Starting phenix.real_space_refine on Tue Feb 13 11:02:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y58_33612/02_2024/7y58_33612.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y58_33612/02_2024/7y58_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y58_33612/02_2024/7y58_33612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y58_33612/02_2024/7y58_33612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y58_33612/02_2024/7y58_33612.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y58_33612/02_2024/7y58_33612.pdb" } 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 Residue "A GLU 48": "OE1" <-> "OE2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 3.54, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.52 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: 1.58 Time building geometry restraints manager: 2.30 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: 96.57 - 104.09: 85 104.09 - 111.60: 2637 111.60 - 119.12: 1998 119.12 - 126.63: 2950 126.63 - 134.15: 86 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 2.440 nonbonded pdb=" OE2 GLU A 473 " pdb=" N GLY B 55 " model vdw 2.246 2.520 nonbonded pdb=" OD1 ASP B 111 " pdb=" N PHE B 112 " model vdw 2.251 2.520 nonbonded pdb=" NE ARG C 69 " pdb=" OG SER C 87 " model vdw 2.279 2.520 ... (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 ========== 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: 2.380 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: 9.680 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 19.460 Find NCS groups from input model: 0.140 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.520 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 0.609 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: 0.1621 time to fit residues: 35.6472 Evaluate side-chains 123 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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: 0.4980 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1836 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= 0.238 Angle : 0.681 7.187 7756 Z= 0.345 Chirality : 0.040 0.136 910 Planarity : 0.005 0.064 959 Dihedral : 6.532 59.322 801 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 5.92 % Allowed : 23.69 % Favored : 70.39 % 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: 1.07 (0.26), residues: 414 sheet: -1.55 (0.58), residues: 87 loop : -2.98 (0.38), 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 0.022 0.002 TYR B 95 ARG 0.005 0.001 ARG C 32 *********************** 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 156 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 121 time to evaluate : 0.603 Fit side-chains REVERT: A 81 TRP cc_start: 0.7355 (t-100) cc_final: 0.6871 (t60) REVERT: A 99 LEU cc_start: 0.6508 (OUTLIER) cc_final: 0.6282 (tt) REVERT: A 155 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7752 (tp) REVERT: A 183 PHE cc_start: 0.6729 (OUTLIER) cc_final: 0.5696 (t80) REVERT: A 233 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7692 (tp30) REVERT: A 285 MET cc_start: 0.7001 (mmt) cc_final: 0.6755 (mmp) REVERT: A 288 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.6397 (t80) REVERT: A 409 MET cc_start: 0.7258 (mmp) cc_final: 0.6806 (mmm) REVERT: A 430 ARG cc_start: 0.8061 (ttp-110) cc_final: 0.7728 (ttm-80) REVERT: C 73 SER cc_start: 0.8689 (t) cc_final: 0.8469 (p) REVERT: C 95 MET cc_start: 0.7190 (tpt) cc_final: 0.6590 (ttt) REVERT: C 97 TYR cc_start: 0.7491 (m-80) cc_final: 0.6711 (m-80) outliers start: 35 outliers final: 18 residues processed: 142 average time/residue: 0.1380 time to fit residues: 26.9287 Evaluate side-chains 136 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 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 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 390 ILE Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 90 ASP 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 53 optimal weight: 0.0570 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2353 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= 0.229 Angle : 0.645 6.881 7756 Z= 0.325 Chirality : 0.040 0.142 910 Planarity : 0.005 0.049 959 Dihedral : 6.281 55.950 800 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 6.09 % Allowed : 24.20 % Favored : 69.71 % 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: -0.63 (0.32), residues: 731 helix: 1.20 (0.26), residues: 407 sheet: -1.31 (0.60), residues: 82 loop : -3.01 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 81 HIS 0.003 0.001 HIS A 449 PHE 0.013 0.001 PHE A 288 TYR 0.018 0.002 