Starting phenix.real_space_refine on Thu Nov 14 10:32:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gb3_29912/11_2024/8gb3_29912.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gb3_29912/11_2024/8gb3_29912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gb3_29912/11_2024/8gb3_29912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gb3_29912/11_2024/8gb3_29912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gb3_29912/11_2024/8gb3_29912.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gb3_29912/11_2024/8gb3_29912.cif" } resolution = 3.7 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= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 242 atoms to isotropic. 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 8 5.16 5 C 3420 2.51 5 N 996 2.21 5 O 1113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 5537 Number of models: 1 Model: "" Number of chains: 3 Chain: "D" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3814 Classifications: {'peptide': 505} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 485} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1051 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 672 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Time building chain proxies: 3.83, per 1000 atoms: 0.69 Number of scatterers: 5537 At special positions: 0 Unit cell: (68.724, 86.112, 106.812, 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 8 16.00 O 1113 8.00 N 996 7.00 C 3420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.37 Conformation dependent library (CDL) restraints added in 737.6 milliseconds 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1346 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 6 sheets defined 46.4% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'D' and resid 51 through 61 removed outlier: 4.390A pdb=" N GLN D 57 " --> pdb=" O PRO D 53 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR D 60 " --> pdb=" O ASN D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 103 removed outlier: 4.289A pdb=" N SER D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'D' and resid 146 through 156 Processing helix chain 'D' and resid 200 through 220 removed outlier: 3.640A pdb=" N TRP D 204 " --> pdb=" O GLY D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 245 Processing helix chain 'D' and resid 274 through 288 removed outlier: 6.054A pdb=" N ASP D 284 " --> pdb=" O ARG D 280 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LEU D 285 " --> pdb=" O ILE D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 300 removed outlier: 4.251A pdb=" N THR D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 330 removed outlier: 3.521A pdb=" N THR D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 343 through 357 removed outlier: 3.508A pdb=" N LYS D 357 " --> pdb=" O ALA D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 496 removed outlier: 3.736A pdb=" N ASP D 487 " --> pdb=" O LYS D 483 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG D 488 " --> pdb=" O GLU D 484 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE D 490 " --> pdb=" O ILE D 486 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS D 491 " --> pdb=" O ASP D 487 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 509 removed outlier: 3.760A pdb=" N GLU D 505 " --> pdb=" O ARG D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 512 No H-bonds generated for 'chain 'D' and resid 510 through 512' Processing helix chain 'E' and resid 45 through 79 removed outlier: 3.592A pdb=" N GLN E 63 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG E 75 " --> pdb=" O ASN E 71 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA E 76 " --> pdb=" O TYR E 72 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU E 77 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG E 78 " --> pdb=" O LYS E 74 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP E 79 " --> pdb=" O ARG E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 94 removed outlier: 3.866A pdb=" N ALA E 84 " --> pdb=" O GLN E 80 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS E 88 " --> pdb=" O ALA E 84 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL E 92 " --> pdb=" O LYS E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 108 Processing helix chain 'E' and resid 114 through 129 removed outlier: 3.950A pdb=" N GLY E 129 " --> pdb=" O SER E 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 83 removed outlier: 3.773A pdb=" N ALA F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU F 77 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 89 removed outlier: 3.677A pdb=" N ALA F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 107 removed outlier: 4.117A pdb=" N GLY F 97 " --> pdb=" O SER F 93 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL F 98 " --> pdb=" O GLN F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 116 No H-bonds generated for 'chain 'F' and resid 114 through 116' Processing helix chain 'F' and resid 117 through 130 removed outlier: 4.119A pdb=" N ASP F 121 " --> pdb=" O LYS F 117 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY F 129 " --> pdb=" O SER F 125 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU F 130 " --> pdb=" O ALA F 126 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 24 through 27 removed outlier: 4.769A pdb=" N VAL D 16 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ALA D 4 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 177 through 181 Processing sheet with id=AA3, first strand: chain 'D' and resid 381 through 386 removed outlier: 3.747A pdb=" N LEU D 385 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU D 373 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN D 413 " --> pdb=" O GLU D 376 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY D 429 " --> pdb=" O VAL D 414 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLN D 416 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU D 427 " --> pdb=" O GLN D 416 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 399 through 400 Processing sheet with id=AA5, first strand: chain 'E' and resid 163 through 169 removed outlier: 3.577A pdb=" N VAL E 163 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY E 185 " --> pdb=" O GLY E 165 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL E 167 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU E 183 " --> pdb=" O VAL E 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 172 through 174 removed outlier: 7.796A pdb=" N TYR E 172 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU E 179 " --> pdb=" O TYR E 172 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU E 174 " --> pdb=" O GLN E 177 " (cutoff:3.500A) 261 hydrogen bonds defined for protein. 762 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: 1.34 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1966 1.34 - 1.46: 768 1.46 - 1.57: 2847 1.57 - 1.69: 0 1.69 - 1.80: 16 Bond restraints: 5597 Sorted by residual: bond pdb=" CA ILE D 39 " pdb=" CB ILE D 39 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.39e+00 bond pdb=" CG PRO D 393 " pdb=" CD PRO D 393 " ideal model delta sigma weight residual 1.503 1.472 0.031 3.40e-02 8.65e+02 8.47e-01 bond pdb=" CB PRO D 148 " pdb=" CG PRO D 148 " ideal model delta sigma weight residual 1.492 1.450 0.042 5.00e-02 4.00e+02 6.93e-01 bond pdb=" CB VAL D 345 " pdb=" CG1 VAL D 345 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.44e-01 bond pdb=" C LYS D 361 " pdb=" O LYS D 361 " ideal model delta sigma weight residual 1.242 1.234 0.008 1.00e-02 1.00e+04 6.26e-01 ... (remaining 5592 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 7272 1.17 - 2.34: 240 2.34 - 3.51: 43 3.51 - 4.68: 10 4.68 - 5.85: 4 Bond angle restraints: 7569 Sorted by residual: angle pdb=" C LYS D 361 " pdb=" CA LYS D 361 " pdb=" CB LYS D 361 " ideal model delta sigma weight residual 116.63 110.78 5.85 1.16e+00 7.43e-01 2.54e+01 angle pdb=" C THR D 391 " pdb=" N ILE D 392 " pdb=" CA ILE D 392 " ideal model delta sigma weight residual 120.43 124.79 -4.36 9.60e-01 1.09e+00 2.06e+01 angle pdb=" C ILE D 144 " pdb=" N VAL D 145 " pdb=" CA VAL D 145 " ideal model delta sigma weight residual 120.49 125.08 -4.59 1.38e+00 5.25e-01 1.10e+01 angle pdb=" CA LYS D 361 " pdb=" C LYS D 361 " pdb=" N ASP D 362 " ideal model delta sigma weight residual 119.63 117.09 2.54 8.10e-01 1.52e+00 9.84e+00 angle pdb=" C ILE D 392 " pdb=" CA ILE D 392 " pdb=" CB ILE D 392 " ideal model delta sigma weight residual 113.70 110.84 2.86 9.50e-01 1.11e+00 9.03e+00 ... (remaining 7564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.77: 3139 15.77 - 31.55: 214 31.55 - 47.32: 59 47.32 - 63.10: 14 63.10 - 78.87: 6 Dihedral angle restraints: 3432 sinusoidal: 