Starting phenix.real_space_refine on Wed Sep 17 18:10:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5fn2_3237/09_2025/5fn2_3237.cif Found real_map, /net/cci-nas-00/data/ceres_data/5fn2_3237/09_2025/5fn2_3237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5fn2_3237/09_2025/5fn2_3237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5fn2_3237/09_2025/5fn2_3237.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5fn2_3237/09_2025/5fn2_3237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5fn2_3237/09_2025/5fn2_3237.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.012 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 40 5.16 5 C 6733 2.51 5 N 1674 2.21 5 O 1829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10276 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: 2339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2339 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 6, 'PTRANS': 10, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 40 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: {'PTRANS': 7, 'TRANS': 235} 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: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 847 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 94} 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: 2.97, per 1000 atoms: 0.29 Number of scatterers: 10276 At special positions: 0 Unit cell: (89.6, 144.2, 105, 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 40 16.00 O 1829 8.00 N 1674 7.00 C 6733 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=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 213 " distance=2.04 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=2.03 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: 0.93 Conformation dependent library (CDL) restraints added in 295.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2462 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 7 sheets defined 58.8% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 35 through 41 Processing helix chain 'A' and resid 78 through 88 removed outlier: 3.773A pdb=" N LEU A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.631A pdb=" N ARG A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 198 Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.821A pdb=" N GLY A 205 " --> pdb=" O SER A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 240 Processing helix chain 'A' and resid 298 through 315 Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 381 through 387 Processing helix chain 'A' and resid 387 through 407 removed outlier: 3.825A pdb=" N GLY A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 481 through 502 Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.742A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.776A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 removed outlier: 3.616A pdb=" N TYR A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 3.620A 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 665 through 693 Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'B' and resid 79 through 103 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 124 through 156 removed outlier: 3.557A pdb=" N ILE B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 156 " --> pdb=" O VAL B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 190 removed outlier: 3.869A pdb=" N HIS B 163 " --> pdb=" O TYR B 159 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 218 through 241 Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.535A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 276 Processing helix chain 'B' and resid 382 through 399 Processing helix chain 'B' and resid 403 through 429 Processing helix chain 'B' and resid 434 through 452 removed outlier: 3.610A pdb=" N ALA B 448 " --> pdb=" O VAL B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 464 removed outlier: 4.398A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 25 Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 28 through 61 Processing helix chain 'C' and resid 64 through 105 removed outlier: 3.810A pdb=" N GLU C 99 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 104 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 143 removed outlier: 4.844A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 185 removed outlier: 3.523A pdb=" N THR C 159 " --> pdb=" O TYR C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 206 Processing helix chain 'C' and resid 213 through 233 Processing helix chain 'C' and resid 235 through 243 removed outlier: 3.783A pdb=" N ILE C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 23 removed outlier: 3.710A pdb=" N PHE D 23 " --> pdb=" O TYR D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 37 Processing helix chain 'D' and resid 37 through 43 Processing helix chain 'D' and resid 49 through 82 Processing helix chain 'D' and resid 86 through 92 Processing sheet with id=AA, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.654A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N VAL A 96 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LEU A 121 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU A 98 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL A 123 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.523A pdb=" N LEU A 53 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'A' and resid 275 through 278 Processing sheet with id=AD, first strand: chain 'A' and resid 361 through 366 Processing sheet with id=AE, first strand: chain 'A' and resid 375 through 377 removed outlier: 3.950A pdb=" N ARG A 414 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'A' and resid 577 through 579 removed outlier: 3.531A pdb=" N THR A 577 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 622 " --> pdb=" O THR A 577 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 579 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.604A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) 610 hydrogen bonds defined for protein. 