TYR B 95 ARG 0.003 0.001 ARG A 114 *********************** 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 151 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 115 time to evaluate : 0.603 Fit side-chains REVERT: A 81 TRP cc_start: 0.7419 (t-100) cc_final: 0.7060 (t60) REVERT: A 99 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6224 (tt) REVERT: A 155 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.7919 (tp) REVERT: A 183 PHE cc_start: 0.6559 (OUTLIER) cc_final: 0.5809 (t80) REVERT: A 233 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7705 (tp30) REVERT: A 285 MET cc_start: 0.7193 (mmt) cc_final: 0.6930 (mmp) REVERT: A 287 MET cc_start: 0.7628 (mmm) cc_final: 0.6730 (tmm) REVERT: A 288 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.6441 (t80) REVERT: A 409 MET cc_start: 0.7237 (mmp) cc_final: 0.6751 (mmm) REVERT: A 430 ARG cc_start: 0.8091 (ttp-110) cc_final: 0.7720 (ttm-80) REVERT: A 434 ASP cc_start: 0.7856 (t0) cc_final: 0.7480 (t0) REVERT: B 120 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7588 (mm-40) REVERT: C 73 SER cc_start: 0.8620 (t) cc_final: 0.8412 (p) REVERT: C 95 MET cc_start: 0.7101 (tpt) cc_final: 0.6481 (ttt) REVERT: C 97 TYR cc_start: 0.7512 (m-80) cc_final: 0.6695 (m-80) outliers start: 36 outliers final: 21 residues processed: 139 average time/residue: 0.1518 time to fit residues: 29.2289 Evaluate side-chains 135 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 26 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 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 259 LEU 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 509 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 chunk 70 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 19 optimal weight: 0.0570 chunk 58 optimal weight: 5.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2605 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= 0.197 Angle : 0.620 6.470 7756 Z= 0.312 Chirality : 0.039 0.160 910 Planarity : 0.004 0.053 959 Dihedral : 6.102 55.204 798 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.80 % Favored : 92.07 % Rotamer: Outliers : 5.41 % Allowed : 25.04 % Favored : 69.54 % 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: 1.28 (0.26), residues: 413 sheet: -1.23 (0.58), residues: 85 loop : -2.89 (0.40), residues: 233 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 288 TYR 0.016 0.002 TYR B 95 ARG 0.002 0.000 ARG A 430 *********************** 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 151 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 119 time to evaluate : 0.820 Fit side-chains REVERT: A 15 LYS cc_start: 0.7766 (mptt) cc_final: 0.7235 (mtmm) REVERT: A 81 TRP cc_start: 0.7388 (t-100) cc_final: 0.6849 (t60) REVERT: A 99 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.6227 (tt) REVERT: A 155 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7880 (tp) REVERT: A 183 PHE cc_start: 0.6671 (OUTLIER) cc_final: 0.5915 (t80) REVERT: A 233 GLU cc_start: 0.8510 (mm-30) cc_final: 0.7730 (tp30) REVERT: A 287 MET cc_start: 0.7638 (mmm) cc_final: 0.6703 (tmm) REVERT: A 288 PHE cc_start: 0.6653 (OUTLIER) cc_final: 0.6307 (t80) REVERT: A 358 TYR cc_start: 0.8508 (t80) cc_final: 0.8298 (t80) REVERT: A 393 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7996 (mt-10) REVERT: A 409 MET cc_start: 0.7275 (mmp) cc_final: 0.6771 (mmm) REVERT: A 434 ASP cc_start: 0.7756 (t0) cc_final: 0.7421 (t0) REVERT: C 95 MET cc_start: 0.6950 (tpt) cc_final: 0.6324 (ttt) REVERT: C 97 TYR cc_start: 0.7615 (m-80) cc_final: 0.6792 (m-80) outliers start: 32 outliers final: 16 residues processed: 139 average time/residue: 0.1504 time to fit residues: 28.5614 Evaluate side-chains 133 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 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 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 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 Chi-restraints excluded: chain C residue 110 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 36 optimal weight: 0.5980 chunk 63 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5720 Z= 0.218 Angle : 0.635 7.280 7756 Z= 0.319 Chirality : 0.040 0.213 910 Planarity : 0.004 0.052 959 Dihedral : 6.118 55.309 798 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 5.08 % Allowed : 25.04 % Favored : 69.88 % 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: -0.40 (0.33), residues: 731 helix: 1.30 (0.26), residues: 412 sheet: -1.25 (0.58), residues: 85 loop : -2.80 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 173 HIS 0.002 0.001 