1348 harmonic: 2084 Sorted by residual: dihedral pdb=" CA ALA D 105 " pdb=" C ALA D 105 " pdb=" N TYR D 106 " pdb=" CA TYR D 106 " ideal model delta harmonic sigma weight residual 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA LEU D 366 " pdb=" C LEU D 366 " pdb=" N ASP D 367 " pdb=" CA ASP D 367 " ideal model delta harmonic sigma weight residual 180.00 161.32 18.68 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ASN D 45 " pdb=" C ASN D 45 " pdb=" N GLY D 46 " pdb=" CA GLY D 46 " ideal model delta harmonic sigma weight residual 180.00 162.88 17.12 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 3429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 498 0.025 - 0.051: 219 0.051 - 0.076: 96 0.076 - 0.102: 43 0.102 - 0.127: 33 Chirality restraints: 889 Sorted by residual: chirality pdb=" CA VAL D 66 " pdb=" N VAL D 66 " pdb=" C VAL D 66 " pdb=" CB VAL D 66 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA ILE D 253 " pdb=" N ILE D 253 " pdb=" C ILE D 253 " pdb=" CB ILE D 253 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CB ILE D 443 " pdb=" CA ILE D 443 " pdb=" CG1 ILE D 443 " pdb=" CG2 ILE D 443 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 886 not shown) Planarity restraints: 1008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 291 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO D 292 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 292 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 292 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 118 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.87e+00 pdb=" N PRO D 119 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 52 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.60e+00 pdb=" N PRO D 53 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 53 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 53 " 0.018 5.00e-02 4.00e+02 ... (remaining 1005 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1115 2.78 - 3.31: 5743 3.31 - 3.84: 9218 3.84 - 4.37: 10395 4.37 - 4.90: 17457 Nonbonded interactions: 43928 Sorted by model distance: nonbonded pdb=" O ILE D 307 " pdb=" NZ LYS D 333 " model vdw 2.245 3.120 nonbonded pdb=" O PHE D 278 " pdb=" OG1 THR D 282 " model vdw 2.248 3.040 nonbonded pdb=" OD2 ASP D 464 " pdb=" OG1 THR D 467 " model vdw 2.249 3.040 nonbonded pdb=" O PRO E 115 " pdb=" OG SER E 118 " model vdw 2.268 3.040 nonbonded pdb=" N GLU E 148 " pdb=" O ALA E 182 " model vdw 2.299 3.120 ... (remaining 43923 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.990 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 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 : 0.003 0.042 5597 Z= 0.194 Angle : 0.522 5.846 7569 Z= 0.305 Chirality : 0.041 0.127 889 Planarity : 0.004 0.038 1008 Dihedral : 12.387 78.869 2086 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.31 % Allowed : 8.97 % Favored : 86.72 % 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: -0.39 (0.33), residues: 723 helix: 1.00 (0.31), residues: 309 sheet: -0.68 (0.55), residues: 101 loop : -1.39 (0.37), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 211 HIS 0.001 0.000 HIS E 147 PHE 0.011 0.001 PHE D 176 TYR 0.006 0.001 TYR D 106 ARG 0.003 0.000 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 ASN cc_start: 0.6699 (m-40) cc_final: 0.6446 (m-40) REVERT: D 100 LYS cc_start: 0.7758 (tttm) cc_final: 0.7533 (tttm) REVERT: D 166 ILE cc_start: 0.7430 (tp) cc_final: 0.7220 (tp) REVERT: D 227 ASP cc_start: 0.6805 (m-30) cc_final: 0.6598 (m-30) REVERT: D 229 MET cc_start: 0.5748 (tpt) cc_final: 0.5399 (tpt) REVERT: D 283 GLN cc_start: 0.6353 (tp-100) cc_final: 0.5803 (tp-100) REVERT: D 333 LYS cc_start: 0.7242 (ttmt) cc_final: 0.6792 (ttmt) REVERT: D 356 LEU cc_start: 0.7988 (mm) cc_final: 0.7552 (mm) REVERT: D 357 LYS cc_start: 0.8056 (pttm) cc_final: 0.7728 (pttm) REVERT: D 359 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6442 (mm-30) REVERT: D 383 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7866 (p) REVERT: D 395 LYS cc_start: 0.7591 (tmtt) cc_final: 0.7304 (tmtt) REVERT: D 416 GLN cc_start: 0.7787 (pm20) cc_final: 0.7439 (pm20) REVERT: D 489 MET cc_start: 0.6065 (mpp) cc_final: 0.5466 (mpp) REVERT: E 63 GLN cc_start: 0.6875 (pm20) cc_final: 0.6522 (pm20) REVERT: F 69 PHE cc_start: 0.7108 (t80) cc_final: 0.6471 (t80) REVERT: F 117 