Starting phenix.real_space_refine on Tue Feb 11 12:09:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y58_33612/02_2025/7y58_33612.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y58_33612/02_2025/7y58_33612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y58_33612/02_2025/7y58_33612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y58_33612/02_2025/7y58_33612.map" model { file = "/net/cci-nas-00/data/ceres_data/7y58_33612/02_2025/7y58_33612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y58_33612/02_2025/7y58_33612.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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 35 5.16 5 C 3639 2.51 5 N 913 2.21 5 O 1019 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5606 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3833 Classifications: {'peptide': 510} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 489} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 902 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 871 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 4.40, per 1000 atoms: 0.78 Number of scatterers: 5606 At special positions: 0 Unit cell: (72.297, 93.072, 116.34, 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 35 16.00 O 1019 8.00 N 913 7.00 C 3639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 106 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 106 " 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: 1.43 Conformation dependent library (CDL) restraints added in 735.5 milliseconds 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1360 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 5 sheets defined 59.2% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 16 through 32 removed outlier: 3.905A pdb=" N ALA A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 27 " --> pdb=" O VAL A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 41 Processing helix chain 'A' and resid 41 through 49 Processing helix chain 'A' and resid 53 through 70 removed outlier: 3.673A pdb=" N LEU A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 60 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TYR A 63 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.609A pdb=" N SER A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 101 removed outlier: 3.712A pdb=" N ILE A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 123 removed outlier: 4.054A pdb=" N ILE A 111 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 136 removed outlier: 3.524A pdb=" N SER A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 170 removed outlier: 3.747A pdb=" N THR A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ALA A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Proline residue: A 161 - end of helix removed outlier: 3.817A pdb=" N GLN A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.641A pdb=" N LEU A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 192 removed outlier: 4.026A pdb=" N PHE A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 186 " --> pdb=" O PRO A 182 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 234 Processing helix chain 'A' and resid 238 through 261 removed outlier: 4.020A pdb=" N SER A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 272 Processing helix chain 'A' and resid 273 through 304 removed outlier: 3.583A pdb=" N GLY A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA A 289 " --> pdb=" O MET A 285 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N MET A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 315 Processing helix chain 'A' and resid 316 through 338 removed outlier: 3.990A pdb=" N ALA A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Proline residue: A 328 - end of helix Proline residue: A 331 - end of helix removed outlier: 3.584A pdb=" N ARG A 336 " --> pdb=" O GLY A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 360 removed outlier: 3.566A pdb=" N VAL A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Proline residue: A 344 - end of helix removed outlier: 3.672A pdb=" N ILE A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR A 358 " --> pdb=" O MET A 354 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 391 removed outlier: 4.283A pdb=" N LEU A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ALA A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 434 removed outlier: 4.158A pdb=" N ALA A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 439 removed outlier: 3.873A pdb=" N SER A 439 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 