HIS A 174 PHE 0.012 0.001 PHE A 284 TYR 0.015 0.002 TYR B 95 ARG 0.002 0.000 ARG A 114 *********************** 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 145 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 115 time to evaluate : 0.642 Fit side-chains REVERT: A 15 LYS cc_start: 0.7735 (mptt) cc_final: 0.7188 (mtmm) REVERT: A 81 TRP cc_start: 0.7391 (t-100) cc_final: 0.6907 (t60) REVERT: A 99 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.6243 (tt) REVERT: A 183 PHE cc_start: 0.6719 (OUTLIER) cc_final: 0.5887 (t80) REVERT: A 233 GLU cc_start: 0.8528 (mm-30) cc_final: 0.7759 (tp30) REVERT: A 287 MET cc_start: 0.7663 (mmm) cc_final: 0.6766 (tmm) REVERT: A 288 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.6366 (t80) REVERT: A 434 ASP cc_start: 0.7766 (t0) cc_final: 0.7437 (t0) REVERT: C 95 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.6311 (ttt) REVERT: C 97 TYR cc_start: 0.7623 (m-80) cc_final: 0.6736 (m-80) outliers start: 30 outliers final: 23 residues processed: 131 average time/residue: 0.1558 time to fit residues: 27.6077 Evaluate side-chains 139 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 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 362 HIS 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 A residue 509 ASP Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 110 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.0370 chunk 70 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.0670 chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5720 Z= 0.164 Angle : 0.612 6.826 7756 Z= 0.303 Chirality : 0.039 0.228 910 Planarity : 0.004 0.054 959 Dihedral : 5.612 53.467 796 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.80 % Favored : 92.07 % Rotamer: Outliers : 4.74 % Allowed : 26.57 % 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: -0.17 (0.33), residues: 731 helix: 1.48 (0.26), residues: 406 sheet: -1.28 (0.58), residues: 85 loop : -2.55 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 173 HIS 0.002 0.001 HIS A 174 PHE 0.013 0.001 PHE A 284 TYR 0.015 0.001 TYR B 95 ARG 0.004 0.000 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 144 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 116 time to evaluate : 0.633 Fit side-chains REVERT: A 15 LYS cc_start: 0.7725 (mptt) cc_final: 0.7169 (mtmm) REVERT: A 81 TRP cc_start: 0.7422 (t-100) cc_final: 0.7005 (t60) REVERT: A 99 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.6233 (tt) REVERT: A 155 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7365 (tp) REVERT: A 233 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7753 (tp30) REVERT: A 288 PHE cc_start: 0.6600 (OUTLIER) cc_final: 0.6280 (t80) REVERT: A 434 ASP cc_start: 0.7738 (t0) cc_final: 0.7468 (t0) REVERT: B 95 TYR cc_start: 0.8413 (m-80) cc_final: 0.7723 (m-10) REVERT: C 95 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6178 (ttp) REVERT: C 97 TYR cc_start: 0.7646 (m-80) cc_final: 0.7098 (m-80) outliers start: 28 outliers final: 15 residues processed: 131 average time/residue: 0.1449 time to fit residues: 25.8745 Evaluate side-chains 129 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 188 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 317 LEU 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 A residue 494 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 Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 110 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3147 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= 0.238 Angle : 0.653 6.779 7756 Z= 0.327 Chirality : 0.040 0.243 910 Planarity : 0.004 0.053 959 Dihedral : 5.719 55.233 796 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.89 % Favored : 90.97 % Rotamer: Outliers : 5.41 % Allowed : 26.57 % Favored : 68.02 % 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: -0.31 (0.33), residues: 731 helix: 1.42 (0.26), residues: 403 sheet: -1.39 (0.58), residues: 86 loop : -2.63 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 81 HIS 0.002 0.001 HIS A 174 PHE 0.011 0.001 PHE A 284 TYR 0.020 0.002 TYR A 410 ARG 0.003 0.000 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 141 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 109 time to evaluate : 0.637 Fit side-chains REVERT: A 15 LYS cc_start: 0.7728 (mptt) cc_final: 0.7174 (mtmm) REVERT: A 81 TRP cc_start: 0.7460 (t-100) cc_final: 0.6867 (t60) REVERT: A 99 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6242 (tt) REVERT: A 155 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7504 (tp) REVERT: A 233 GLU cc_start: 0.8523 (mm-30) cc_final: 