1797 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: 1.83 Time building geometry restraints manager: 1.24 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: 1689 1.32 - 1.45: 2961 1.45 - 1.58: 5831 1.58 - 1.70: 2 1.70 - 1.83: 61 Bond restraints: 10544 Sorted by residual: bond pdb=" CA ASP A 458 " pdb=" C ASP A 458 " ideal model delta sigma weight residual 1.523 1.586 -0.062 1.34e-02 5.57e+03 2.17e+01 bond pdb=" C THR B 116 " pdb=" N PRO B 117 " ideal model delta sigma weight residual 1.332 1.389 -0.057 1.30e-02 5.92e+03 1.93e+01 bond pdb=" CA VAL B 87 " pdb=" CB VAL B 87 " ideal model delta sigma weight residual 1.539 1.563 -0.024 5.40e-03 3.43e+04 1.90e+01 bond pdb=" N PRO B 117 " pdb=" CD PRO B 117 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.66e+01 bond pdb=" N PRO B 264 " pdb=" CD PRO B 264 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.62e+01 ... (remaining 10539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 13247 2.93 - 5.87: 1034 5.87 - 8.80: 86 8.80 - 11.74: 12 11.74 - 14.67: 4 Bond angle restraints: 14383 Sorted by residual: angle pdb=" C ASN A 91 " pdb=" N PRO A 92 " pdb=" CA PRO A 92 " ideal model delta sigma weight residual 120.38 132.33 -11.95 1.03e+00 9.43e-01 1.35e+02 angle pdb=" N PRO A 92 " pdb=" CA PRO A 92 " pdb=" C PRO A 92 " ideal model delta sigma weight residual 110.70 122.17 -11.47 1.22e+00 6.72e-01 8.84e+01 angle pdb=" CA VAL B 87 " pdb=" C VAL B 87 " pdb=" N PRO B 88 " ideal model delta sigma weight residual 120.83 115.48 5.35 6.10e-01 2.69e+00 7.69e+01 angle pdb=" N ARG B 108 " pdb=" CA ARG B 108 " pdb=" C ARG B 108 " ideal model delta sigma weight residual 109.52 122.31 -12.79 1.55e+00 4.16e-01 6.81e+01 angle pdb=" N ILE B 227 " pdb=" CA ILE B 227 " pdb=" CB ILE B 227 " ideal model delta sigma weight residual 110.55 119.16 -8.61 1.17e+00 7.31e-01 5.41e+01 ... (remaining 14378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 5154 17.08 - 34.15: 725 34.15 - 51.22: 207 51.22 - 68.30: 65 68.30 - 85.37: 10 Dihedral angle restraints: 6161 sinusoidal: 2343 harmonic: 3818 Sorted by residual: dihedral pdb=" CA CYS B 263 " pdb=" C CYS B 263 " pdb=" N PRO B 264 " pdb=" CA PRO B 264 " ideal model delta harmonic sigma weight residual -180.00 -123.15 -56.85 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -171.37 85.37 1 1.00e+01 1.00e-02 8.83e+01 dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual -86.00 -155.64 69.64 1 1.00e+01 1.00e-02 6.26e+01 ... (remaining 6158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1331 0.118 - 0.236: 285 0.236 - 0.353: 43 0.353 - 0.471: 12 0.471 - 0.589: 1 Chirality restraints: 1672 Sorted by residual: 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 1.92 0.59 2.00e-01 2.50e+01 8.67e+00 chirality pdb=" CA PHE B 388 " pdb=" N PHE B 388 " pdb=" C PHE B 388 " pdb=" CB PHE B 388 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" CA PHE A 525 " pdb=" N PHE A 525 " pdb=" C PHE A 525 " pdb=" CB PHE A 525 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.49e+00 ... (remaining 1669 not shown) Planarity restraints: 1789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 178 " -0.058 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO A 179 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 179 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 179 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 215 " -0.058 5.00e-02 4.00e+02 8.75e-02 1.23e+01 pdb=" N PRO C 216 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO C 216 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 216 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 266 " -0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO B 267 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 267 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 267 " -0.043 5.00e-02 4.00e+02 ... (remaining 1786 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 55 2.49 - 3.09: 7753 3.09 - 3.70: 16942 3.70 - 4.30: 22833 4.30 - 4.90: 38468 Nonbonded interactions: 86051 Sorted by model distance: nonbonded pdb=" O CYS B 263 " pdb=" N GLY B 266 " model vdw 1.890 3.120 nonbonded pdb=" CD2 LEU B 113 " pdb=" O TYR B 240 " model vdw 2.001 3.460 nonbonded pdb=" O ILE B 114 " pdb=" CD PRO B 117 " model vdw 2.060 3.440 nonbonded pdb=" ND1 HIS B 163 " pdb=" OE1 GLU B 280 " model vdw 2.106 3.120 nonbonded pdb=" O CYS B 263 " pdb=" CD PRO B 267 " model vdw 2.152 3.440 ... (remaining 86046 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: 0.410 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.880 Find NCS groups from input model: 0.040 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5693 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 : 0.009 0.066 10549 Z= 0.653 Angle : 1.735 14.672 14393 Z= 1.240 Chirality : 0.101 0.589 1672 Planarity : 0.008 0.088 1789 Dihedral : 17.975 83.353 3684 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 3.93 % Allowed : 11.93 % Favored : 84.14 % Rotamer: Outliers : 11.69 % Allowed : 14.66 % Favored : 73.65 % Cbeta Deviations : 1.87 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 3.39 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.20), residues: 1299 helix: 0.96 (0.15), residues: 745 sheet: -3.87 (0.50), residues: 57 loop : -4.43 (0.20), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 184 TYR 0.042 0.004 TYR C 119 PHE 0.052 0.004 PHE A 302 TRP 0.026 0.003 TRP D 58 HIS 0.011 0.003 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00950 (10544) covalent geometry : angle 1.73478 (14383) SS BOND : bond 0.00723 ( 5) SS BOND : angle 1.88664 ( 10) hydrogen bonds : bond 0.14911 ( 610) hydrogen bonds : angle 6.45132 ( 1797) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 457 time to evaluate : 0.431 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: A 50 CYS cc_start: 0.8637 (OUTLIER) cc_final: 0.7854 (p) REVERT: A 86 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6136 (mp) REVERT: A 87 THR cc_start: 0.7955 (t) cc_final: 0.7657 (t) REVERT: A 95 MET cc_start: 0.7656 (mmt) cc_final: 0.7274 (mmm) REVERT: A 221 MET cc_start: 0.8672 (mmp) cc_final: 0.8413 (mmp) REVERT: A 326 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6681 (tmm) REVERT: A 426 SER cc_start: 0.8703 (t) cc_final: 0.8398 (m) REVERT: A 443 ASP cc_start: 0.6079 (OUTLIER) cc_final: 0.5693 (t70) REVERT: A 444 HIS cc_start: 0.8256 (p-80) cc_final: 