Starting phenix.real_space_refine on Thu Mar 6 08:57:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y58_33612/03_2025/7y58_33612.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y58_33612/03_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_33612/03_2025/7y58_33612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y58_33612/03_2025/7y58_33612.map" model { file = "/net/cci-nas-00/data/ceres_data/7y58_33612/03_2025/7y58_33612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y58_33612/03_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-5624/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: 4.46, per 1000 atoms: 0.80 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: 1.36 Conformation dependent library (CDL) restraints added in 672.7 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: 0.54 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: 1.67 Time building geometry restraints manager: 1.62 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: 2.970 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.710 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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: 23.710 ------------------------------------------------------------------------------- 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 : 0.551 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: 0.1609 time to fit residues: 35.0307 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 : 0.555 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.132800 restraints weight = 7509.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.137226 restraints weight = 4065.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.140210 restraints weight = 2708.596| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 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 56.820 801 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 : 0.539 Fit side-chains REVERT: A 99 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6860 (tt) REVERT: A 183 PHE cc_start: 0.6679 (OUTLIER) cc_final: 0.5825 (t80) REVERT: A 233 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7615 (tp30) REVERT: A 288 PHE cc_start: 0.7366 (OUTLIER) cc_final: 0.6923 (t80) REVERT: A 409 MET cc_start: 0.7900 (mmp) cc_final: 0.7390 (mmm) REVERT: A 430 ARG cc_start: 0.8400 (ttp-110) cc_final: 0.8077 (ttm-80) REVERT: C 73 SER cc_start: 0.8527 (t) cc_final: 0.8234 (p) REVERT: C 95 MET cc_start: 0.7568 (tpt) cc_final: 0.6720 (ttp) REVERT: C 97 TYR cc_start: 0.7353 (m-80) cc_final: 0.6839 (m-80) outliers start: 32 outliers final: 14 residues processed: 137 average time/residue: 0.1328 time to fit residues: 24.9333 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 : 0.533 ------------------------------------------------------------------------------- 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: 0.9990 chunk 56 optimal weight: 1.9990 chunk 67 optimal weight: 0.0570 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.0470 chunk 11 optimal weight: 0.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.171868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.136992 restraints weight = 7800.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.141453 restraints weight = 4340.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144503 restraints weight = 2972.082| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5720 Z= 0.185 Angle : 0.631 6.686 7756 Z= 0.318 Chirality : 0.040 0.140 910 Planarity : 0.005 0.050 959 Dihedral : 5.909 52.542 796 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.80 % Favored : 92.07 % Rotamer: Outliers : 4.40 % Allowed : 24.87 % Favored : 70.73 % 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: 1.22 (0.26), residues: 407 sheet: -1.61 (0.57), residues: 87 loop : -2.86 (0.38), residues: 237 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 0.020 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 143 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.592 Fit side-chains REVERT: A 81 TRP cc_start: 0.7628 (t-100) cc_final: 0.7360 (t60) REVERT: A 183 PHE cc_start: 0.6552 (OUTLIER) cc_final: 0.5998 (t80) REVERT: A 233 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7631 (tp30) REVERT: A 285 MET cc_start: 0.7593 (mmt) cc_final: 0.7390 (mmp) REVERT: A 288 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.6774 (t80) REVERT: A 380 MET cc_start: 0.7756 (tpp) cc_final: 0.7525 (tpp) REVERT: A 409 MET cc_start: 0.7953 (mmp) cc_final: 0.7404 (mmm) REVERT: A 434 ASP cc_start: 0.8102 (t0) cc_final: 0.7806 (t0) REVERT: B 30 TYR cc_start: 0.8929 (m-80) cc_final: 0.8706 (m-80) REVERT: C 73 SER cc_start: 0.8422 (t) cc_final: 0.8125 (p) REVERT: C 95 MET cc_start: 0.7610 (tpt) cc_final: 0.6647 (ttt) REVERT: C 97 TYR cc_start: 0.7351 (m-80) cc_final: 0.6464 (m-80) outliers start: 26 outliers final: 14 residues processed: 132 average time/residue: 0.1400 time to fit residues: 25.3648 Evaluate side-chains 126 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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: 0.9980 chunk 55 optimal weight: 0.0970 chunk 26 optimal weight: 0.3980 chunk 72 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 0.0270 chunk 48 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.169319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.134245 restraints weight = 7868.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.138848 restraints weight = 4307.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.141979 restraints weight = 2888.951| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5720 Z= 0.189 Angle : 0.621 6.674 7756 Z= 0.312 Chirality : 0.040 0.174 910 Planarity : 0.005 0.053 959 Dihedral : 5.737 53.283 796 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.11 % Favored : 92.75 % Rotamer: Outliers : 5.25 % Allowed : 25.55 % Favored : 69.20 % 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: 1.37 (0.26), residues: 407 sheet: -1.46 (0.58), residues: 85 loop : -2.64 (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 0.012 0.001 PHE A 284 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 152 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.596 Fit side-chains REVERT: A 40 MET cc_start: 0.7296 (ttm) cc_final: 0.7063 (ttm) REVERT: A 81 TRP cc_start: 0.7630 (t-100) cc_final: 0.7271 (t60) REVERT: A 154 SER cc_start: 0.8454 (m) cc_final: 0.7797 (m) REVERT: A 183 PHE cc_start: 0.6645 (OUTLIER) cc_final: 0.5921 (t80) REVERT: A 233 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7673 (tp30) REVERT: A 285 MET cc_start: 0.7443 (mmt) cc_final: 0.7016 (mmp) REVERT: A 288 PHE cc_start: 0.7184 (OUTLIER) cc_final: 0.6734 (t80) REVERT: A 358 TYR cc_start: 0.8532 (t80) cc_final: 0.8290 (t80) REVERT: A 380 MET cc_start: 0.7488 (tpp) cc_final: 0.7267 (tpp) REVERT: A 434 ASP cc_start: 0.7972 (t0) cc_final: 0.7696 (t0) REVERT: C 73 SER cc_start: 0.8431 (t) cc_final: 0.8132 (p) REVERT: C 95 MET cc_start: 0.7435 (tpt) cc_final: 0.6332 (ttp) REVERT: C 97 TYR cc_start: 0.7450 (m-80) cc_final: 0.6877 (m-80) outliers start: 31 outliers final: 21 residues processed: 139 average time/residue: 0.1462 time to fit residues: 27.9313 Evaluate side-chains 136 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 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 362 HIS 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 15 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.166657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.131771 restraints weight = 7696.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.136159 restraints weight = 4274.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.139101 restraints weight = 2896.997| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5720 Z= 0.237 Angle : 0.653 6.534 7756 Z= 0.330 Chirality : 0.041 0.254 910 Planarity : 0.005 0.052 959 Dihedral : 5.777 53.631 796 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.48 % Favored : 91.38 % Rotamer: Outliers : 6.26 % Allowed : 24.87 % 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: -0.33 (0.33), residues: 731 helix: 1.34 (0.26), residues: 406 sheet: -1.43 (0.58), residues: 85 loop : -2.54 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 173 HIS 0.002 0.001 HIS A 449 PHE 0.014 0.001 PHE A 288 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 153 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 0.546 Fit side-chains REVERT: A 15 LYS cc_start: 0.7783 (mptt) cc_final: 0.7264 (mtmm) REVERT: A 40 MET cc_start: 0.7249 (ttm) cc_final: 0.6952 (ttm) REVERT: A 81 TRP cc_start: 0.7674 (t-100) cc_final: 0.7191 (t60) REVERT: A 154 SER cc_start: 0.8510 (m) cc_final: 0.7864 (m) REVERT: A 183 PHE cc_start: 0.6766 (OUTLIER) cc_final: 0.6031 (t80) REVERT: A 233 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7690 (tp30) REVERT: A 285 MET cc_start: 0.7583 (mmt) cc_final: 0.7231 (mmp) REVERT: A 287 MET cc_start: 0.7417 (tpp) cc_final: 0.6829 (mmm) REVERT: A 288 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.6822 (t80) REVERT: A 409 MET cc_start: 0.7889 (mmp) cc_final: 0.7331 (mmm) REVERT: A 434 ASP cc_start: 0.7974 (t0) cc_final: 0.7712 (t0) REVERT: B 29 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8178 (mtm180) REVERT: C 73 SER cc_start: 0.8400 (t) cc_final: 0.8144 (p) REVERT: C 95 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.6460 (ttp) REVERT: C 97 TYR cc_start: 0.7507 (m-80) cc_final: 0.6929 (m-80) outliers start: 37 outliers final: 23 residues processed: 139 average time/residue: 0.1497 time to fit residues: 28.5377 Evaluate side-chains 140 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 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 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: 0.0270 chunk 18 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.167005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.132022 restraints weight = 7765.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.136416 restraints weight = 4320.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.139364 restraints weight = 2933.393| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5720 Z= 0.226 Angle : 0.651 7.254 7756 Z= 0.325 Chirality : 0.040 0.234 910 Planarity : 0.005 0.054 959 Dihedral : 5.764 54.143 796 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.66 % Favored : 92.20 % Rotamer: Outliers : 5.25 % Allowed : 26.06 % 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: -0.36 (0.33), residues: 731 helix: 1.31 (0.26), residues: 404 sheet: -1.43 (0.57), residues: 85 loop : -2.51 (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 0.013 0.001 PHE A 288 TYR 0.016 0.002 TYR A 410 ARG 0.002 0.000 ARG B 29 *********************** 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 146 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.536 Fit side-chains REVERT: A 15 LYS cc_start: 0.7783 (mptt) cc_final: 0.7268 (mtmm) REVERT: A 81 TRP cc_start: 0.7739 (t-100) cc_final: 0.7282 (t60) REVERT: A 183 PHE cc_start: 0.6760 (OUTLIER) cc_final: 0.5973 (t80) REVERT: A 233 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7694 (tp30) REVERT: A 285 MET cc_start: 0.7505 (mmt) cc_final: 0.7232 (mmp) REVERT: A 287 MET cc_start: 0.7447 (tpp) cc_final: 0.6929 (mmm) REVERT: A 288 PHE cc_start: 0.7153 (OUTLIER) cc_final: 0.6701 (t80) REVERT: A 321 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8024 (mm) REVERT: A 409 MET cc_start: 0.7809 (mmp) cc_final: 0.7320 (mmm) REVERT: A 434 ASP cc_start: 0.7907 (t0) cc_final: 0.7679 (t0) REVERT: B 29 ARG cc_start: 0.8436 (mtp85) cc_final: 0.8171 (mtm180) REVERT: C 23 CYS cc_start: 0.6319 (m) cc_final: 0.6052 (m) REVERT: C 73 SER cc_start: 0.8415 (t) cc_final: 0.8186 (p) REVERT: C 95 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.6418 (ttp) REVERT: C 97 TYR cc_start: 0.7536 (m-80) cc_final: 0.6972 (m-80) outliers start: 31 outliers final: 22 residues processed: 133 average time/residue: 0.1467 time to fit residues: 26.5736 Evaluate side-chains 138 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 16 optimal weight: 0.0270 chunk 57 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 28 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 = 0.3895 r_free = 0.3895 target = 0.166835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.131681 restraints weight = 7659.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.136087 restraints weight = 4322.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.139055 restraints weight = 2940.409| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3124 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= 0.188 Angle : 0.624 6.425 7756 Z= 0.310 Chirality : 0.040 0.197 910 Planarity : 0.004 0.052 959 Dihedral : 5.623 54.032 796 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.66 % Favored : 92.07 % Rotamer: Outliers : 4.40 % Allowed : 28.09 % Favored : 67.51 % 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: -0.20 (0.33), residues: 731 helix: 1.44 (0.26), residues: 406 sheet: -1.44 (0.57), residues: 85 loop : -2.43 (0.41), residues: 240 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 0.013 0.001 PHE A 284 TYR 0.017 0.002 TYR A 410 ARG 0.002 0.000 ARG A 114 *********************** 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 142 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.545 Fit side-chains REVERT: A 15 LYS cc_start: 0.7773 (mptt) cc_final: 0.7263 (mtmm) REVERT: A 81 TRP cc_start: 0.7750 (t-100) cc_final: 0.7317 (t60) REVERT: A 183 PHE cc_start: 0.6690 (OUTLIER) cc_final: 0.5874 (t80) REVERT: A 233 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7563 (tm-30) REVERT: A 285 MET cc_start: 0.7434 (mmt) cc_final: 0.7108 (mmp) REVERT: A 288 PHE