454 Processing helix chain 'A' and resid 454 through 466 Processing helix chain 'A' and resid 468 through 504 removed outlier: 3.684A pdb=" N ASN A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 8 removed outlier: 3.886A pdb=" N GLN B 6 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR B 78 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 73 " --> pdb=" O THR B 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 48 removed outlier: 3.607A pdb=" N TYR B 114 " --> pdb=" O GLY B 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 52 Processing sheet with id=AA4, first strand: chain 'C' and resid 22 through 24 removed outlier: 3.814A pdb=" N CYS C 23 " --> pdb=" O VAL C 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 59 through 62 removed outlier: 4.016A pdb=" N ALA C 50 " --> pdb=" O TRP C 37 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N CYS C 34 " --> pdb=" O ASP C 101 " (cutoff:3.500A) 325 hydrogen bonds defined for protein. 957 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: 1.74 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 885 1.29 - 1.42: 1477 1.42 - 1.55: 3296 1.55 - 1.68: 0 1.68 - 1.82: 62 Bond restraints: 5720 Sorted by residual: bond pdb=" CA ILE A 151 " pdb=" C ILE A 151 " ideal model delta sigma weight residual 1.524 1.435 0.089 1.22e-02 6.72e+03 5.26e+01 bond pdb=" C ILE A 151 " pdb=" O ILE A 151 " ideal model delta sigma weight residual 1.237 1.160 0.077 1.13e-02 7.83e+03 4.62e+01 bond pdb=" CA ILE A 151 " pdb=" CB ILE A 151 " ideal model delta sigma weight residual 1.540 1.471 0.068 1.17e-02 7.31e+03 3.39e+01 bond pdb=" CA ILE A 155 " pdb=" C ILE A 155 " ideal model delta sigma weight residual 1.521 1.444 0.077 1.45e-02 4.76e+03 2.78e+01 bond pdb=" CA ILE A 155 " pdb=" CB ILE A 155 " ideal model delta sigma weight residual 1.545 1.476 0.069 1.45e-02 4.76e+03 2.23e+01 ... (remaining 5715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.04: 7694 4.04 - 8.07: 55 8.07 - 12.11: 6 12.11 - 16.15: 0 16.15 - 20.18: 1 Bond angle restraints: 7756 Sorted by residual: angle pdb=" C ARG C 32 " pdb=" CA ARG C 32 " pdb=" CB ARG C 32 " ideal model delta sigma weight residual 110.42 130.60 -20.18 1.99e+00 2.53e-01 1.03e+02 angle pdb=" N ILE A 155 " pdb=" CA ILE A 155 " pdb=" C ILE A 155 " ideal model delta sigma weight residual 112.76 103.59 9.17 1.27e+00 6.20e-01 5.21e+01 angle pdb=" C LEU C 19 " pdb=" N ARG C 20 " pdb=" CA ARG C 20 " ideal model delta sigma weight residual 121.87 110.57 11.30 1.64e+00 3.72e-01 4.75e+01 angle pdb=" N ILE A 151 " pdb=" CA ILE A 151 " pdb=" C ILE A 151 " ideal model delta sigma weight residual 110.42 104.18 6.24 9.60e-01 1.09e+00 4.23e+01 angle pdb=" C GLN C 40 " pdb=" CA GLN C 40 " pdb=" CB GLN C 40 " ideal model delta sigma weight residual 109.68 98.56 11.12 1.98e+00 2.55e-01 3.15e+01 ... (remaining 7751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 2907 17.94 - 35.88: 342 35.88 - 53.82: 104 53.82 - 71.76: 19 71.76 - 89.70: 9 Dihedral angle restraints: 3381 sinusoidal: 1259 harmonic: 2122 Sorted by residual: dihedral pdb=" CD ARG C 32 " pdb=" NE ARG C 32 " pdb=" CZ ARG C 32 " pdb=" NH1 ARG C 32 " ideal model delta sinusoidal sigma weight residual 0.00 71.16 -71.16 1 1.00e+01 1.00e-02 6.50e+01 dihedral pdb=" C ARG C 32 " pdb=" N ARG C 32 " pdb=" CA ARG C 32 " pdb=" CB ARG C 32 " ideal model delta harmonic sigma weight residual -122.60 -139.39 16.79 0 2.50e+00 1.60e-01 4.51e+01 dihedral pdb=" CB CYS C 34 " pdb=" SG CYS C 34 " pdb=" SG CYS C 106 " pdb=" CB CYS C 106 " ideal model delta sinusoidal sigma weight residual 93.00 148.32 -55.32 1 1.00e+01 1.00e-02 4.14e+01 ... (remaining 3378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 873 0.098 - 0.197: 31 0.197 - 0.295: 2 0.295 - 0.393: 3 0.393 - 0.491: 1 Chirality restraints: 910 Sorted by residual: chirality pdb=" CA ARG C 32 " pdb=" N ARG C 32 " pdb=" C ARG C 32 " pdb=" CB ARG C 32 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" CA GLU B 89 " pdb=" N GLU B 89 " pdb=" C GLU B 89 " pdb=" CB GLU B 89 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA ILE C 41 " pdb=" N ILE C 41 " pdb=" C ILE C 41 " pdb=" CB ILE C 41 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 907 not shown) Planarity restraints: 959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 32 " 1.028 9.50e-02 1.11e+02 4.61e-01 1.28e+02 pdb=" NE ARG C 32 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG C 32 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG C 32 