0.7780 (tp30) REVERT: A 287 MET cc_start: 0.7795 (tpp) cc_final: 0.7157 (tpp) REVERT: A 288 PHE cc_start: 0.6813 (OUTLIER) cc_final: 0.6546 (t80) REVERT: A 358 TYR cc_start: 0.8362 (t80) cc_final: 0.8150 (t80) REVERT: A 359 PHE cc_start: 0.7982 (m-10) cc_final: 0.7647 (m-10) REVERT: A 380 MET cc_start: 0.7538 (tpp) cc_final: 0.7114 (tpp) REVERT: A 409 MET cc_start: 0.7235 (mmp) cc_final: 0.6786 (mmm) REVERT: A 434 ASP cc_start: 0.7782 (t0) cc_final: 0.7476 (t0) REVERT: C 95 MET cc_start: 0.6873 (OUTLIER) cc_final: 0.6217 (ttp) REVERT: C 97 TYR cc_start: 0.7704 (m-80) cc_final: 0.7127 (m-80) outliers start: 32 outliers final: 22 residues processed: 127 average time/residue: 0.1513 time to fit residues: 26.0858 Evaluate side-chains 135 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 109 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 71 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 155 ILE 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 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 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 A residue 494 ILE Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 110 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 55 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 chunk 67 optimal weight: 0.0040 chunk 61 optimal weight: 0.9980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3259 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= 0.191 Angle : 0.637 7.793 7756 Z= 0.315 Chirality : 0.040 0.227 910 Planarity : 0.005 0.052 959 Dihedral : 5.581 54.001 794 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.66 % Favored : 92.20 % Rotamer: Outliers : 5.25 % Allowed : 26.73 % Favored : 68.02 % 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: -0.17 (0.33), residues: 731 helix: 1.53 (0.26), residues: 405 sheet: -1.34 (0.58), residues: 85 loop : -2.60 (0.40), residues: 241 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 0.012 0.001 PHE A 284 TYR 0.017 0.001 TYR A 410 ARG 0.004 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 143 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 112 time to evaluate : 0.652 Fit side-chains REVERT: A 15 LYS cc_start: 0.7727 (mptt) cc_final: 0.7171 (mtmm) REVERT: A 81 TRP cc_start: 0.7430 (t-100) cc_final: 0.6866 (t60) REVERT: A 99 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.6201 (tt) REVERT: A 155 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7423 (tp) REVERT: A 233 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7577 (tm-30) REVERT: A 287 MET cc_start: 0.7674 (tpp) cc_final: 0.7038 (tpp) REVERT: A 288 PHE cc_start: 0.6688 (OUTLIER) cc_final: 0.6363 (t80) REVERT: A 359 PHE cc_start: 0.7781 (m-10) cc_final: 0.7472 (m-10) REVERT: A 409 MET cc_start: 0.7179 (mmp) cc_final: 0.6782 (mmm) REVERT: A 434 ASP cc_start: 0.7789 (t0) cc_final: 0.7468 (t0) REVERT: C 95 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6198 (ttp) REVERT: C 97 TYR cc_start: 0.7756 (m-80) cc_final: 0.7173 (m-80) outliers start: 31 outliers final: 20 residues processed: 130 average time/residue: 0.1535 time to fit residues: 26.8332 Evaluate side-chains 134 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 151 ILE Chi-restraints excluded: chain A residue 155 ILE 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 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 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 A residue 509 ASP 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 Chi-restraints excluded: chain C residue 110 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 62 optimal weight: 0.0980 chunk 43 optimal weight: 0.0770 chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3389 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= 0.201 Angle : 0.663 8.719 7756 Z= 0.322 Chirality : 0.040 0.215 910 Planarity : 0.005 0.054 959 Dihedral : 5.613 54.118 794 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.89 % Favored : 90.97 % Rotamer: Outliers : 4.91 % Allowed : 27.24 % Favored : 67.85 % 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: 1.53 (0.26), residues: 403 sheet: -1.19 (0.59), residues: 85 loop : -2.70 (0.39), residues: 243 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 0.012 0.001 PHE A 284 TYR 0.018 0.002 TYR A 410 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 140 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 0.625 Fit side-chains REVERT: A 15 LYS cc_start: 0.7721 (mptt) cc_final: 0.7167 (mtmm) REVERT: A 81 TRP cc_start: 0.7448 (t-100) cc_final: 0.6872 (t60) REVERT: A 99 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6216 (tt) REVERT: A 155 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7414 (tp) REVERT: A 233 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7576 (tm-30) REVERT: A 287 MET cc_start: 0.7550 (tpp) cc_final: 0.6866 (tpp) REVERT: A 288 PHE cc_start: 0.6695 (OUTLIER) cc_final: 0.6371 (t80) REVERT: A 409 MET cc_start: 0.7189 (mmp) cc_final: 0.6777 (mmm) REVERT: A 434 ASP cc_start: 0.7765 (t0) cc_final: 0.7467 (t0) REVERT: C 95 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6237 (ttp) REVERT: C 97 TYR cc_start: 0.7740 (m-80) cc_final: 0.7181 (m-80) outliers start: 29 outliers final: 24 residues processed: 126 average time/residue: 0.1545 time to fit residues: 26.1793 Evaluate side-chains 139 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 71 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 155 ILE 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 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 A residue 494 ILE Chi-restraints excluded: chain A residue 509 ASP 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 73 SER Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 110 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 0.4980 chunk 48 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 0.0000 chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 17 optimal weight: 0.0980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5720 Z= 0.170 Angle : 0.648 7.729 7756 Z= 0.316 Chirality : 0.040 0.214 910 Planarity : 0.005 0.053 959 Dihedral : 5.554 53.424 794 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.66 % Favored : 92.20 % Rotamer: Outliers : 4.06 % Allowed : 27.92 % Favored : 68.02 % 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: -0.14 (0.33), residues: 731 helix: 1.64 (0.26), residues: 399 sheet: -1.21 (0.58), residues: 85 loop : -2.72 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 81 HIS 0.009 0.002 HIS A 362 PHE 0.013 0.001 PHE A 360 TYR 0.017 0.001 TYR A 410 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 137 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 0.632 Fit side-chains REVERT: A 15 LYS cc_start: 0.7716 (mptt) cc_final: 0.7164 (mtmm) REVERT: A 81 TRP cc_start: 0.7446 (t-100) cc_final: 0.6906 (t60) REVERT: A 99 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6236 (tt) REVERT: A 155 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7372 (tp) REVERT: A 233 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7586 (tm-30) REVERT: A 287 MET cc_start: 0.7545 (tpp) cc_final: 0.6948 (tpp) REVERT: A 288 PHE cc_start: 0.6578 (OUTLIER) cc_final: 0.6231 (t80) REVERT: A 409 MET cc_start: 0.7172 (mmp) cc_final: 0.6764 (mmm) REVERT: A 434 ASP cc_start: 0.7752 (t0) cc_final: 0.7473 (t0) REVERT: B 95 TYR cc_start: 0.8317 (m-80) cc_final: 0.7567 (m-10) REVERT: C 95 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.6228 (ttp) outliers start: 24 outliers final: 19 residues processed: 125 average time/residue: 0.1549 time to fit residues: 26.4109 Evaluate side-chains 134 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 99 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 155 ILE 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 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 A residue 509 ASP 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 Chi-restraints excluded: chain C residue 73 SER 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 53 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** 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 = 0.3887 r_free = 0.3887 target = 0.165803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.130952 restraints weight = 7740.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.135325 restraints weight = 4335.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.138277 restraints weight = 2944.888| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5720 Z= 0.241 Angle : 0.673 8.195 7756 Z= 0.332 Chirality : 0.041 0.215 910 Planarity : 0.005 0.051 959 Dihedral : 5.663 54.691 794 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.17 % Favored : 90.70 % Rotamer: Outliers : 4.23 % Allowed : 27.75 % Favored : 68.02 % 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: -0.25 (0.33), residues: 731 helix: 1.49 (0.26), residues: 403 sheet: -1.22 (0.58), residues: 85 loop : -2.72 (0.39), residues: 243 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 0.015 0.001 PHE A 360 TYR 0.020 0.002 TYR A 410 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: 1471.37 seconds wall clock time: 27 minutes 8.76 seconds (1628.76 seconds total)