cc_start: 0.7130 (OUTLIER) cc_final: 0.6728 (t80) REVERT: A 357 MET cc_start: 0.9272 (tpp) cc_final: 0.9052 (tpp) REVERT: A 380 MET cc_start: 0.7607 (tpp) cc_final: 0.7169 (tpp) REVERT: A 409 MET cc_start: 0.7799 (mmp) cc_final: 0.7318 (mmm) REVERT: A 434 ASP cc_start: 0.7927 (t0) cc_final: 0.7715 (t0) REVERT: C 73 SER cc_start: 0.8530 (t) cc_final: 0.8274 (p) REVERT: C 95 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6291 (ttp) REVERT: C 97 TYR cc_start: 0.7593 (m-80) cc_final: 0.6976 (m-80) outliers start: 26 outliers final: 21 residues processed: 129 average time/residue: 0.1406 time to fit residues: 24.8590 Evaluate side-chains 137 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 20 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 23 optimal weight: 0.0010 chunk 42 optimal weight: 0.9980 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.168200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.132981 restraints weight = 7676.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.137424 restraints weight = 4287.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.140402 restraints weight = 2917.863| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5720 Z= 0.201 Angle : 0.634 7.607 7756 Z= 0.315 Chirality : 0.040 0.178 910 Planarity : 0.004 0.053 959 Dihedral : 5.570 54.514 796 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.93 % Favored : 91.79 % Rotamer: Outliers : 5.08 % Allowed : 28.26 % Favored : 66.67 % 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: -0.23 (0.33), residues: 731 helix: 1.43 (0.26), residues: 404 sheet: -1.49 (0.57), residues: 85 loop : -2.45 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 81 HIS 0.002 0.001 HIS A 174 PHE 0.013 0.001 PHE A 284 TYR 0.014 0.001 TYR B 95 ARG 0.003 0.000 ARG B 29 *********************** 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 143 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.556 Fit side-chains REVERT: A 15 LYS cc_start: 0.7776 (mptt) cc_final: 0.7258 (mtmm) REVERT: A 81 TRP cc_start: 0.7774 (t-100) cc_final: 0.7326 (t60) REVERT: A 183 PHE cc_start: 0.6770 (OUTLIER) cc_final: 0.5924 (t80) REVERT: A 233 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7578 (tm-30) REVERT: A 285 MET cc_start: 0.7407 (mmt) cc_final: 0.7113 (mmp) REVERT: A 288 PHE cc_start: 0.7077 (OUTLIER) cc_final: 0.6611 (t80) REVERT: A 321 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.7992 (mm) REVERT: A 409 MET cc_start: 0.7830 (mmp) cc_final: 0.7305 (mmm) REVERT: A 434 ASP cc_start: 0.7924 (t0) cc_final: 0.7709 (t0) REVERT: B 73 ASP cc_start: 0.7962 (p0) cc_final: 0.7705 (p0) REVERT: C 73 SER cc_start: 0.8458 (t) cc_final: 0.8226 (p) REVERT: C 95 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6293 (ttp) REVERT: C 97 TYR cc_start: 0.7520 (m-80) cc_final: 0.6911 (m-80) outliers start: 30 outliers final: 21 residues processed: 129 average time/residue: 0.1463 time to fit residues: 25.5550 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 : 0.545 ------------------------------------------------------------------------------- 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 151 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 44 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 0.0020 chunk 72 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.166194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.131470 restraints weight = 7625.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.135833 restraints weight = 4227.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.138747 restraints weight = 2858.550| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3350 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= 0.224 Angle : 0.645 6.768 7756 Z= 0.321 Chirality : 0.040 0.172 910 Planarity : 0.005 0.059 959 Dihedral : 5.577 53.865 794 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.21 % Favored : 91.52 % Rotamer: Outliers : 4.40 % Allowed : 29.44 % Favored : 66.16 % 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: -0.18 (0.33), residues: 731 helix: 1.46 (0.26), residues: 404 sheet: -1.35 (0.58), residues: 85 loop : -2.46 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 81 HIS 0.002 0.001 HIS A 174 PHE 0.013 0.001 PHE A 284 TYR 0.016 0.002 TYR A 429 ARG 0.004 0.000 ARG B 29 *********************** 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 137 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.536 Fit side-chains REVERT: A 15 LYS cc_start: 0.7771 (mptt) cc_final: 0.7252 (mtmm) REVERT: A 81 TRP cc_start: 0.7774 (t-100) cc_final: 