0.7908 (p90) REVERT: A 454 GLN cc_start: 0.7887 (pt0) cc_final: 0.7630 (mp10) REVERT: A 561 THR cc_start: 0.6861 (OUTLIER) cc_final: 0.6619 (p) REVERT: A 575 THR cc_start: 0.8077 (p) cc_final: 0.7792 (p) REVERT: B 174 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8555 (tt) REVERT: B 203 TRP cc_start: 0.6969 (t-100) cc_final: 0.6732 (t-100) REVERT: B 222 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8750 (tm-30) REVERT: C 62 ARG cc_start: 0.6636 (tpt-90) cc_final: 0.6088 (ptp-110) REVERT: C 174 TRP cc_start: 0.8117 (m-10) cc_final: 0.7554 (m-90) REVERT: C 206 LEU cc_start: 0.8303 (mp) cc_final: 0.8013 (tp) REVERT: C 207 ASN cc_start: 0.7250 (t0) cc_final: 0.5741 (t0) REVERT: C 214 LEU cc_start: 0.8046 (tp) cc_final: 0.7742 (tp) REVERT: C 218 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7669 (m-80) REVERT: C 231 THR cc_start: 0.6993 (p) cc_final: 0.6654 (p) REVERT: C 236 LEU cc_start: 0.7549 (mt) cc_final: 0.7101 (tp) REVERT: C 243 LEU cc_start: 0.5667 (OUTLIER) cc_final: 0.5240 (mt) REVERT: D 6 VAL cc_start: 0.4617 (t) cc_final: 0.3878 (t) REVERT: D 34 ILE cc_start: 0.8012 (mt) cc_final: 0.7725 (mt) REVERT: D 40 GLU cc_start: 0.8278 (mp0) cc_final: 0.7769 (mp0) REVERT: D 64 PHE cc_start: 0.7213 (t80) cc_final: 0.6986 (t80) REVERT: D 84 ARG cc_start: 0.7865 (mtt90) cc_final: 0.7618 (ttp-170) REVERT: D 94 PHE cc_start: 0.7342 (t80) cc_final: 0.6961 (t80) REVERT: D 95 THR cc_start: 0.7508 (m) cc_final: 0.6297 (t) outliers start: 130 outliers final: 49 residues processed: 525 average time/residue: 0.0977 time to fit residues: 73.6372 Evaluate side-chains 384 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 326 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN A 199 HIS A 237 GLN A 313 GLN ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN B 464 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN C 150 HIS C 171 HIS D 8 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.094234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.082861 restraints weight = 36973.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.084913 restraints weight = 22954.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.086287 restraints weight = 15917.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.087327 restraints weight = 12084.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.087978 restraints weight = 9697.498| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 10549 Z= 0.229 Angle : 0.954 12.697 14393 Z= 0.501 Chirality : 0.051 0.224 1672 Planarity : 0.007 0.068 1789 Dihedral : 7.175 43.249 1410 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 1.23 % Allowed : 9.01 % Favored : 89.76 % Rotamer: Outliers : 0.63 % Allowed : 4.86 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 1.69 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.24), residues: 1299 helix: 1.84 (0.19), residues: 752 sheet: -3.74 (0.37), residues: 102 loop : -3.90 (0.24), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 432 TYR 0.026 0.003 TYR B 466 PHE 0.057 0.003 PHE C 132 TRP 0.021 0.002 TRP B 247 HIS 0.008 0.002 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00511 (10544) covalent geometry : angle 0.95138 (14383) SS BOND : bond 0.00898 ( 5) SS BOND : angle 2.65855 ( 10) hydrogen bonds : bond 0.05389 ( 610) hydrogen bonds : angle 5.31070 ( 1797) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 433 time to evaluate : 0.414 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: A 58 HIS cc_start: 0.7011 (m90) cc_final: 0.6685 (m90) REVERT: A 175 ASP cc_start: 0.8015 (t0) cc_final: 0.7074 (p0) REVERT: A 182 LEU cc_start: 0.9111 (tp) cc_final: 0.8864 (tp) REVERT: A 330 PHE cc_start: 0.8622 (m-80) cc_final: 0.8060 (m-80) REVERT: A 333 GLU cc_start: 0.9000 (mp0) cc_final: 0.7954 (mp0) REVERT: A 335 PHE cc_start: 0.9260 (m-80) cc_final: 0.8861 (m-10) REVERT: A 411 VAL cc_start: 0.9269 (t) cc_final: 0.9041 (t) REVERT: A 474 GLU cc_start: 0.8137 (mp0) cc_final: 0.7928 (mp0) REVERT: A 555 ILE cc_start: 0.8764 (mp) cc_final: 0.8523 (mt) REVERT: A 566 VAL cc_start: 0.9551 (t) cc_final: 0.9319 (p) REVERT: A 574 LEU cc_start: 0.9038 (mp) cc_final: 0.8825 (mp) REVERT: A 662 LEU cc_start: 0.9082 (mt) cc_final: 0.8572 (mt) REVERT: B 203 TRP cc_start: 0.8578 (t-100) cc_final: 0.8298 (t-100) REVERT: B 222 GLN cc_start: 0.8551 (tm-30) cc_final: 0.7977 (tm-30) REVERT: B 223 GLN cc_start: 0.8946 (mt0) cc_final: 0.8044 (mp10) REVERT: B 233 MET cc_start: 0.8214 (ttm) cc_final: 0.8011 (ttm) REVERT: B 257 ASP cc_start: 0.8915 (m-30) cc_final: 0.8632 (m-30) REVERT: B 406 THR cc_start: 0.8786 (m) cc_final: 0.8497 (t) REVERT: B 416 ILE cc_start: 0.8517 (mm) cc_final: 0.7990 (mm) REVERT: B 423 LEU cc_start: 0.8655 (mt) cc_final: 0.8030 (pp) REVERT: B 466 TYR cc_start: 0.7453 (m-10) cc_final: 0.7097 (m-10) REVERT: C 87 ARG cc_start: 0.8545 (ttm-80) cc_final: 0.8001 (ttm110) REVERT: C 92 LYS cc_start: 0.8176 (mptt) cc_final: 0.7589 (mmtm) REVERT: C 117 MET cc_start: 0.7511 (mtm) cc_final: 0.7141 (mtm) REVERT: C 134 VAL cc_start: 0.8870 (p) cc_final: 0.8637 (p) REVERT: C 140 ASP cc_start: 0.8980 (m-30) cc_final: 0.8677 (m-30) REVERT: C 173 PHE cc_start: 0.7938 (m-10) cc_final: 0.7675 (m-80) REVERT: C 198 LEU cc_start: 0.8487 (tt) cc_final: 0.8221 (tp) REVERT: C 200 THR cc_start: 0.8765 (p) cc_final: 0.8504 (p) REVERT: C 206 LEU cc_start: 0.8479 (mp) cc_final: 0.7880 (tp) REVERT: C 214 LEU cc_start: 0.7803 (tp) cc_final: 0.7313 (tp) REVERT: D 36 TRP cc_start: 0.8710 (t60) cc_final: 0.8428 (t60) REVERT: D 40 GLU cc_start: 0.8231 (mp0) cc_final: 0.7801 (mp0) REVERT: D 64 PHE cc_start: 0.7861 (t80) cc_final: 0.7174 (t80) REVERT: D 92 LEU cc_start: 0.9115 (pp) cc_final: 0.8564 (pp) REVERT: D 95 THR cc_start: 0.8854 (m) cc_final: 0.8275 (t) outliers start: 7 outliers final: 0 residues processed: 436 average time/residue: 0.0909 time to fit residues: 58.3823 Evaluate side-chains 299 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 81 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN A 516 GLN A 573 ASN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 GLN ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN C 171 HIS ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.090618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.080564 restraints weight = 37484.