243 " pdb=" CA LEU C 243 " ideal model delta sigma weight residual 1.457 1.528 -0.070 1.29e-02 6.01e+03 2.98e+01 bond pdb=" CA VAL A 579 " pdb=" C VAL A 579 " ideal model delta sigma weight residual 1.520 1.578 -0.058 1.07e-02 8.73e+03 2.95e+01 bond pdb=" CA LEU B 452 " pdb=" C LEU B 452 " ideal model delta sigma weight residual 1.525 1.476 0.050 1.02e-02 9.61e+03 2.37e+01 bond pdb=" CA LEU C 243 " pdb=" C LEU C 243 " ideal model delta sigma weight residual 1.523 1.582 -0.059 1.34e-02 5.57e+03 1.95e+01 ... (remaining 9889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 11297 2.57 - 5.15: 1993 5.15 - 7.72: 166 7.72 - 10.30: 23 10.30 - 12.87: 9 Bond angle restraints: 13488 Sorted by residual: angle pdb=" N VAL C 120 " pdb=" CA VAL C 120 " pdb=" CB VAL C 120 " ideal model delta sigma weight residual 110.55 119.51 -8.96 1.17e+00 7.31e-01 5.87e+01 angle pdb=" N GLY A 547 " pdb=" CA GLY A 547 " pdb=" C GLY A 547 " ideal model delta sigma weight residual 112.57 102.37 10.20 1.37e+00 5.33e-01 5.54e+01 angle pdb=" N ALA B 400 " pdb=" CA ALA B 400 " pdb=" C ALA B 400 " ideal model delta sigma weight residual 109.40 121.49 -12.09 1.63e+00 3.76e-01 5.50e+01 angle pdb=" CA PHE C 88 " pdb=" C PHE C 88 " pdb=" N ALA C 89 " ideal model delta sigma weight residual 117.07 108.95 8.12 1.14e+00 7.69e-01 5.07e+01 angle pdb=" C ILE B 387 " pdb=" CA ILE B 387 " pdb=" CB ILE B 387 " ideal model delta sigma weight residual 111.97 102.87 9.10 1.28e+00 6.10e-01 5.06e+01 ... (remaining 13483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 4792 17.40 - 34.79: 691 34.79 - 52.19: 221 52.19 - 69.59: 57 69.59 - 86.99: 10 Dihedral angle restraints: 5771 sinusoidal: 2196 harmonic: 3575 Sorted by residual: dihedral pdb=" CA ALA B 400 " pdb=" C ALA B 400 " pdb=" N SER B 401 " pdb=" CA SER B 401 " ideal model delta harmonic sigma weight residual -180.00 -128.06 -51.94 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CB CYS A 230 " pdb=" SG CYS A 230 " pdb=" SG CYS A 248 " pdb=" CB CYS A 248 " ideal model delta sinusoidal sigma weight residual 93.00 179.99 -86.99 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CA TYR B 106 " pdb=" C TYR B 106 " pdb=" N THR B 107 " pdb=" CA THR B 107 " ideal model delta harmonic sigma weight residual 180.00 132.58 47.42 0 5.00e+00 4.00e-02 8.99e+01 ... (remaining 5768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 1341 0.151 - 0.301: 185 0.301 - 0.452: 26 0.452 - 0.602: 6 0.602 - 0.753: 2 Chirality restraints: 1560 Sorted by residual: chirality pdb=" CA PHE A 218 " pdb=" N PHE A 218 " pdb=" C PHE A 218 " pdb=" CB PHE A 218 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CA PHE A 302 " pdb=" N PHE A 302 " pdb=" C PHE A 302 " pdb=" CB PHE A 302 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CA TYR B 225 " pdb=" N TYR B 225 " pdb=" C TYR B 225 " pdb=" CB TYR B 225 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.45e+00 ... (remaining 1557 not shown) Planarity restraints: 1680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 559 " 0.072 5.00e-02 4.00e+02 1.10e-01 1.92e+01 pdb=" N PRO A 560 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 87 " 0.064 5.00e-02 4.00e+02 9.62e-02 1.48e+01 pdb=" N PRO B 88 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO B 88 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 88 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 388 " 0.038 2.00e-02 2.50e+03 2.64e-02 1.22e+01 pdb=" CG PHE B 388 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE B 388 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE B 388 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE B 388 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 388 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 388 " 0.011 2.00e-02 2.50e+03 ... (remaining 1677 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 132 2.64 - 3.20: 9550 3.20 - 3.77: 16000 3.77 - 4.33: 20541 4.33 - 4.90: 33144 Nonbonded interactions: 79367 Sorted by model distance: nonbonded pdb=" O ILE C 34 " pdb=" OH TYR C 90 " model vdw 2.074 3.040 nonbonded pdb=" O ALA B 396 " pdb=" OG1 THR B 399 " model vdw 2.219 3.040 nonbonded pdb=" O LEU A 397 " pdb=" OG1 THR A 400 " model vdw 2.247 3.040 nonbonded pdb=" O LEU C 35 " pdb=" OG SER C 124 " model vdw 2.263 3.040 nonbonded pdb=" O ALA C 76 " pdb=" OG SER C 79 " model vdw 2.280 3.040 ... (remaining 79362 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.290 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.970 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 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 : 0.012 0.095 9894 Z= 0.780 Angle : 1.850 12.870 13488 Z= 1.292 Chirality : 0.113 0.753 1560 Planarity : 0.008 0.110 1680 Dihedral : 18.823 81.957 3448 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 4.30 % Allowed : 11.41 % Favored : 84.28 % Rotamer: Outliers : 14.00 % Allowed : 16.49 % Favored : 69.51 % Cbeta Deviations : 2.43 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 1.85 % Twisted General : 1.29 % 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 (0.22), residues: 1209 helix: 1.07 (0.16), residues: 660 sheet: -3.39 (0.45), residues: 100 loop : -4.58 (0.22), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP D 36 HIS 0.013 0.003 HIS A 74 PHE 0.059 0.005 PHE A 302 TYR 0.042 0.004 TYR B 225 ARG 0.008 0.001 ARG A 657 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 240 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.6710 (OUTLIER) cc_final: 0.6345 (p) REVERT: A 95 MET cc_start: 0.9170 (mmt) cc_final: 0.8700 (mmm) REVERT: A 129 SER cc_start: 0.7373 (OUTLIER) cc_final: 0.6535 (t) REVERT: A 237 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8194 (tp-100) REVERT: A 333 GLU cc_start: 0.9323 (OUTLIER) cc_final: 0.8792 (mp0) REVERT: A 378 MET cc_start: 0.9135 (mpt) cc_final: 0.8745 (mpp) REVERT: A 425 SER cc_start: 0.8302 (OUTLIER) cc_final: 0.7908 (t) REVERT: A 426 SER cc_start: 0.9586 (t) cc_final: 0.8770 (p) REVERT: A 430 PHE cc_start: 0.9607 (m-80) cc_final: 0.9003 (m-80) REVERT: A 512 GLN cc_start: 0.9340 (OUTLIER) cc_final: 0.8960 (pp30) REVERT: A 522 LEU cc_start: 0.9666 (OUTLIER) cc_final: 0.9433 (mt) REVERT: A 555 ILE cc_start: 0.7981 (mt) cc_final: 0.6549 (mt) REVERT: A 574 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8803 (mt) REVERT: A 624 THR cc_start: 0.7194 (OUTLIER) cc_final: 0.6823 (m) REVERT: A 644 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8895 (pp20) REVERT: A 655 ASP cc_start: 0.8547 (m-30) cc_final: 0.8202 (p0) REVERT: B 80 LYS cc_start: 0.9357 (tttt) cc_final: 0.9022 (mttm) REVERT: B 105 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8396 (t80) REVERT: B 184 GLU cc_start: 0.9375 (OUTLIER) cc_final: 0.9130 (mm-30) REVERT: B 194 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8142 (p0) REVERT: B 195 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.8656 (m-80) REVERT: B 386 PHE cc_start: 0.8150 (t80) cc_final: 0.7820 (t80) REVERT: B 405 ASN cc_start: 0.8830 (t0) cc_final: 0.8514 (t0) REVERT: B 438 SER cc_start: 0.8016 (OUTLIER) cc_final: 0.7749 (p) REVERT: C 9 CYS cc_start: 0.8973 (m) cc_final: 0.8604 (p) REVERT: C 83 GLN cc_start: 0.9499 (mt0) cc_final: 0.9275 (mp10) REVERT: C 84 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8619 (mm-30) REVERT: C 132 PHE cc_start: 0.9522 (m-10) cc_final: 0.9304 (m-10) REVERT: C 136 ASN cc_start: 0.9112 (m-40) cc_final: 0.8562 (p0) REVERT: D 5 ARG cc_start: 0.8240 (mtm180) cc_final: 0.8029 (ptt90) REVERT: D 28 PHE cc_start: 0.9231 (t80) cc_final: 0.8868 (t80) REVERT: D 84 ARG cc_start: 0.9253 (mtt180) cc_final: 0.9022 (mpt-90) REVERT: D 96 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7658 (mm) outliers start: 146 outliers final: 47 residues processed: 346 average time/residue: 0.2056 time to fit residues: 98.7282 Evaluate side-chains 223 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 160 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 70 optimal weight: 0.4980 chunk 109 optimal weight: 5.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 237 GLN ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN A 535 GLN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN C 171 HIS ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 9894 Z= 0.287 Angle : 0.873 11.272 13488 Z= 0.454 Chirality : 0.048 0.197 1560 Planarity : 0.006 0.090 1680 Dihedral : 7.200 35.800 1319 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 1.08 % Allowed : 8.35 % Favored : 90.57 % Rotamer: Outliers : 0.86 % Allowed : 3.93 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 3.70 % Twisted General : 0.17 % 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: -0.59 (0.25), residues: 1209 helix: 1.87 (0.20), residues: 692 sheet: -2.88 (0.44), residues: 109 loop : -3.92 (0.25), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 257 HIS 0.009 0.002 HIS A 553 PHE 0.038 0.003 PHE A 302 TYR 0.023 0.002 TYR C 69 ARG 0.004 0.001 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 225 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 PHE cc_start: 0.9198 (m-80) cc_final: 0.8926 (m-80) REVERT: A 305 GLN cc_start: 0.9450 (tp-100) cc_final: 0.9071 (tt0) REVERT: A 347 MET cc_start: 0.9214 (tpp) cc_final: 0.8998 (tpp) REVERT: A 378 MET cc_start: 0.9140 (mpp) cc_final: 0.8904 (mpp) REVERT: A 553 HIS cc_start: 0.9186 (m-70) cc_final: 0.8957 (m90) REVERT: A 655 ASP cc_start: 0.8710 (m-30) cc_final: 0.8280 (p0) REVERT: B 194 ASP cc_start: 0.8893 (p0) cc_final: 0.8500 (p0) REVERT: B 210 MET cc_start: 0.9114 (mmp) cc_final: 0.8807 (mmm) REVERT: B 225 TYR cc_start: 0.8496 (m-10) cc_final: 0.8241 (m-80) REVERT: B 445 PHE cc_start: 0.9134 (t80) cc_final: 0.8855 (t80) REVERT: B 457 MET cc_start: 0.9692 (mmp) cc_final: 0.9303 (ptt) REVERT: B 463 HIS cc_start: 0.9401 (m90) cc_final: 0.9122 (t-90) REVERT: C 109 ARG cc_start: 0.8223 (pmt-80) cc_final: 0.7925 (ptm-80) REVERT: C 132 PHE cc_start: 0.9475 (m-10) cc_final: 0.9253 (m-10) REVERT: C 135 ILE cc_start: 0.8960 (tp) cc_final: 0.8668 (tp) REVERT: C 140 ASP cc_start: 0.7767 (m-30) cc_final: 0.7070 (m-30) REVERT: C 197 HIS cc_start: 0.9692 (t-170) cc_final: 0.9453 (t-170) REVERT: D 28 PHE cc_start: 0.9329 (t80) cc_final: 0.9023 (t80) REVERT: D 69 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8958 (tp) outliers start: 9 outliers final: 2 residues processed: 230 average time/residue: 0.2125 time to fit residues: 70.5647 Evaluate side-chains 150 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 chunk 118 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9894 Z= 0.286 Angle : 0.779 11.109 13488 Z= 0.405 Chirality : 0.045 0.181 1560 Planarity : 0.006 0.098 1680 Dihedral : 6.561 33.861 1319 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.91 % Allowed : 8.93 % Favored : 90.16 % Rotamer: Outliers : 0.19 % Allowed : 6.33 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 