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7079 (ttmm) outliers start: 25 outliers final: 10 residues processed: 137 average time/residue: 0.2342 time to fit residues: 39.2187 Evaluate side-chains 116 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 42 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 ASN E 80 GLN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 5597 Z= 0.427 Angle : 0.698 10.679 7569 Z= 0.369 Chirality : 0.048 0.203 889 Planarity : 0.005 0.044 1008 Dihedral : 7.803 58.157 809 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 5.52 % Allowed : 11.90 % Favored : 82.59 % 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: -0.97 (0.32), residues: 723 helix: 0.35 (0.29), residues: 321 sheet: -0.62 (0.55), residues: 101 loop : -1.72 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 204 HIS 0.006 0.001 HIS D 72 PHE 0.022 0.002 PHE D 176 TYR 0.013 0.002 TYR D 155 ARG 0.008 0.001 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 ASN cc_start: 0.6748 (m-40) cc_final: 0.6428 (m-40) REVERT: D 49 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.7038 (mp) REVERT: D 166 ILE cc_start: 0.7491 (tp) cc_final: 0.7260 (tp) REVERT: D 182 GLU cc_start: 0.4510 (mt-10) cc_final: 0.4033 (mt-10) REVERT: D 229 MET cc_start: 0.5975 (tpt) cc_final: 0.5734 (tpt) REVERT: D 283 GLN cc_start: 0.6313 (tp-100) cc_final: 0.5800 (tp-100) REVERT: D 333 LYS cc_start: 0.7217 (ttmt) cc_final: 0.6843 (ttmt) REVERT: D 356 LEU cc_start: 0.8053 (mm) cc_final: 0.7659 (mm) REVERT: D 359 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6531 (mm-30) REVERT: D 395 LYS cc_start: 0.7765 (tmtt) cc_final: 0.7416 (tmtt) REVERT: D 416 GLN cc_start: 0.7874 (pm20) cc_final: 0.7629 (pm20) REVERT: E 63 GLN cc_start: 0.6806 (pm20) cc_final: 0.6516 (pm20) REVERT: F 69 PHE cc_start: 0.7221 (t80) cc_final: 0.6437 (t80) REVERT: F 75 ARG cc_start: 0.7336 (ttp-110) cc_final: 0.7036 (ttp-110) REVERT: F 78 ARG cc_start: 0.7052 (mmm160) cc_final: 0.6408 (mmm160) REVERT: F 102 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5743 (pp) REVERT: F 117 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7275 (tppp) outliers start: 32 outliers final: 19 residues processed: 132 average time/residue: 0.2361 time to fit residues: 38.2152 Evaluate side-chains 129 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 384 ARG Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 0.0010 chunk 20 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5972 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5597 Z= 0.243 Angle : 0.612 12.375 7569 Z= 0.318 Chirality : 0.044 0.153 889 Planarity : 0.004 0.038 1008 Dihedral : 7.078 59.712 804 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 5.00 % Allowed : 15.17 % Favored : 79.83 % 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: -0.75 (0.32), residues: 723 helix: 0.65 (0.29), residues: 315 sheet: -0.54 (0.55), residues: 99 loop : -1.70 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 204 HIS 0.005 0.001 HIS D 459 PHE 0.017 0.002 PHE D 122 TYR 0.008 0.001 TYR D 155 ARG 0.006 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 45 ASN cc_start: 0.6673 (m-40) cc_final: 0.6304 (m-40) REVERT: D 166 ILE cc_start: 0.7415 (tp) cc_final: 0.7201 (tp) REVERT: D 182 GLU cc_start: 0.4540 (mt-10) cc_final: 0.4301 (mt-10) REVERT: D 229 MET cc_start: 0.5750 (tpt) cc_final: 0.5375 (tpt) REVERT: D 231 MET cc_start: 0.5342 (mmt) cc_final: 0.4716 (mmt) REVERT: D 249 GLN cc_start: 0.7640 (pp30) cc_final: 0.7405 (pp30) REVERT: D 283 GLN cc_start: 0.6270 (tp-100) cc_final: 0.5734 (tp-100) REVERT: D 297 ILE cc_start: 0.2741 (OUTLIER) cc_final: 0.2345 (tt) REVERT: D 356 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7583 (mm) REVERT: D 357 LYS cc_start: 0.7983 (pttm) cc_final: 0.7591 (pttm) REVERT: D 359 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6476 (mm-30) REVERT: D 395 LYS cc_start: 0.7749 (tmtt) cc_final: 0.7378 (tmtt) REVERT: D 416 GLN cc_start: 0.7838 (pm20) cc_final: 0.7634 (pm20) REVERT: E 63 GLN cc_start: 0.6840 (pm20) cc_final: 0.6509 (pm20) REVERT: F 69 PHE cc_start: 0.7166 (t80) cc_final: 0.6454 (t80) REVERT: F 78 ARG cc_start: 0.6927 (mmm160) cc_final: 0.6293 (mmm160) REVERT: F 117 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7233 (tppp) outliers start: 29 outliers final: 15 residues processed: 125 average time/residue: 0.2285 time to fit residues: 