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 32 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 46 " -0.672 9.50e-02 1.11e+02 3.01e-01 5.52e+01 pdb=" NE ARG C 46 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG C 46 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 46 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 46 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 39 " -0.017 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C ARG C 39 " 0.057 2.00e-02 2.50e+03 pdb=" O ARG C 39 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN C 40 " -0.019 2.00e-02 2.50e+03 ... (remaining 956 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 74 2.63 - 3.20: 5413 3.20 - 3.77: 8635 3.77 - 4.33: 10937 4.33 - 4.90: 18186 Nonbonded interactions: 43245 Sorted by model distance: nonbonded pdb=" O ARG C 32 " pdb=" CE1 TYR C 53 " model vdw 2.068 3.340 nonbonded pdb=" O TYR A 315 " pdb=" OH TYR A 366 " model vdw 2.197 3.040 nonbonded pdb=" OE2 GLU A 473 " pdb=" N GLY B 55 " model vdw 2.246 3.120 nonbonded pdb=" OD1 ASP B 111 " pdb=" N PHE B 112 " model vdw 2.251 3.120 nonbonded pdb=" NE ARG C 69 " pdb=" OG SER C 87 " model vdw 2.279 3.120 ... (remaining 43240 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.770 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 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 : 0.005 0.089 5720 Z= 0.316 Angle : 0.884 20.185 7756 Z= 0.498 Chirality : 0.050 0.491 910 Planarity : 0.018 0.461 959 Dihedral : 18.111 89.698 2009 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 3.38 % Allowed : 24.87 % Favored : 71.74 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.32), residues: 731 helix: 0.64 (0.27), residues: 399 sheet: -2.12 (0.55), residues: 83 loop : -3.19 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 300 HIS 0.002 0.001 HIS A 174 PHE 0.013 0.001 PHE A 288 TYR 0.018 0.002 TYR A 410 ARG 0.004 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.616 Fit side-chains REVERT: A 233 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7638 (tp30) REVERT: A 380 MET cc_start: 0.7942 (tpp) cc_final: 0.7530 (tpp) REVERT: A 393 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7959 (mt-10) REVERT: A 409 MET cc_start: 0.7100 (mmp) cc_final: 0.6704 (mmm) REVERT: C 73 SER cc_start: 0.8697 (t) cc_final: 0.8468 (p) REVERT: C 95 MET cc_start: 0.7206 (tpt) cc_final: 0.6510 (ttp) REVERT: C 97 TYR cc_start: 0.7300 (m-80) cc_final: 0.6798 (m-80) outliers start: 20 outliers final: 7 residues processed: 165 average time/residue: 0.1639 time to fit residues: 35.5885 Evaluate side-chains 123 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 60 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN ** A 401 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 = 0.3893 r_free = 0.3893 target = 0.166766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.132802 restraints weight = 7509.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.137223 restraints weight = 4065.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.140220 restraints weight = 2709.167| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5720 Z= 0.251 Angle : 0.695 6.970 7756 Z= 0.354 Chirality : 0.041 0.134 910 Planarity : 0.005 0.065 959 Dihedral : 6.583 56.821 801 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 5.41 % Allowed : 23.01 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.32), residues: 731 helix: 1.06 (0.26), residues: 414 sheet: -1.59 (0.58), residues: 87 loop : -2.96 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 81 HIS 0.004 0.001 HIS A 449 PHE 0.014 0.001 PHE A 94 TYR 0.024 0.002 TYR B 95 ARG 0.004 0.001 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.590 Fit side-chains REVERT: A 99 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6865 (tt) REVERT: A 183 PHE cc_start: 0.6677 (OUTLIER) cc_final: 0.5821 (t80) REVERT: A 233 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7613 (tp30) REVERT: A 288 PHE cc_start: 0.7367 (OUTLIER) cc_final: 0.6924 (t80) REVERT: A 409 MET cc_start: 0.7902 (mmp) cc_final: 0.7392 (mmm) REVERT: A 430 ARG cc_start: 0.8399 (ttp-110) cc_final: 0.8076 (ttm-80) REVERT: C 73 SER cc_start: 0.8531 (t) cc_final: 0.8238 (p) REVERT: C 95 MET cc_start: 0.7562 (tpt) cc_final: 0.6718 (ttp) REVERT: C 97 TYR cc_start: 0.7353 (m-80) cc_final: 0.6841 (m-80) outliers start: 32 outliers final: 14 residues processed: 137 average time/residue: 0.1394 time to fit residues: 26.2827 Evaluate side-chains 133 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 60 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 67 optimal weight: 0.0770 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 50 optimal weight: 0.0050 chunk 11 optimal weight: 0.9990 overall best weight: 0.5152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.171080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.135979 restraints weight = 7796.