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.082252 restraints weight = 24405.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.083491 restraints weight = 17605.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.084309 restraints weight = 13533.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.084924 restraints weight = 11044.847| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 10549 Z= 0.290 Angle : 0.928 13.358 14393 Z= 0.491 Chirality : 0.050 0.229 1672 Planarity : 0.007 0.084 1789 Dihedral : 6.897 38.739 1410 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 21.76 Ramachandran Plot: Outliers : 1.00 % Allowed : 10.32 % Favored : 88.68 % Rotamer: Outliers : 0.45 % Allowed : 4.95 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.23), residues: 1299 helix: 1.15 (0.18), residues: 749 sheet: -3.48 (0.38), residues: 105 loop : -3.59 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 429 TYR 0.041 0.003 TYR B 389 PHE 0.040 0.003 PHE A 218 TRP 0.030 0.002 TRP C 174 HIS 0.007 0.002 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00647 (10544) covalent geometry : angle 0.92605 (14383) SS BOND : bond 0.00648 ( 5) SS BOND : angle 2.40121 ( 10) hydrogen bonds : bond 0.05081 ( 610) hydrogen bonds : angle 5.33734 ( 1797) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 341 time to evaluate : 0.418 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 335 PHE cc_start: 0.9122 (m-80) cc_final: 0.8780 (m-10) REVERT: A 427 LEU cc_start: 0.8795 (tp) cc_final: 0.8435 (tp) REVERT: A 555 ILE cc_start: 0.8752 (mp) cc_final: 0.8522 (mt) REVERT: A 662 LEU cc_start: 0.9043 (mt) cc_final: 0.8490 (mt) REVERT: B 130 LEU cc_start: 0.8163 (mt) cc_final: 0.7905 (mt) REVERT: B 163 HIS cc_start: 0.6162 (m170) cc_final: 0.5440 (m-70) REVERT: B 204 ASN cc_start: 0.8430 (m-40) cc_final: 0.7898 (t0) REVERT: B 222 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7814 (tm-30) REVERT: B 223 GLN cc_start: 0.9017 (mt0) cc_final: 0.8528 (mt0) REVERT: B 233 MET cc_start: 0.7895 (ttm) cc_final: 0.7656 (ttm) REVERT: B 267 PRO cc_start: 0.6798 (OUTLIER) cc_final: 0.6460 (Cg_endo) REVERT: B 390 SER cc_start: 0.9297 (m) cc_final: 0.8887 (t) REVERT: B 419 CYS cc_start: 0.7969 (p) cc_final: 0.7613 (p) REVERT: B 423 LEU cc_start: 0.8484 (mt) cc_final: 0.7956 (pp) REVERT: C 72 LEU cc_start: 0.8925 (mt) cc_final: 0.8690 (mt) REVERT: C 87 ARG cc_start: 0.8477 (ttm-80) cc_final: 0.8165 (ttm-80) REVERT: C 173 PHE cc_start: 0.7938 (m-10) cc_final: 0.7657 (m-80) REVERT: C 198 LEU cc_start: 0.8210 (tt) cc_final: 0.7931 (tp) REVERT: C 206 LEU cc_start: 0.8232 (mp) cc_final: 0.7655 (tp) REVERT: D 4 GLU cc_start: 0.6817 (mp0) cc_final: 0.6504 (mp0) REVERT: D 36 TRP cc_start: 0.8488 (t60) cc_final: 0.8278 (t60) REVERT: D 92 LEU cc_start: 0.9118 (pp) cc_final: 0.8872 (pp) outliers start: 5 outliers final: 0 residues processed: 344 average time/residue: 0.0817 time to fit residues: 43.1048 Evaluate side-chains 266 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 26 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 305 GLN ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN C 171 HIS ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.092815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.080503 restraints weight = 37926.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.082805 restraints weight = 22222.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.084281 restraints weight = 14910.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.085525 restraints weight = 11139.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.086182 restraints weight = 8635.450| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 10549 Z= 0.213 Angle : 0.855 12.017 14393 Z= 0.447 Chirality : 0.048 0.245 1672 Planarity : 0.007 0.088 1789 Dihedral : 6.561 36.500 1410 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 1.00 % Allowed : 9.31 % Favored : 89.68 % Rotamer: Outliers : 0.45 % Allowed : 4.50 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.23), residues: 1299 helix: 1.09 (0.18), residues: 746 sheet: -3.30 (0.39), residues: 108 loop : -3.36 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 652 TYR 0.029 0.002 TYR D 56 PHE 0.040 0.003 PHE B 86 TRP 0.018 0.002 TRP A 653 HIS 0.012 0.002 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00479 (10544) covalent geometry : angle 0.85383 (14383) SS BOND : bond 0.00739 ( 5) SS BOND : angle 2.06276 ( 10) hydrogen bonds : bond 0.04642 ( 610) hydrogen bonds : angle 5.20081 ( 1797) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 344 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 CYS cc_start: 0.5052 (t) cc_final: 0.4582 (t) REVERT: A 282 LEU cc_start: 0.8100 (tt) cc_final: 0.7826 (tt) REVERT: A 290 ASN cc_start: 0.8075 (p0) cc_final: 0.7840 (p0) REVERT: A 335 PHE cc_start: 0.8947 (m-80) cc_final: 0.8590 (m-10) REVERT: A 427 LEU cc_start: 0.8614 (tp) cc_final: 0.8250 (tp) REVERT: A 462 ASN cc_start: 0.7487 (t0) cc_final: 0.7048 (t0) REVERT: A 645 TYR cc_start: 0.7414 (m-80) cc_final: 0.7208 (m-80) REVERT: A 662 LEU cc_start: 0.8799 (mt) cc_final: 0.8330 (mt) REVERT: B 163 HIS cc_start: 0.6125 (m170) cc_final: 0.5502 (m-70) REVERT: B 187 LYS cc_start: 0.8631 (mmtt) cc_final: 0.8290 (mtmt) REVERT: B 204 ASN cc_start: 0.8174 (m-40) cc_final: 0.7750 (t0) REVERT: B 213 ILE cc_start: 0.8933 (mm) cc_final: 0.8677 (mm) REVERT: B 223 GLN cc_start: 0.8835 (mt0) cc_final: 0.8402 (mt0) REVERT: B 257 ASP cc_start: 0.8081 (m-30) cc_final: 0.7875 (m-30) REVERT: B 390 SER cc_start: 0.9192 (m) cc_final: 0.8779 (t) REVERT: B 419 CYS cc_start: 0.7723 (p) cc_final: 0.7203 (p) REVERT: B 423 LEU cc_start: 0.8347 (mt) cc_final: 0.7900 (pp) REVERT: C 87 ARG cc_start: 0.8271 (ttm-80) cc_final: 0.7680 (ttm-80) REVERT: C 133 SER cc_start: 0.9153 (p) cc_final: 0.8867 (p) REVERT: C 169 LEU cc_start: 0.9112 (mt) cc_final: 0.8330 (mt) REVERT: C 173 PHE cc_start: 0.7841 (m-10) cc_final: 0.7630 (m-80) REVERT: C 206 LEU cc_start: 0.8109 (mp) cc_final: 0.7656 (tp) REVERT: C 218 TYR cc_start: 0.8099 (m-10) cc_final: 0.7804 (m-10) REVERT: D 78 PHE cc_start: 0.7725 (t80) cc_final: 0.7521 (t80) outliers start: 5 outliers final: 0 residues processed: 347 average time/residue: 0.0795 time to fit residues: 42.0809 Evaluate side-chains 265 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 129 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN C 171 HIS ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.092211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.080027 restraints weight = 37795.