0.7335 (t60) REVERT: A 183 PHE cc_start: 0.6806 (OUTLIER) cc_final: 0.5954 (t80) REVERT: A 233 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7572 (tm-30) REVERT: A 285 MET cc_start: 0.7536 (mmt) cc_final: 0.7238 (mmp) REVERT: A 288 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.6648 (t80) REVERT: A 321 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.8026 (mm) REVERT: A 371 LEU cc_start: 0.8157 (mm) cc_final: 0.7193 (tp) REVERT: A 380 MET cc_start: 0.7436 (tpp) cc_final: 0.6945 (tpp) REVERT: A 409 MET cc_start: 0.7812 (mmp) cc_final: 0.7307 (mmm) REVERT: A 434 ASP cc_start: 0.7937 (t0) cc_final: 0.7702 (t0) REVERT: C 73 SER cc_start: 0.8460 (t) cc_final: 0.8249 (p) REVERT: C 95 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.6348 (ttp) outliers start: 26 outliers final: 19 residues processed: 124 average time/residue: 0.1489 time to fit residues: 24.7991 Evaluate side-chains 134 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 151 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 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: 0.9980 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.167744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.133211 restraints weight = 7748.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.137553 restraints weight = 4357.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.140382 restraints weight = 2966.150| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3444 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= 0.195 Angle : 0.628 7.067 7756 Z= 0.312 Chirality : 0.040 0.162 910 Planarity : 0.005 0.051 959 Dihedral : 5.500 54.562 794 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.93 % Favored : 91.79 % Rotamer: Outliers : 4.23 % Allowed : 29.95 % 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: -0.12 (0.33), residues: 731 helix: 1.51 (0.26), residues: 404 sheet: -1.35 (0.58), residues: 85 loop : -2.42 (0.41), residues: 242 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 0.014 0.001 PHE A 284 TYR 0.014 0.001 TYR A 410 ARG 0.003 0.000 ARG B 29 ********************** 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 136 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.549 Fit side-chains REVERT: A 15 LYS cc_start: 0.7775 (mptt) cc_final: 0.7226 (mtmm) REVERT: A 81 TRP cc_start: 0.7771 (t-100) cc_final: 0.7360 (t60) REVERT: A 183 PHE cc_start: 0.6702 (OUTLIER) cc_final: 0.5888 (t80) REVERT: A 233 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7578 (tm-30) REVERT: A 288 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6715 (t80) REVERT: A 321 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8023 (mm) REVERT: A 371 LEU cc_start: 0.8093 (mm) cc_final: 0.7143 (tp) REVERT: A 380 MET cc_start: 0.7285 (tpp) cc_final: 0.7013 (tpp) REVERT: A 409 MET cc_start: 0.7838 (mmp) cc_final: 0.7350 (mmm) REVERT: C 73 SER cc_start: 0.8460 (t) cc_final: 0.8239 (p) REVERT: C 95 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.6539 (ttp) outliers start: 25 outliers final: 19 residues processed: 124 average time/residue: 0.1557 time to fit residues: 25.9838 Evaluate side-chains 134 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 151 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 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 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: 0.0670 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 37 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.165919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.131739 restraints weight = 7522.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.136094 restraints weight = 4134.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.139016 restraints weight = 2761.998| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3493 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= 0.193 Angle : 0.636 6.938 7756 Z= 0.316 Chirality : 0.040 0.160 910 Planarity : 0.005 0.053 959 Dihedral : 5.495 53.266 794 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.21 % Favored : 91.66 % Rotamer: Outliers : 3.89 % Allowed : 30.29 % 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: -0.08 (0.33), residues: 731 helix: 1.52 (0.26), residues: 404 sheet: -1.28 (0.58), residues: 85 loop : -2.38 (0.41), residues: 242 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 0.014 0.001 PHE A 284 TYR 0.015 0.001 TYR A 429 ARG 0.003 0.000 ARG B 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1992.92 seconds wall clock time: 35 minutes 14.59 seconds (2114.59 seconds total)