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.140531 restraints weight = 4330.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.143584 restraints weight = 2945.022| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5720 Z= 0.192 Angle : 0.632 6.691 7756 Z= 0.319 Chirality : 0.040 0.140 910 Planarity : 0.005 0.050 959 Dihedral : 5.909 52.617 796 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.21 % Favored : 91.66 % Rotamer: Outliers : 4.40 % Allowed : 25.38 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.32), residues: 731 helix: 1.23 (0.26), residues: 406 sheet: -1.61 (0.57), residues: 87 loop : -2.89 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 81 HIS 0.003 0.001 HIS A 174 PHE 0.013 0.001 PHE A 94 TYR 0.021 0.002 TYR B 95 ARG 0.002 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.662 Fit side-chains REVERT: A 81 TRP cc_start: 0.7616 (t-100) cc_final: 0.7379 (t60) REVERT: A 183 PHE cc_start: 0.6549 (OUTLIER) cc_final: 0.5983 (t80) REVERT: A 233 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7642 (tp30) REVERT: A 288 PHE cc_start: 0.7279 (OUTLIER) cc_final: 0.6795 (t80) REVERT: A 380 MET cc_start: 0.7703 (tpp) cc_final: 0.7497 (tpp) REVERT: A 409 MET cc_start: 0.7933 (mmp) cc_final: 0.7374 (mmm) REVERT: A 434 ASP cc_start: 0.8081 (t0) cc_final: 0.7798 (t0) REVERT: B 30 TYR cc_start: 0.8944 (m-80) cc_final: 0.8697 (m-80) REVERT: C 73 SER cc_start: 0.8407 (t) cc_final: 0.8112 (p) REVERT: C 95 MET cc_start: 0.7637 (tpt) cc_final: 0.6676 (ttt) REVERT: C 97 TYR cc_start: 0.7352 (m-80) cc_final: 0.6463 (m-80) outliers start: 26 outliers final: 14 residues processed: 131 average time/residue: 0.1396 time to fit residues: 24.8882 Evaluate side-chains 123 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 60 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 71 optimal weight: 3.9990 chunk 53 optimal weight: 0.1980 chunk 55 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 0.0270 chunk 48 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.168479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.134431 restraints weight = 7690.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.138920 restraints weight = 4151.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.141993 restraints weight = 2753.699| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5720 Z= 0.190 Angle : 0.621 6.714 7756 Z= 0.313 Chirality : 0.040 0.162 910 Planarity : 0.005 0.054 959 Dihedral : 5.725 53.301 796 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.11 % Favored : 92.75 % Rotamer: Outliers : 5.25 % Allowed : 25.72 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.33), residues: 731 helix: 1.35 (0.26), residues: 407 sheet: -1.43 (0.58), residues: 85 loop : -2.62 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 81 HIS 0.003 0.001 HIS A 174 PHE 0.011 0.001 PHE A 288 TYR 0.018 0.002 TYR B 95 ARG 0.003 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.612 Fit side-chains REVERT: A 40 MET cc_start: 0.7305 (ttm) cc_final: 0.7080 (ttm) REVERT: A 81 TRP cc_start: 0.7652 (t-100) cc_final: 0.7284 (t60) REVERT: A 183 PHE cc_start: 0.6666 (OUTLIER) cc_final: 0.5958 (t80) REVERT: A 233 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7677 (tp30) REVERT: A 288 PHE cc_start: 0.7159 (OUTLIER) cc_final: 0.6749 (t80) REVERT: A 358 TYR cc_start: 0.8509 (t80) cc_final: 0.8277 (t80) REVERT: A 434 ASP cc_start: 0.7965 (t0) cc_final: 0.7694 (t0) REVERT: C 73 SER cc_start: 0.8459 (t) cc_final: 0.8163 (p) REVERT: C 95 MET cc_start: 0.7418 (tpt) cc_final: 0.6491 (ttt) REVERT: C 97 TYR cc_start: 0.7460 (m-80) cc_final: 0.6550 (m-80) outliers start: 31 outliers final: 20 residues processed: 137 average time/residue: 0.1548 time to fit residues: 28.9580 Evaluate side-chains 136 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 60 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 15 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.167526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.132658 restraints weight = 7723.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.137137 restraints weight = 4264.