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.082316 restraints weight = 22204.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.083939 restraints weight = 14848.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.084899 restraints weight = 10819.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.085816 restraints weight = 8635.206| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10549 Z= 0.219 Angle : 0.847 13.824 14393 Z= 0.444 Chirality : 0.047 0.277 1672 Planarity : 0.006 0.071 1789 Dihedral : 6.414 34.797 1410 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.01 % Favored : 90.07 % Rotamer: Outliers : 0.09 % Allowed : 4.41 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.23), residues: 1299 helix: 0.95 (0.18), residues: 742 sheet: -2.64 (0.45), residues: 95 loop : -3.34 (0.25), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 432 TYR 0.037 0.002 TYR B 389 PHE 0.044 0.003 PHE B 86 TRP 0.043 0.002 TRP D 36 HIS 0.012 0.002 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00489 (10544) covalent geometry : angle 0.84518 (14383) SS BOND : bond 0.00618 ( 5) SS BOND : angle 2.08620 ( 10) hydrogen bonds : bond 0.04567 ( 610) hydrogen bonds : angle 5.19804 ( 1797) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 335 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.8258 (p) cc_final: 0.7851 (p) REVERT: A 195 CYS cc_start: 0.4735 (t) cc_final: 0.4306 (t) REVERT: A 215 MET cc_start: 0.6524 (tmm) cc_final: 0.5891 (ttt) REVERT: A 327 PHE cc_start: 0.7172 (m-80) cc_final: 0.6552 (m-10) REVERT: A 427 LEU cc_start: 0.8452 (tp) cc_final: 0.8053 (tp) REVERT: A 462 ASN cc_start: 0.7294 (t0) cc_final: 0.6940 (t0) REVERT: A 538 LEU cc_start: 0.8443 (mp) cc_final: 0.8227 (tp) REVERT: A 662 LEU cc_start: 0.8611 (mt) cc_final: 0.8216 (mt) REVERT: B 103 VAL cc_start: 0.8810 (t) cc_final: 0.7899 (t) REVERT: B 163 HIS cc_start: 0.5679 (m170) cc_final: 0.5337 (m-70) REVERT: B 204 ASN cc_start: 0.8115 (m-40) cc_final: 0.7638 (t0) REVERT: B 222 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7803 (tm-30) REVERT: B 223 GLN cc_start: 0.8488 (mt0) cc_final: 0.7699 (mt0) REVERT: B 236 VAL cc_start: 0.9433 (t) cc_final: 0.9224 (t) REVERT: B 390 SER cc_start: 0.8978 (m) cc_final: 0.8637 (m) REVERT: B 406 THR cc_start: 0.8434 (m) cc_final: 0.7987 (t) REVERT: B 416 ILE cc_start: 0.8618 (mm) cc_final: 0.8254 (mm) REVERT: B 466 TYR cc_start: 0.7579 (m-10) cc_final: 0.7368 (m-10) REVERT: C 72 LEU cc_start: 0.8750 (mt) cc_final: 0.8530 (mt) REVERT: C 87 ARG cc_start: 0.8050 (ttm-80) cc_final: 0.7476 (ttm-80) REVERT: C 114 ILE cc_start: 0.8092 (mm) cc_final: 0.7854 (mm) REVERT: C 133 SER cc_start: 0.9099 (p) cc_final: 0.8846 (p) REVERT: C 169 LEU cc_start: 0.9039 (mt) cc_final: 0.8148 (mt) REVERT: C 170 LEU cc_start: 0.8327 (tp) cc_final: 0.8126 (tp) REVERT: C 173 PHE cc_start: 0.7716 (m-10) cc_final: 0.7460 (m-80) REVERT: C 206 LEU cc_start: 0.7961 (mp) cc_final: 0.7456 (tp) REVERT: C 218 TYR cc_start: 0.7914 (m-10) cc_final: 0.7559 (m-10) REVERT: C 231 THR cc_start: 0.8927 (p) cc_final: 0.8708 (p) REVERT: D 4 GLU cc_start: 0.6743 (mp0) cc_final: 0.6507 (mp0) REVERT: D 26 LEU cc_start: 0.8419 (mp) cc_final: 0.8131 (mp) REVERT: D 28 PHE cc_start: 0.6546 (t80) cc_final: 0.5525 (t80) REVERT: D 64 PHE cc_start: 0.7410 (t80) cc_final: 0.6743 (t80) outliers start: 1 outliers final: 0 residues processed: 335 average time/residue: 0.0787 time to fit residues: 40.1911 Evaluate side-chains 260 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 9 optimal weight: 0.9990 chunk 87 optimal weight: 0.0070 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 28 optimal weight: 30.0000 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN A 573 ASN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 HIS C 171 HIS ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.092222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.079728 restraints weight = 38162.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.082058 restraints weight = 22234.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.083696 restraints weight = 14818.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.084666 restraints weight = 10849.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.085478 restraints weight = 8690.841| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10549 Z= 0.217 Angle : 0.838 12.478 14393 Z= 0.439 Chirality : 0.048 0.271 1672 Planarity : 0.006 0.073 1789 Dihedral : 6.320 32.660 1410 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.39 % Favored : 89.68 % Rotamer: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.23), residues: 1299 helix: 0.92 (0.18), residues: 748 sheet: -2.43 (0.49), residues: 88 loop : -3.27 (0.25), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 657 TYR 0.031 0.002 TYR B 189 PHE 0.040 0.003 PHE B 86 TRP 0.028 0.002 TRP D 36 HIS 0.011 0.002 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00485 (10544) covalent geometry : angle 0.83676 (14383) SS BOND : bond 0.00575 ( 5) SS BOND : angle 1.76565 ( 10) hydrogen bonds : bond 0.04572 ( 610) hydrogen bonds : angle 5.32610 ( 1797) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 323 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 THR cc_start: 0.8347 (p) cc_final: 0.8107 (p) REVERT: A 95 MET cc_start: 0.7861 (mmp) cc_final: 0.7311 (mmm) REVERT: A 195 CYS cc_start: 0.4792 (t) cc_final: 0.4439 (t) REVERT: A 305 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7568 (tm-30) REVERT: A 327 PHE cc_start: 0.7394 (m-80) cc_final: 0.6922 (m-10) REVERT: A 335 PHE cc_start: 0.8412 (m-80) cc_final: 0.8076 (m-10) REVERT: A 427 LEU cc_start: 0.8571 (tp) cc_final: 0.8192 (tp) REVERT: A 462 ASN cc_start: 0.7317 (t0) cc_final: 0.6935 (t0) REVERT: A 662 LEU cc_start: 0.8769 (mt) cc_final: 0.8346 (mt) REVERT: B 204 ASN cc_start: 0.7756 (m-40) cc_final: 0.7155 (t0) REVERT: B 222 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7703 (tm-30) REVERT: B 223 GLN cc_start: 0.8498 (mt0) cc_final: 0.7611 (mt0) REVERT: B 236 VAL cc_start: 0.9419 (t) cc_final: 0.9152 (t) REVERT: B 257 ASP cc_start: 0.8076 (m-30) cc_final: 0.7840 (m-30) REVERT: B 390 SER cc_start: 0.9021 (m) cc_final: 0.8593 (t) REVERT: B 406 THR cc_start: 0.8368 (m) cc_final: 0.8009 (t) REVERT: C 87 ARG cc_start: 0.8102 (ttm-80) cc_final: 0.7721 (ttm-80) REVERT: C 92 LYS cc_start: 0.8499 (mptt) cc_final: 0.8014 (mmtm) REVERT: C 133 SER cc_start: 0.9131 (p) cc_final: 0.8782 (p) REVERT: C 169 LEU cc_start: 0.9079 (mt) cc_final: 0.8206 (mt) REVERT: C 170 LEU cc_start: 0.8678 (tp) cc_final: 0.8434 (tp) REVERT: C 206 LEU cc_start: 0.8122 (mp) cc_final: 0.7664 (tp) REVERT: C 218 TYR cc_start: 0.7966 (m-10) cc_final: 0.7716 (m-10) REVERT: D 4 GLU cc_start: 0.6911 (mp0) cc_final: 0.5363 (tm-30) REVERT: D 26 LEU cc_start: 0.8416 (mp) cc_final: 0.8154 (mp) REVERT: D 78 PHE cc_start: 0.7649 (t80) cc_final: 0.7438 (t80) REVERT: D 94 PHE cc_start: 0.7874 (t80) cc_final: 0.7578 (t80) outliers start: 1 outliers final: 0 residues processed: 324 average time/residue: 0.0798 time to fit residues: 39.5889 Evaluate side-chains 250 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 97 optimal weight: 9.9990 chunk 61 optimal weight: 0.1980 chunk 106 optimal weight: 40.0000 chunk 59 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN C 171 HIS ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.094278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.083850 restraints weight = 36704.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.085631 restraints weight = 23466.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.086925 restraints weight = 16617.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.087870 restraints weight = 12675.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.088406 restraints weight = 10204.210| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.6746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 10549 Z= 0.185 Angle : 0.856 13.760 14393 Z= 0.442 Chirality : 0.049 0.574 1672 Planarity : 0.006 0.079 1789 Dihedral : 6.143 30.932 1410 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.85 % Allowed : 9.08 % Favored : 90.07 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.23), residues: 1299 helix: 0.85 (0.18), residues: 747 sheet: -2.17 (0.49), residues: 100 loop : -3.15 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 626 TYR 0.047 0.002 TYR B 389 PHE 0.040 0.002 PHE B 86 TRP 0.063 0.002 TRP C 227 HIS 0.013 0.002 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00411 (10544) covalent geometry : angle 0.85515 (14383) SS BOND : bond 0.00489 ( 5) SS BOND : angle 1.53400 ( 10) hydrogen bonds : bond 0.04494 ( 610) hydrogen bonds : angle 5.34327 ( 1797) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8097 (mmp) cc_final: 0.7355 (mmm) REVERT: A 305 GLN cc_start: 0.8662 (tm-30) cc_final: 0.7629 (tm-30) REVERT: A 310 GLU cc_start: 0.8151 (tp30) cc_final: 0.7903 (tp30) REVERT: A 333 GLU cc_start: 0.8679 (mp0) cc_final: 0.8136 (mp0) REVERT: A 335 PHE cc_start: 0.8669 (m-80) cc_final: 0.8379 (m-10) REVERT: A 347 MET cc_start: 0.7532 (mmm) cc_final: 0.6945 (tpp) REVERT: A 376 LEU cc_start: 0.9267 (tp) cc_final: 0.9027 (tp) REVERT: A 427 LEU cc_start: 0.8968 (tp) cc_final: 0.8671 (tp) REVERT: A 462 ASN cc_start: 0.7443 (t0) cc_final: 0.7044 (t0) REVERT: A 662 LEU cc_start: 0.9061 (mt) cc_final: 0.8592 (mt) REVERT: B 204 ASN cc_start: 0.7751 (m-40) cc_final: 0.7124 (t0) REVERT: B 222 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8450 (tm-30) REVERT: B 223 GLN cc_start: 0.9100 (mt0) cc_final: 0.8322 (mt0) REVERT: B 257 ASP cc_start: 0.8129 (m-30) cc_final: 0.7837 (m-30) REVERT: B 390 SER cc_start: 0.9226 (m) cc_final: 0.8895 (t) REVERT: B 397 SER cc_start: 0.9063 (p) cc_final: 0.8808 (p) REVERT: B 406 THR cc_start: 0.8846 (m) cc_final: 0.8394 (t) REVERT: B 466 TYR cc_start: 0.7667 (m-10) cc_final: 0.7275 (m-10) REVERT: C 81 LEU cc_start: 0.8608 (pp) cc_final: 0.8063 (mm) REVERT: C 87 ARG cc_start: 0.8641 (ttm-80) cc_final: 0.8227 (ttm-80) REVERT: C 133 SER cc_start: 0.9067 (p) cc_final: 0.8820 (p) REVERT: C 167 ILE cc_start: 0.9131 (mm) cc_final: 0.8921 (mm) REVERT: C 169 LEU cc_start: 0.9402 (mt) cc_final: 0.8620 (mt) REVERT: C 174 TRP cc_start: 0.7873 (m-10) cc_final: 0.7458 (m-10) REVERT: C 180 ASP cc_start: 0.7906 (t0) cc_final: 0.7419 (t0) REVERT: C 206 LEU cc_start: 0.8273 (mp) cc_final: 0.7792 (tp) REVERT: C 224 MET cc_start: 0.7865 (mmp) cc_final: 0.7404 (mmm) REVERT: C 231 THR cc_start: 0.8808 (p) cc_final: 0.8487 (p) REVERT: D 4 GLU cc_start: 0.6743 (mp0) cc_final: 0.5555 (tm-30) REVERT: D 26 LEU cc_start: 0.8611 (mp) cc_final: 0.8122 (mp) REVERT: D 74 TRP cc_start: 0.8499 (t-100) cc_final: 0.8201 (t-100) REVERT: D 94 PHE cc_start: 0.8085 (t80) cc_final: 0.7832 (t80) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.0830 time to fit residues: 41.4184 Evaluate side-chains 277 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 47 optimal weight: 0.0670 chunk 56 optimal weight: 0.0020 chunk 31 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.1730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN A 562 ASN A 573 ASN A 587 GLN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.095895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.083527 restraints weight = 36969.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.085896 restraints weight = 21702.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.087484 restraints weight = 14486.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.088730 restraints weight = 10653.