1.85 % Twisted General : 0.17 % 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: -0.82 (0.24), residues: 1209 helix: 1.32 (0.19), residues: 690 sheet: -2.47 (0.46), residues: 107 loop : -3.41 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 84 HIS 0.008 0.002 HIS C 58 PHE 0.034 0.002 PHE A 302 TYR 0.023 0.002 TYR B 446 ARG 0.021 0.001 ARG A 659 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 186 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8610 (mmt) cc_final: 0.7862 (mmt) REVERT: A 97 LEU cc_start: 0.9489 (tp) cc_final: 0.9195 (tp) REVERT: A 182 LEU cc_start: 0.9458 (tp) cc_final: 0.9164 (pp) REVERT: A 210 PHE cc_start: 0.9092 (m-80) cc_final: 0.8754 (m-80) REVERT: A 347 MET cc_start: 0.9299 (tpp) cc_final: 0.8943 (tpp) REVERT: A 367 GLN cc_start: 0.8911 (mp10) cc_final: 0.8392 (tt0) REVERT: A 378 MET cc_start: 0.9137 (mpp) cc_final: 0.8790 (mpp) REVERT: B 194 ASP cc_start: 0.8944 (p0) cc_final: 0.8579 (p0) REVERT: B 210 MET cc_start: 0.9138 (mmp) cc_final: 0.8859 (mmm) REVERT: B 386 PHE cc_start: 0.8146 (t80) cc_final: 0.7592 (t80) REVERT: B 391 VAL cc_start: 0.9256 (t) cc_final: 0.9024 (t) REVERT: B 463 HIS cc_start: 0.9393 (m90) cc_final: 0.9087 (t-90) REVERT: C 109 ARG cc_start: 0.8242 (pmt-80) cc_final: 0.7815 (ptm-80) REVERT: C 132 PHE cc_start: 0.9585 (m-80) cc_final: 0.9268 (m-80) REVERT: C 197 HIS cc_start: 0.9714 (t-170) cc_final: 0.9389 (t-170) REVERT: D 28 PHE cc_start: 0.9341 (t80) cc_final: 0.9105 (t80) outliers start: 2 outliers final: 0 residues processed: 188 average time/residue: 0.1810 time to fit residues: 49.8332 Evaluate side-chains 131 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 HIS A 449 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN A 606 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9894 Z= 0.395 Angle : 0.850 11.215 13488 Z= 0.443 Chirality : 0.046 0.228 1560 Planarity : 0.007 0.088 1680 Dihedral : 6.620 35.041 1319 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 23.09 Ramachandran Plot: Outliers : 0.91 % Allowed : 8.77 % Favored : 90.32 % Rotamer: Outliers : 0.19 % Allowed : 4.89 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 1.85 % Twisted General : 0.09 % 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: -1.25 (0.24), residues: 1209 helix: 0.82 (0.19), residues: 684 sheet: -2.43 (0.46), residues: 110 loop : -3.29 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 53 HIS 0.009 0.002 HIS A 74 PHE 0.034 0.003 PHE A 302 TYR 0.021 0.002 TYR C 90 ARG 0.008 0.001 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 172 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.9316 (pt0) cc_final: 0.8903 (tm-30) REVERT: A 108 MET cc_start: 0.9667 (mmp) cc_final: 0.9401 (mmm) REVERT: A 182 LEU cc_start: 0.9419 (tp) cc_final: 0.9142 (pp) REVERT: A 210 PHE cc_start: 0.9029 (m-80) cc_final: 0.8759 (m-80) REVERT: A 347 MET cc_start: 0.9301 (tpp) cc_final: 0.8996 (tpp) REVERT: A 367 GLN cc_start: 0.8751 (mp10) cc_final: 0.8255 (mt0) REVERT: A 378 MET cc_start: 0.9040 (mpp) cc_final: 0.8756 (mpp) REVERT: B 210 MET cc_start: 0.9030 (mmp) cc_final: 0.8828 (mmm) REVERT: B 225 TYR cc_start: 0.8623 (m-80) cc_final: 0.8398 (m-80) REVERT: B 386 PHE cc_start: 0.8435 (t80) cc_final: 0.8194 (t80) REVERT: C 84 GLU cc_start: 0.9561 (pp20) cc_final: 0.9324 (pp20) REVERT: C 99 GLU cc_start: 0.9037 (pp20) cc_final: 0.8787 (pt0) REVERT: C 132 PHE cc_start: 0.9534 (m-80) cc_final: 0.9178 (m-80) REVERT: D 28 PHE cc_start: 0.9399 (t80) cc_final: 0.9131 (t80) outliers start: 2 outliers final: 1 residues processed: 173 average time/residue: 0.1858 time to fit residues: 46.8941 Evaluate