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.140173 restraints weight = 2877.569| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5720 Z= 0.221 Angle : 0.645 6.650 7756 Z= 0.324 Chirality : 0.040 0.216 910 Planarity : 0.005 0.052 959 Dihedral : 5.725 53.610 796 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.34 % Favored : 91.52 % Rotamer: Outliers : 5.92 % Allowed : 25.21 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.33), residues: 731 helix: 1.37 (0.26), residues: 406 sheet: -1.42 (0.58), residues: 85 loop : -2.51 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 173 HIS 0.002 0.001 HIS A 449 PHE 0.018 0.001 PHE A 284 TYR 0.017 0.002 TYR B 95 ARG 0.003 0.001 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.629 Fit side-chains REVERT: A 15 LYS cc_start: 0.7780 (mptt) cc_final: 0.7264 (mtmm) REVERT: A 19 THR cc_start: 0.8490 (p) cc_final: 0.7885 (t) REVERT: A 40 MET cc_start: 0.7283 (ttm) cc_final: 0.7012 (ttm) REVERT: A 81 TRP cc_start: 0.7709 (t-100) cc_final: 0.7219 (t60) REVERT: A 183 PHE cc_start: 0.6743 (OUTLIER) cc_final: 0.5995 (t80) REVERT: A 233 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7692 (tp30) REVERT: A 288 PHE cc_start: 0.7124 (OUTLIER) cc_final: 0.6741 (t80) REVERT: A 359 PHE cc_start: 0.7672 (m-10) cc_final: 0.7251 (m-10) REVERT: A 434 ASP cc_start: 0.7966 (t0) cc_final: 0.7707 (t0) REVERT: C 73 SER cc_start: 0.8431 (t) cc_final: 0.8141 (p) REVERT: C 95 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6451 (ttp) REVERT: C 97 TYR cc_start: 0.7506 (m-80) cc_final: 0.6933 (m-80) outliers start: 35 outliers final: 22 residues processed: 137 average time/residue: 0.1488 time to fit residues: 27.6086 Evaluate side-chains 138 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 95 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.169756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.133246 restraints weight = 7913.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.137691 restraints weight = 4484.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.140696 restraints weight = 3079.166| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5720 Z= 0.237 Angle : 0.673 9.265 7756 Z= 0.334 Chirality : 0.041 0.242 910 Planarity : 0.005 0.053 959 Dihedral : 5.731 54.196 796 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.80 % Favored : 92.07 % Rotamer: Outliers : 5.08 % Allowed : 26.23 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.33), residues: 731 helix: 1.28 (0.26), residues: 404 sheet: -1.42 (0.58), residues: 85 loop : -2.50 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 81 HIS 0.002 0.001 HIS A 174 PHE 0.018 0.001 PHE A 284 TYR 0.015 0.002 TYR B 95 ARG 0.004 0.001 ARG C 109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.567 Fit side-chains REVERT: A 15 LYS cc_start: 0.7778 (mptt) cc_final: 0.7262 (mtmm) REVERT: A 19 THR cc_start: 0.8467 (p) cc_final: 0.7866 (t) REVERT: A 81 TRP cc_start: 0.7751 (t-100) cc_final: 0.7306 (t60) REVERT: A 183 PHE cc_start: 0.6836 (OUTLIER) cc_final: 0.6019 (t80) REVERT: A 233 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7710 (tp30) REVERT: A 288 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6676 (t80) REVERT: A 409 MET cc_start: 0.7823 (mmp) cc_final: 0.7295 (mmm) REVERT: A 434 ASP cc_start: 0.7904 (t0) cc_final: 0.7682 (t0) REVERT: C 23 CYS cc_start: 0.6320 (m) cc_final: 0.6056 (m) REVERT: C 73 SER cc_start: 0.8445 (t) cc_final: 0.8168 (p) REVERT: C 95 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.6407 (ttp) REVERT: C 97 TYR cc_start: 0.7561 (m-80) cc_final: 0.7007 (m-80) outliers start: 30 outliers final: 25 residues processed: 130 average time/residue: 0.1758 time to fit residues: 30.9246 Evaluate side-chains 139 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 95 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.163765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.129718 restraints weight = 7607.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.133985 restraints weight = 4202.