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.089362 restraints weight = 8281.464| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.6969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10549 Z= 0.168 Angle : 0.822 12.966 14393 Z= 0.423 Chirality : 0.047 0.250 1672 Planarity : 0.006 0.083 1789 Dihedral : 6.023 29.345 1410 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 1.00 % Allowed : 8.93 % Favored : 90.07 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.23), residues: 1299 helix: 0.87 (0.18), residues: 751 sheet: -1.82 (0.48), residues: 106 loop : -3.11 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 108 TYR 0.016 0.002 TYR A 565 PHE 0.039 0.002 PHE B 86 TRP 0.039 0.002 TRP A 653 HIS 0.018 0.002 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00379 (10544) covalent geometry : angle 0.82059 (14383) SS BOND : bond 0.00472 ( 5) SS BOND : angle 2.23937 ( 10) hydrogen bonds : bond 0.04413 ( 610) hydrogen bonds : angle 5.25561 ( 1797) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 THR cc_start: 0.7901 (p) cc_final: 0.7625 (p) REVERT: A 95 MET cc_start: 0.8037 (mmp) cc_final: 0.7658 (mmm) REVERT: A 195 CYS cc_start: 0.4609 (t) cc_final: 0.4117 (t) REVERT: A 335 PHE cc_start: 0.8454 (m-80) cc_final: 0.8151 (m-10) REVERT: A 347 MET cc_start: 0.7181 (mmm) cc_final: 0.6951 (tpp) REVERT: A 376 LEU cc_start: 0.8908 (tp) cc_final: 0.8629 (tp) REVERT: A 427 LEU cc_start: 0.8527 (tp) cc_final: 0.8176 (tp) REVERT: A 645 TYR cc_start: 0.6902 (m-80) cc_final: 0.6652 (m-80) REVERT: A 662 LEU cc_start: 0.8655 (mt) cc_final: 0.8227 (mt) REVERT: B 138 ILE cc_start: 0.7346 (mt) cc_final: 0.6971 (tt) REVERT: B 204 ASN cc_start: 0.7552 (m-40) cc_final: 0.7080 (t0) REVERT: B 219 LEU cc_start: 0.8054 (mm) cc_final: 0.7764 (mm) REVERT: B 222 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7945 (tm-30) REVERT: B 223 GLN cc_start: 0.8375 (mt0) cc_final: 0.8012 (mp10) REVERT: B 236 VAL cc_start: 0.9384 (t) cc_final: 0.9107 (t) REVERT: B 257 ASP cc_start: 0.8029 (m-30) cc_final: 0.7823 (m-30) REVERT: B 387 ILE cc_start: 0.8808 (mt) cc_final: 0.8562 (mt) REVERT: B 390 SER cc_start: 0.9028 (m) cc_final: 0.8704 (t) REVERT: B 397 SER cc_start: 0.8993 (p) cc_final: 0.8778 (p) REVERT: B 464 GLN cc_start: 0.7707 (tp40) cc_final: 0.7474 (tp40) REVERT: B 466 TYR cc_start: 0.7480 (m-10) cc_final: 0.7264 (m-10) REVERT: C 81 LEU cc_start: 0.8372 (pp) cc_final: 0.7845 (mm) REVERT: C 87 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7754 (ttm-80) REVERT: C 133 SER cc_start: 0.8803 (p) cc_final: 0.8410 (p) REVERT: C 136 ASN cc_start: 0.7773 (p0) cc_final: 0.7570 (p0) REVERT: C 172 THR cc_start: 0.9424 (p) cc_final: 0.9160 (p) REVERT: C 206 LEU cc_start: 0.7864 (mp) cc_final: 0.7445 (tp) REVERT: C 224 MET cc_start: 0.7604 (mmp) cc_final: 0.7293 (mmm) REVERT: D 25 PHE cc_start: 0.6230 (m-80) cc_final: 0.5910 (m-80) REVERT: D 26 LEU cc_start: 0.8199 (mp) cc_final: 0.7912 (mp) REVERT: D 79 GLN cc_start: 0.7702 (tm-30) cc_final: 0.7402 (tm-30) REVERT: D 81 TYR cc_start: 0.6632 (m-10) cc_final: 0.6272 (m-10) REVERT: D 94 PHE cc_start: 0.7483 (t80) cc_final: 0.7249 (t80) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.0792 time to fit residues: 41.4627 Evaluate side-chains 271 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 103 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 128 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 207 ASN ** 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 = 0.3612 r_free = 0.3612 target = 0.097072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.086388 restraints weight = 36617.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.088241 restraints weight = 23570.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.089404 restraints weight = 16738.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.090421 restraints weight = 12997.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.091012 restraints weight = 10495.156| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.7281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10549 Z= 0.165 Angle : 0.831 13.032 14393 Z= 0.427 Chirality : 0.047 0.313 1672 Planarity : 0.006 0.083 1789 Dihedral : 5.881 29.436 1410 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 1.00 % Allowed : 9.16 % Favored : 89.84 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.23), residues: 1299 helix: 0.90 (0.19), residues: 751 sheet: -1.65 (0.49), residues: 105 loop : -3.11 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 108 TYR 0.054 0.002 TYR B 389 PHE 0.045 0.002 PHE D 78 TRP 0.035 0.002 TRP B 247 HIS 0.008 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00365 (10544) covalent geometry : angle 0.82871 (14383) SS BOND : bond 0.00446 ( 5) SS BOND : angle 2.34974 ( 10) hydrogen bonds : bond 0.04325 ( 610) hydrogen bonds : angle 5.26656 ( 1797) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8320 (mmp) cc_final: 0.7882 (mmm) REVERT: A 195 CYS cc_start: 0.5404 (t) cc_final: 0.5069 (t) REVERT: A 290 ASN cc_start: 0.7499 (p0) cc_final: 0.7254 (p0) REVERT: A 305 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7853 (tm-30) REVERT: A 327 PHE cc_start: 0.8019 (m-10) cc_final: 0.7554 (m-10) REVERT: A 335 PHE cc_start: 0.8677 (m-80) cc_final: 0.8314 (m-10) REVERT: A 347 MET cc_start: 0.7691 (mmm) cc_final: 0.6981 (tpp) REVERT: A 376 LEU cc_start: 0.9080 (tp) cc_final: 0.8776 (tp) REVERT: A 427 LEU cc_start: 0.8814 (tp) cc_final: 0.8439 (tp) REVERT: A 645 TYR cc_start: 0.7092 (m-80) cc_final: 0.6807 (m-80) REVERT: A 662 LEU cc_start: 0.8975 (mt) cc_final: 0.8544 (mt) REVERT: B 204 ASN cc_start: 0.7798 (m-40) cc_final: 0.7023 (t0) REVERT: B 222 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8557 (tm-30) REVERT: B 223 GLN cc_start: 0.8936 (mt0) cc_final: 0.8154 (mp10) REVERT: B 257 ASP cc_start: 0.8160 (m-30) cc_final: 0.7860 (m-30) REVERT: B 387 ILE cc_start: 0.9175 (mt) cc_final: 0.8751 (mt) REVERT: B 390 SER cc_start: 0.9298 (m) cc_final: 0.8990 (t) REVERT: B 397 SER cc_start: 0.9011 (p) cc_final: 0.8747 (p) REVERT: B 415 LEU cc_start: 0.9132 (mp) cc_final: 0.8794 (mp) REVERT: B 464 GLN cc_start: 0.8087 (tp40) cc_final: 0.7799 (tp40) REVERT: B 466 TYR cc_start: 0.7612 (m-10) cc_final: 0.7073 (m-10) REVERT: C 81 LEU cc_start: 0.8616 (pp) cc_final: 0.8057 (mm) REVERT: C 87 ARG cc_start: 0.8503 (ttm-80) cc_final: 0.8275 (ttm-80) REVERT: C 114 ILE cc_start: 0.7981 (mm) cc_final: 0.7777 (mm) REVERT: C 133 SER cc_start: 0.8799 (p) cc_final: 0.8500 (p) REVERT: C 136 ASN cc_start: 0.8061 (p0) cc_final: 0.7702 (m-40) REVERT: C 137 ILE cc_start: 0.8738 (tt) cc_final: 0.8343 (tt) REVERT: C 169 LEU cc_start: 0.9372 (mt) cc_final: 0.8975 (mt) REVERT: C 180 ASP cc_start: 0.8478 (t70) cc_final: 0.8058 (t70) REVERT: C 206 LEU cc_start: 0.8138 (mp) cc_final: 0.7712 (tp) REVERT: C 224 MET cc_start: 0.8191 (mmp) cc_final: 0.7747 (mmm) REVERT: D 25 PHE cc_start: 0.6777 (m-80) cc_final: 0.6469 (m-80) REVERT: D 26 LEU cc_start: 0.8451 (mp) cc_final: 0.7980 (mp) REVERT: D 79 GLN cc_start: 0.7703 (tm-30) cc_final: 0.7459 (tm-30) REVERT: D 81 TYR cc_start: 0.7483 (m-10) cc_final: 0.7082 (m-10) REVERT: D 94 PHE cc_start: 0.7771 (t80) cc_final: 0.7561 (t80) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.0754 time to fit residues: 40.2437 Evaluate side-chains 275 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 8 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 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 = 0.3568 r_free = 0.3568 target = 0.094555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.083932 restraints weight = 36617.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.085766 restraints weight = 23346.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.087004 restraints weight = 16378.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.087936 restraints weight = 12544.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.088566 restraints weight = 10089.672| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.7352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10549 Z= 0.207 Angle : 0.842 11.670 14393 Z= 0.434 Chirality : 0.048 0.282 1672 Planarity : 0.006 0.084 1789 Dihedral : 5.991 29.422 1410 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 1.00 % Allowed : 9.24 % Favored : 89.76 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.23), residues: 1299 helix: 0.79 (0.18), residues: 750 sheet: -1.71 (0.47), residues: 110 loop : -3.06 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 52 TYR 0.037 0.002 TYR D 56 PHE 0.038 0.003 PHE B 86 TRP 0.038 0.002 TRP B 247 HIS 0.020 0.002 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00471 (10544) covalent geometry : angle 0.84095 (14383) SS BOND : bond 0.00530 ( 5) SS BOND : angle 2.09674 ( 10) hydrogen bonds : bond 0.04559 ( 610) hydrogen bonds : angle 5.38483 ( 1797) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8477 (mmp) cc_final: 0.7925 (mmm) REVERT: A 305 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8253 (tm-30) REVERT: A 327 PHE cc_start: 0.8223 (m-10) cc_final: 0.7757 (m-10) REVERT: A 335 PHE cc_start: 0.8836 (m-80) cc_final: 0.8495 (m-10) REVERT: A 347 MET cc_start: 0.7898 (mmm) cc_final: 0.6993 (tpp) REVERT: A 376 LEU cc_start: 0.9199 (tp) cc_final: 0.8994 (tp) REVERT: A 427 LEU cc_start: 0.8949 (tp) cc_final: 0.8624 (tp) REVERT: A 662 LEU cc_start: 0.9119 (mt) cc_final: 0.8695 (mt) REVERT: B 93 MET cc_start: 0.8321 (mpp) cc_final: 0.8114 (mpp) REVERT: B 204 ASN cc_start: 0.7844 (m-40) cc_final: 0.7260 (t0) REVERT: B 222 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8644 (tm-30) REVERT: B 223 GLN cc_start: 0.9204 (mt0) cc_final: 0.8339 (mp10) REVERT: B 236 VAL cc_start: 0.9483 (t) cc_final: 0.9223 (t) REVERT: B 257 ASP cc_start: 0.8337 (m-30) cc_final: 0.7959 (m-30) REVERT: B 397 SER cc_start: 0.9148 (p) cc_final: 0.8832 (p) REVERT: B 406 THR cc_start: 0.8803 (m) cc_final: 0.8388 (t) REVERT: B 466 TYR cc_start: 0.7762 (m-10) cc_final: 0.7340 (m-10) REVERT: C 81 LEU cc_start: 0.8615 (pp) cc_final: 0.8040 (mm) REVERT: C 133 SER cc_start: 0.8915 (p) cc_final: 0.8672 (p) REVERT: C 136 ASN cc_start: 0.8205 (p0) cc_final: 0.7778 (m-40) REVERT: C 173 PHE cc_start: 0.7958 (m-80) cc_final: 0.7684 (m-80) REVERT: C 198 LEU cc_start: 0.7688 (tt) cc_final: 0.7467 (tp) REVERT: C 206 LEU cc_start: 0.8222 (mp) cc_final: 0.7768 (tp) REVERT: C 224 MET cc_start: 0.8161 (mmp) cc_final: 0.7636 (mmm) REVERT: D 25 PHE cc_start: 0.7328 (m-80) cc_final: 0.7012 (m-80) REVERT: D 26 LEU cc_start: 0.8688 (mp) cc_final: 0.8269 (mp) REVERT: D 81 TYR cc_start: 0.7648 (m-10) cc_final: 0.7218 (m-10) REVERT: D 94 PHE cc_start: 0.7978 (t80) cc_final: 0.7742 (t80) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.0780 time to fit residues: 38.1281 Evaluate side-chains 265 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 112 optimal weight: 8.9990 chunk 82 optimal weight: 0.2980 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 85 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 92 optimal weight: 0.3980 chunk 50 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 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 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN B 405 ASN B 464 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.095191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.084190 restraints weight = 37153.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.085981 restraints weight = 23815.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.087304 restraints weight = 16897.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.088088 restraints weight = 12971.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.088820 restraints weight = 10756.541| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.7455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10549 Z= 0.190 Angle : 0.829 11.794 14393 Z= 0.425 Chirality : 0.047 0.256 1672 Planarity : 0.006 0.088 1789 Dihedral : 5.982 31.039 1410 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.92 % Allowed : 8.78 % Favored : 90.30 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.23), residues: 1299 helix: 0.77 (0.18), residues: 750 sheet: -1.72 (0.46), residues: 109 loop : -3.01 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 108 TYR 0.038 0.002 TYR B 389 PHE 0.038 0.003 PHE B 86 TRP 0.042 0.002 TRP B 247 HIS 0.010 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00429 (10544) covalent geometry : angle 0.82719 (14383) SS BOND : bond 0.00529 ( 5) SS BOND : angle 2.06081 ( 10) hydrogen bonds : bond 0.04394 ( 610) hydrogen bonds : angle 5.38511 ( 1797) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1655.87 seconds wall clock time: 29 minutes 32.53 seconds (1772.53 seconds total)