side-chains 122 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.1980 chunk 1 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 0 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 39 optimal weight: 0.2980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9894 Z= 0.220 Angle : 0.738 11.472 13488 Z= 0.374 Chirality : 0.043 0.197 1560 Planarity : 0.006 0.090 1680 Dihedral : 5.998 32.916 1319 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.94 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 1.85 % 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: -0.76 (0.25), residues: 1209 helix: 1.19 (0.19), residues: 694 sheet: -2.19 (0.48), residues: 108 loop : -3.12 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 67 HIS 0.012 0.001 HIS C 197 PHE 0.030 0.002 PHE A 302 TYR 0.016 0.002 TYR C 90 ARG 0.004 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.9302 (pt0) cc_final: 0.8917 (tm-30) REVERT: A 70 THR cc_start: 0.7845 (t) cc_final: 0.7638 (t) REVERT: A 108 MET cc_start: 0.9578 (mmp) cc_final: 0.9235 (mmp) REVERT: A 182 LEU cc_start: 0.9403 (tp) cc_final: 0.9176 (pp) REVERT: A 210 PHE cc_start: 0.9063 (m-80) cc_final: 0.8792 (m-80) REVERT: A 347 MET cc_start: 0.9337 (tpp) cc_final: 0.9058 (tpp) REVERT: A 367 GLN cc_start: 0.8704 (mp10) cc_final: 0.8198 (mt0) REVERT: A 378 MET cc_start: 0.9106 (mpp) cc_final: 0.8821 (mpp) REVERT: A 655 ASP cc_start: 0.8735 (t0) cc_final: 0.8198 (t0) REVERT: B 175 PHE cc_start: 0.9053 (m-10) cc_final: 0.8747 (m-80) REVERT: B 210 MET cc_start: 0.8987 (mmp) cc_final: 0.8602 (mmm) REVERT: B 221 LEU cc_start: 0.7874 (mt) cc_final: 0.7634 (mt) REVERT: B 225 TYR cc_start: 0.8511 (m-80) cc_final: 0.8306 (m-80) REVERT: B 233 MET cc_start: 0.9440 (mmp) cc_final: 0.9201 (tpt) REVERT: C 53 TRP cc_start: 0.9045 (t60) cc_final: 0.8759 (t60) REVERT: C 84 GLU cc_start: 0.9560 (pp20) cc_final: 0.9298 (pp20) REVERT: C 99 GLU cc_start: 0.8995 (pp20) cc_final: 0.8756 (pt0) REVERT: C 132 PHE cc_start: 0.9456 (m-80) cc_final: 0.9088 (m-80) REVERT: C 133 SER cc_start: 0.8971 (t) cc_final: 0.8609 (p) REVERT: D 28 PHE cc_start: 0.9370 (t80) cc_final: 0.9119 (t80) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1841 time to fit residues: 49.3062 Evaluate side-chains 138 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 10.0000 chunk 23 optimal weight: 0.0020 chunk 68 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 overall best weight: 6.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 HIS ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.6201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9894 Z= 0.405 Angle : 0.845 11.479 13488 Z= 0.440 Chirality : 0.046 0.174 1560 Planarity : 0.007 0.084 1680 Dihedral : 6.327 32.206 1319 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 23.66 Ramachandran Plot: Outliers : 0.83 % Allowed : 10.09 % Favored : 89.08 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 1.85 % Twisted General : 0.09 % 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: -1.18 (0.24), residues: 1209 helix: 0.77 (0.19), residues: 688 sheet: -2.20 (0.47), residues: 108 loop : -3.13 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 244 HIS 0.011 0.003 HIS A 102 PHE 0.030 0.003 PHE A 302 TYR 0.025 0.002 TYR C 90 ARG 0.011 0.001 ARG A 657 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8433 (mpp) cc_final: 0.7619 (mpp) REVERT: A 108 MET cc_start: 0.9537 (mmp) cc_final: 0.9228 (mmp) REVERT: A 182 LEU cc_start: 0.9419 (tp) cc_final: 0.9079 (pp) REVERT: A 210 PHE cc_start: 0.9070 (m-80) cc_final: 0.8813 (m-80) REVERT: A 347 MET cc_start: 0.9285 (tpp) cc_final: 0.9005 (tpp) REVERT: A 367 GLN cc_start: 0.8724 (mp10) cc_final: 0.8220 (mt0) REVERT: A 378 MET cc_start: 0.8923 (mpp) cc_final: 0.8602 (mpp) REVERT: A 553 HIS cc_start: 0.9214 (m-70) cc_final: 0.8896 (m90) REVERT: B 210 MET cc_start: 0.9018 (mmp) cc_final: 0.8787 (mmm) REVERT: C 84 GLU cc_start: 0.9598 (pp20) cc_final: 0.9330 (pp20) REVERT: C 132 PHE cc_start: 0.9418 (m-80) cc_final: 0.9094 (m-80) REVERT: C 171 HIS cc_start: 0.9585 (m90) cc_final: 0.9275 (m90) REVERT: C 218 TYR cc_start: 0.9090 (m-80) cc_final: 0.8861 (m-80) REVERT: D 28 PHE cc_start: 0.9489 (t80) cc_final: 0.9270 (t80) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1818 time to fit residues: 43.0916 Evaluate side-chains 121 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.6409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9894 Z= 0.334 Angle : 0.794 11.699 13488 Z= 0.415 Chirality : 0.045 0.180 1560 Planarity : 0.006 0.081 1680 Dihedral : 6.137 32.827 1319 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 22.57 Ramachandran Plot: Outliers : 0.83 % Allowed : 8.44 % Favored : 90.74 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.24), residues: 1209 helix: 0.79 (0.19), residues: 686 sheet: -1.99 (0.49), residues: 105 loop : -3.15 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 67 HIS 0.012 0.002 HIS C 197 PHE 0.029 0.002 PHE A 302 TYR 0.020 0.002 TYR B 195 ARG 0.004 0.001 ARG A 434 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8530 (mpp) cc_final: 0.7940 (mpp) REVERT: A 97 LEU cc_start: 0.9510 (tp) cc_final: 0.9279 (tt) REVERT: A 108 MET cc_start: 0.9571 (mmp) cc_final: 0.9347 (mmm) REVERT: A 182 LEU cc_start: 0.9392 (tp) cc_final: 0.9036 (pp) REVERT: A 210 PHE cc_start: 0.9090 (m-80) cc_final: 0.8854 (m-80) REVERT: A 305 GLN cc_start: 0.9668 (tp-100) cc_final: 0.9426 (tt0) REVERT: A 347 MET cc_start: 0.9345 (tpp) cc_final: 0.9049 (tpp) REVERT: A 367 GLN cc_start: 0.8827 (mp10) cc_final: 0.8401 (mt0) REVERT: A 378 MET cc_start: 0.8910 (mpp) cc_final: 0.8577 (mpp) REVERT: B 175 PHE cc_start: 0.9240 (m-10) cc_final: 0.8966 (m-80) REVERT: B 195 TYR cc_start: 0.8891 (m-80) cc_final: 0.8599 (m-10) REVERT: B 198 VAL cc_start: 0.9156 (t) cc_final: 0.8910 (t) REVERT: B 210 MET cc_start: 0.9083 (mmp) cc_final: 0.8676 (mmm) REVERT: C 9 CYS cc_start: 0.9431 (m) cc_final: 0.9117 (p) REVERT: C 53 TRP cc_start: 0.9027 (t60) cc_final: 0.8669 (t60) REVERT: C 84 GLU cc_start: 0.9613 (pp20) cc_final: 0.9311 (pp20) REVERT: C 98 ASP cc_start: 0.9626 (t0) cc_final: 0.9393 (m-30) REVERT: C 133 SER cc_start: 0.9099 (t) cc_final: 0.8758 (p) REVERT: C 171 HIS cc_start: 0.9584 (m90) cc_final: 0.9211 (m90) REVERT: C 218 TYR cc_start: 0.9060 (m-80) cc_final: 0.8703 (m-80) REVERT: D 5 ARG cc_start: 0.8849 (mtm180) cc_final: 0.8581 (mmp80) REVERT: D 28 PHE cc_start: 0.9403 (t80) cc_final: 0.8965 (t80) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1840 time to fit residues: 44.0360 Evaluate side-chains 125 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 111 optimal weight: 30.0000 chunk 101 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.6603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9894 Z= 0.271 Angle : 0.768 11.687 13488 Z= 0.397 Chirality : 0.045 0.221 1560 Planarity : 0.006 0.078 1680 Dihedral : 5.911 31.781 1319 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.83 % Allowed : 8.85 % Favored : 90.32 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 1.85 % 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: -1.04 (0.24), residues: 1209 helix: 0.85 (0.19), residues: 692 sheet: -1.92 (0.49), residues: 105 loop : -3.10 