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.136843 restraints weight = 2826.866| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5720 Z= 0.276 Angle : 0.680 7.027 7756 Z= 0.342 Chirality : 0.042 0.235 910 Planarity : 0.005 0.052 959 Dihedral : 5.850 53.910 796 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.76 % Favored : 90.97 % Rotamer: Outliers : 5.75 % Allowed : 27.41 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.32), residues: 731 helix: 1.20 (0.26), residues: 406 sheet: -1.47 (0.57), residues: 86 loop : -2.61 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 81 HIS 0.002 0.001 HIS A 449 PHE 0.017 0.002 PHE A 288 TYR 0.015 0.002 TYR A 410 ARG 0.004 0.001 ARG C 109 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 0.631 Fit side-chains REVERT: A 15 LYS cc_start: 0.7772 (mptt) cc_final: 0.7252 (mtmm) REVERT: A 81 TRP cc_start: 0.7810 (t-100) cc_final: 0.7355 (t60) REVERT: A 183 PHE cc_start: 0.6895 (OUTLIER) cc_final: 0.6101 (t80) REVERT: A 233 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7733 (tp30) REVERT: A 285 MET cc_start: 0.7806 (mmp) cc_final: 0.7539 (mmp) REVERT: A 288 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.6832 (t80) REVERT: A 302 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8193 (mt0) REVERT: A 321 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8116 (mm) REVERT: A 409 MET cc_start: 0.7809 (mmp) cc_final: 0.7334 (mmm) REVERT: A 434 ASP cc_start: 0.7905 (t0) cc_final: 0.7677 (t0) REVERT: C 23 CYS cc_start: 0.6440 (m) cc_final: 0.6204 (m) REVERT: C 73 SER cc_start: 0.8457 (t) cc_final: 0.8252 (p) REVERT: C 95 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6309 (ttp) REVERT: C 97 TYR cc_start: 0.7623 (m-80) cc_final: 0.7123 (m-80) outliers start: 34 outliers final: 25 residues processed: 134 average time/residue: 0.1517 time to fit residues: 27.4409 Evaluate side-chains 138 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 302 GLN Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 95 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.161868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.127704 restraints weight = 7601.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.131925 restraints weight = 4173.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.134810 restraints weight = 2800.771| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5720 Z= 0.264 Angle : 0.669 7.251 7756 Z= 0.336 Chirality : 0.041 0.171 910 Planarity : 0.005 0.053 959 Dihedral : 5.840 53.804 796 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.21 % Favored : 91.52 % Rotamer: Outliers : 5.75 % Allowed : 28.43 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.32), residues: 731 helix: 1.26 (0.26), residues: 400 sheet: -1.41 (0.59), residues: 80 loop : -2.55 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 81 HIS 0.002 0.001 HIS A 174 PHE 0.013 0.001 PHE A 284 TYR 0.015 0.002 TYR A 410 ARG 0.003 0.000 ARG C 109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.645 Fit side-chains REVERT: A 15 LYS cc_start: 0.7779 (mptt) cc_final: 0.7254 (mtmm) REVERT: A 81 TRP cc_start: 0.7802 (t-100) cc_final: 0.7381 (t60) REVERT: A 183 PHE cc_start: 0.6908 (OUTLIER) cc_final: 0.6117 (t80) REVERT: A 233 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7686 (tp30) REVERT: A 288 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.6925 (t80) REVERT: A 321 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8102 (mm) REVERT: A 409 MET cc_start: 0.7819 (mmp) cc_final: 0.7363 (mmm) REVERT: C 23 CYS cc_start: 0.6462 (m) cc_final: 0.6160 (m) REVERT: C 73 SER cc_start: 0.8503 (t) cc_final: 0.8297 (p) REVERT: C 95 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6298 (ttp) REVERT: C 97 TYR cc_start: 0.7629 (m-80) cc_final: 0.7092 (m-80) outliers start: 34 outliers final: 25 residues processed: 134 average time/residue: 0.1521 time to fit residues: 27.7272 Evaluate side-chains 139 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 95 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 44 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 0.0570 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 46 optimal weight: 0.6980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.166759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.132894 restraints weight = 7580.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.137253 restraints weight = 4130.