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 404 HIS 0.008 0.002 HIS C 197 PHE 0.036 0.002 PHE C 205 TYR 0.035 0.002 TYR A 554 ARG 0.003 0.000 ARG D 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8601 (mpp) cc_final: 0.8158 (mpp) REVERT: A 108 MET cc_start: 0.9537 (mmp) cc_final: 0.9273 (mmp) REVERT: A 182 LEU cc_start: 0.9352 (tp) cc_final: 0.9004 (pp) REVERT: A 305 GLN cc_start: 0.9668 (tp-100) cc_final: 0.9451 (tt0) REVERT: A 347 MET cc_start: 0.9283 (tpp) cc_final: 0.9071 (tpp) REVERT: A 367 GLN cc_start: 0.8903 (mp10) cc_final: 0.8449 (mt0) REVERT: A 378 MET cc_start: 0.8915 (mpp) cc_final: 0.8574 (mpp) REVERT: A 430 PHE cc_start: 0.9157 (m-80) cc_final: 0.8931 (m-80) REVERT: B 210 MET cc_start: 0.9081 (mmp) cc_final: 0.8801 (mmm) REVERT: B 457 MET cc_start: 0.9753 (mmp) cc_final: 0.9537 (mmp) REVERT: C 9 CYS cc_start: 0.9421 (m) cc_final: 0.9117 (p) REVERT: C 53 TRP cc_start: 0.9038 (t60) cc_final: 0.8686 (t60) REVERT: C 84 GLU cc_start: 0.9522 (pp20) cc_final: 0.9266 (pp20) REVERT: C 132 PHE cc_start: 0.9464 (m-10) cc_final: 0.9220 (m-80) REVERT: C 133 SER cc_start: 0.9062 (t) cc_final: 0.8779 (p) REVERT: C 218 TYR cc_start: 0.9048 (m-80) cc_final: 0.8647 (m-80) REVERT: D 28 PHE cc_start: 0.9438 (t80) cc_final: 0.9079 (t80) REVERT: D 32 VAL cc_start: 0.9716 (t) cc_final: 0.9515 (t) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1851 time to fit residues: 45.5066 Evaluate side-chains 127 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 40.0000 chunk 65 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 71 optimal weight: 0.0970 chunk 114 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.6784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9894 Z= 0.255 Angle : 0.772 11.783 13488 Z= 0.398 Chirality : 0.045 0.245 1560 Planarity : 0.006 0.076 1680 Dihedral : 5.766 30.757 1319 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.91 % Allowed : 8.11 % Favored : 90.98 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 1.85 % 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: -0.96 (0.24), residues: 1209 helix: 0.87 (0.19), residues: 690 sheet: -1.87 (0.49), residues: 105 loop : -2.98 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 67 HIS 0.007 0.001 HIS C 58 PHE 0.035 0.002 PHE C 205 TYR 0.021 0.002 TYR A 41 ARG 0.005 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8588 (mpp) cc_final: 0.8289 (mpp) REVERT: A 108 MET cc_start: 0.9547 (mmp) cc_final: 0.9301 (mmp) REVERT: A 182 LEU cc_start: 0.9353 (tp) cc_final: 0.9008 (pp) REVERT: A 305 GLN cc_start: 0.9668 (tp-100) cc_final: 0.9454 (tt0) REVERT: A 347 MET cc_start: 0.9229 (tpp) cc_final: 0.9009 (tpp) REVERT: A 367 GLN cc_start: 0.8911 (mp10) cc_final: 0.8451 (mt0) REVERT: A 378 MET cc_start: 0.8909 (mpp) cc_final: 0.8570 (mpp) REVERT: A 430 PHE cc_start: 0.9213 (m-80) cc_final: 0.8990 (m-80) REVERT: A 553 HIS cc_start: 0.9113 (m-70) cc_final: 0.8802 (m90) REVERT: B 103 VAL cc_start: 0.8321 (t) cc_final: 0.7949 (t) REVERT: B 198 VAL cc_start: 0.9161 (t) cc_final: 0.8925 (t) REVERT: B 210 MET cc_start: 0.9051 (mmp) cc_final: 0.8766 (mmm) REVERT: B 457 MET cc_start: 0.9767 (mmp) cc_final: 0.9557 (mmp) REVERT: C 35 LEU cc_start: 0.9190 (mm) cc_final: 0.8989 (mm) REVERT: C 53 TRP cc_start: 0.9044 (t60) cc_final: 0.8671 (t60) REVERT: C 84 GLU cc_start: 0.9587 (pp20) cc_final: 0.9339 (pp20) REVERT: C 132 PHE cc_start: 0.9461 (m-10) cc_final: 0.9249 (m-10) REVERT: C 133 SER cc_start: 0.9112 (t) cc_final: 0.8821 (p) REVERT: C 218 TYR cc_start: 0.9094 (m-80) cc_final: 0.8686 (m-80) REVERT: D 28 PHE cc_start: 0.9427 (t80) cc_final: 0.9079 (t80) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1818 time to fit residues: 43.9938 Evaluate side-chains 127 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 120 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.6891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9894 Z= 0.305 Angle : 0.808 11.807 13488 Z= 0.422 Chirality : 0.046 0.257 1560 Planarity : 0.006 0.081 1680 Dihedral : 5.860 31.842 1319 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.10 % Favored : 90.07 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 1.85 % 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: -1.05 (0.24), residues: 1209 helix: 0.77 (0.19), residues: 685 sheet: -1.86 (0.49), residues: 105 loop : -2.93 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 404 HIS 0.009 0.002 HIS A 74 PHE 0.031 0.002 PHE A 302 TYR 0.020 0.002 TYR C 90 ARG 0.003 0.000 ARG A 657 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8614 (mpp) cc_final: 0.8186 (mpp) REVERT: A 108 MET cc_start: 0.9544 (mmp) cc_final: 0.9278 (mmp) REVERT: A 182 LEU cc_start: 0.9427 (tp) cc_final: 0.9095 (pp) REVERT: A 213 CYS cc_start: 0.8604 (t) cc_final: 0.8279 (m) REVERT: A 347 MET cc_start: 0.9221 (tpp) cc_final: 0.9008 (tpp) REVERT: A 367 GLN cc_start: 0.8816 (mp10) cc_final: 0.8339 (mt0) REVERT: A 378 MET cc_start: 0.8860 (mpp) cc_final: 0.8527 (mpp) REVERT: A 553 HIS cc_start: 0.9102 (m-70) cc_final: 0.8758 (m90) REVERT: B 103 VAL cc_start: 0.8350 (t) cc_final: 0.8109 (t) REVERT: B 198 VAL cc_start: 0.9173 (t) cc_final: 0.8905 (t) REVERT: B 210 MET cc_start: 0.9106 (mmp) cc_final: 0.8750 (mmm) REVERT: B 228 MET cc_start: 0.9241 (mpp) cc_final: 0.9038 (mpp) REVERT: B 457 MET cc_start: 0.9777 (mmp) cc_final: 0.9565 (mmp) REVERT: C 53 TRP cc_start: 0.9019 (t60) cc_final: 0.8488 (t60) REVERT: C 84 GLU cc_start: 0.9618 (pp20) cc_final: 0.9377 (pp20) REVERT: C 132 PHE cc_start: 0.9490 (m-10) cc_final: 0.9288 (m-10) REVERT: C 133 SER cc_start: 0.9138 (t) cc_final: 0.8838 (p) REVERT: C 140 ASP cc_start: 0.7897 (m-30) cc_final: 0.7648 (m-30) REVERT: C 218 TYR cc_start: 0.9105 (m-80) cc_final: 0.8681 (m-80) REVERT: D 28 PHE cc_start: 0.9439 (t80) cc_final: 0.9083 (t80) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1800 time to fit residues: 44.0750 Evaluate side-chains 131 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 17 optimal weight: 0.0370 chunk 84 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 69 optimal weight: 0.3980 overall best weight: 1.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.049602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.042404 restraints weight = 73176.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.043383 restraints weight = 47938.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.044116 restraints weight = 35188.386| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.7015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9894 Z= 0.232 Angle : 0.779 11.877 13488 Z= 0.401 Chirality : 0.045 0.220 1560 Planarity : 0.006 0.081 1680 Dihedral : 5.617 31.232 1319 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.74 % Allowed : 8.19 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 1.85 % 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: -0.89 (0.25), residues: 1209 helix: 0.89 (0.20), residues: 691 sheet: -1.90 (0.48), residues: 110 loop : -2.86 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 67 HIS 0.009 0.001 HIS C 197 PHE 0.039 0.002 PHE D 66 TYR 0.017 0.001 TYR C 119 ARG 0.003 0.000 ARG D 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1876.42 seconds wall clock time: 34 minutes 35.98 seconds (2075.98 seconds total)