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.140214 restraints weight = 2754.976| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5720 Z= 0.196 Angle : 0.670 9.658 7756 Z= 0.331 Chirality : 0.040 0.237 910 Planarity : 0.005 0.051 959 Dihedral : 5.751 52.826 796 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.80 % Favored : 91.93 % Rotamer: Outliers : 4.23 % Allowed : 30.29 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.33), residues: 731 helix: 1.37 (0.26), residues: 401 sheet: -1.42 (0.57), residues: 85 loop : -2.43 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 81 HIS 0.002 0.001 HIS A 174 PHE 0.011 0.001 PHE A 284 TYR 0.014 0.001 TYR B 95 ARG 0.004 0.000 ARG C 109 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.638 Fit side-chains REVERT: A 15 LYS cc_start: 0.7781 (mptt) cc_final: 0.7249 (mtmm) REVERT: A 81 TRP cc_start: 0.7765 (t-100) cc_final: 0.7350 (t60) REVERT: A 183 PHE cc_start: 0.6796 (OUTLIER) cc_final: 0.6042 (t80) REVERT: A 233 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7579 (tm-30) REVERT: A 288 PHE cc_start: 0.7088 (OUTLIER) cc_final: 0.6631 (t80) REVERT: A 321 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8120 (mm) REVERT: A 409 MET cc_start: 0.7721 (mmp) cc_final: 0.7252 (mmm) REVERT: C 95 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6273 (ttp) REVERT: C 97 TYR cc_start: 0.7640 (m-80) cc_final: 0.7053 (m-80) outliers start: 25 outliers final: 19 residues processed: 126 average time/residue: 0.2019 time to fit residues: 33.7996 Evaluate side-chains 133 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 95 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 52 optimal weight: 0.0070 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 54 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 19 optimal weight: 0.0470 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.170363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.136542 restraints weight = 7648.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.141061 restraints weight = 4126.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.144096 restraints weight = 2725.580| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5720 Z= 0.162 Angle : 0.640 8.134 7756 Z= 0.317 Chirality : 0.040 0.209 910 Planarity : 0.005 0.052 959 Dihedral : 5.550 54.918 794 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.39 % Favored : 92.34 % Rotamer: Outliers : 3.55 % Allowed : 30.80 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.33), residues: 731 helix: 1.50 (0.26), residues: 406 sheet: -1.41 (0.58), residues: 85 loop : -2.36 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 59 HIS 0.002 0.001 HIS A 174 PHE 0.009 0.001 PHE A 288 TYR 0.013 0.001 TYR B 95 ARG 0.004 0.000 ARG C 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.686 Fit side-chains REVERT: A 15 LYS cc_start: 0.7783 (mptt) cc_final: 0.7216 (mtmm) REVERT: A 81 TRP cc_start: 0.7732 (t-100) cc_final: 0.7310 (t60) REVERT: A 183 PHE cc_start: 0.6623 (OUTLIER) cc_final: 0.5795 (t80) REVERT: A 233 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7603 (tm-30) REVERT: A 288 PHE cc_start: 0.6997 (OUTLIER) cc_final: 0.6549 (t80) REVERT: A 321 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8078 (mm) REVERT: A 409 MET cc_start: 0.7816 (mmp) cc_final: 0.7306 (mmm) REVERT: B 73 ASP cc_start: 0.8048 (p0) cc_final: 0.7742 (p0) REVERT: C 95 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6378 (ttp) REVERT: C 97 TYR cc_start: 0.7568 (m-80) cc_final: 0.7090 (m-80) outliers start: 21 outliers final: 16 residues processed: 129 average time/residue: 0.1609 time to fit residues: 27.7929 Evaluate side-chains 135 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 95 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 0 optimal weight: 8.9990 chunk 33 optimal weight: 0.0470 chunk 15 optimal weight: 0.3980 chunk 10 optimal weight: 0.3980 chunk 68 optimal weight: 6.9990 chunk 19 optimal weight: 0.0980 chunk 37 optimal weight: 0.0670 chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 overall best weight: 0.1816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.176229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.140716 restraints weight = 7747.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.145351 restraints weight = 4299.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.148418 restraints weight = 2899.831| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5720 Z= 0.153 Angle : 0.647 8.699 7756 Z= 0.315 Chirality : 0.040 0.197 910 Planarity : 0.005 0.052 959 Dihedral : 5.542 59.929 794 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.80 % Favored : 91.93 % Rotamer: Outliers : 3.05 % Allowed : 30.96 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.33), residues: 731 helix: 1.61 (0.26), residues: 400 sheet: -1.31 (0.59), residues: 85 loop : -2.42 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 173 HIS 0.005 0.001 HIS A 174 PHE 0.011 0.001 PHE A 284 TYR 0.022 0.001 TYR A 358 ARG 0.004 0.000 ARG C 109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2027.25 seconds wall clock time: 37 minutes 10.27 seconds (2230.27 seconds total)