34.9935 Evaluate side-chains 122 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 5597 Z= 0.333 Angle : 0.656 12.206 7569 Z= 0.344 Chirality : 0.046 0.145 889 Planarity : 0.005 0.040 1008 Dihedral : 7.243 58.781 804 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 5.86 % Allowed : 14.83 % Favored : 79.31 % 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: -0.84 (0.31), residues: 723 helix: 0.65 (0.29), residues: 315 sheet: -0.63 (0.58), residues: 91 loop : -1.79 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 204 HIS 0.006 0.001 HIS D 459 PHE 0.017 0.002 PHE D 122 TYR 0.012 0.001 TYR D 155 ARG 0.006 0.000 ARG F 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 ASN cc_start: 0.6681 (m-40) cc_final: 0.6297 (m-40) REVERT: D 182 GLU cc_start: 0.4608 (mt-10) cc_final: 0.4303 (mt-10) REVERT: D 215 LYS cc_start: 0.6769 (tptp) cc_final: 0.6457 (tptp) REVERT: D 229 MET cc_start: 0.5863 (tpt) cc_final: 0.5509 (tpt) REVERT: D 231 MET cc_start: 0.5236 (mmt) cc_final: 0.4722 (mmt) REVERT: D 249 GLN cc_start: 0.7761 (pp30) cc_final: 0.7229 (pp30) REVERT: D 272 GLN cc_start: 0.6869 (OUTLIER) cc_final: 0.6638 (pm20) REVERT: D 283 GLN cc_start: 0.6183 (tp-100) cc_final: 0.5719 (tp-100) REVERT: D 356 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7590 (mm) REVERT: D 357 LYS cc_start: 0.7989 (pttm) cc_final: 0.7658 (pttm) REVERT: D 359 GLU cc_start: 0.6923 (mm-30) cc_final: 0.6452 (mm-30) REVERT: D 395 LYS cc_start: 0.7751 (tmtt) cc_final: 0.7215 (tmtt) REVERT: E 63 GLN cc_start: 0.6862 (pm20) cc_final: 0.6514 (pm20) REVERT: F 64 ARG cc_start: 0.7210 (mmm-85) cc_final: 0.6865 (mmm-85) REVERT: F 69 PHE cc_start: 0.7183 (t80) cc_final: 0.6387 (t80) REVERT: F 78 ARG cc_start: 0.6942 (mmm160) cc_final: 0.6280 (mmm160) REVERT: F 102 LEU cc_start: 0.6148 (OUTLIER) cc_final: 0.5773 (pp) REVERT: F 117 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7279 (tppp) outliers start: 34 outliers final: 19 residues processed: 126 average time/residue: 0.2552 time to fit residues: 39.4742 Evaluate side-chains 128 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 0 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5597 Z= 0.295 Angle : 0.632 12.364 7569 Z= 0.332 Chirality : 0.045 0.153 889 Planarity : 0.005 0.041 1008 Dihedral : 7.275 59.118 804 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 5.86 % Allowed : 15.86 % Favored : 78.28 % 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: -0.85 (0.32), residues: 723 helix: 0.72 (0.30), residues: 312 sheet: -0.77 (0.58), residues: 91 loop : -1.82 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 204 HIS 0.005 0.001 HIS D 459 PHE 0.018 0.002 PHE D 122 TYR 0.013 0.001 TYR D 155 ARG 0.010 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 182 GLU cc_start: 0.4588 (mt-10) cc_final: 0.4303 (mt-10) REVERT: D 229 MET cc_start: 0.5851 (tpt) cc_final: 0.5542 (tpt) REVERT: D 249 GLN cc_start: 0.7743 (pp30) cc_final: 0.7228 (pp30) REVERT: D 272 GLN cc_start: 0.6867 (OUTLIER) cc_final: 0.6664 (pm20) REVERT: D 283 GLN cc_start: 0.6165 (tp-100) cc_final: 0.5705 (tp-100) REVERT: D 356 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7568 (mm) REVERT: D 357 LYS cc_start: 0.8012 (pttm) cc_final: 0.7682 (pttm) REVERT: D 359 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6403 (mm-30) REVERT: D 384 ARG cc_start: 0.6971 (ttm170) cc_final: 0.6668 (ttm170) REVERT: D 395 LYS cc_start: 0.7749 (tmtt) cc_final: 0.7391 (tmtt) REVERT: E 63 GLN cc_start: 0.6879 (pm20) cc_final: 0.6587 (pm20) REVERT: E 106 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7537 (ttp-170) REVERT: F 69 PHE cc_start: 0.7164 (t80) cc_final: 0.6381 (t80) REVERT: F 102 LEU cc_start: 0.6253 (OUTLIER) cc_final: 0.5868 (pp) REVERT: F 117 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7320 (tppp) outliers start: 34 outliers final: 20 residues processed: 126 average time/residue: 0.2509 time to fit residues: 38.4700 Evaluate side-chains 130 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 0.0170 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5597 Z= 0.213 Angle : 0.602 11.026 7569 Z= 0.310 Chirality : 0.044 0.298 889 Planarity : 0.004 0.037 1008 Dihedral : 7.143 59.628 804 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 6.03 % Allowed : 15.52 % Favored : 78.45 % 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: -0.58 (0.32), residues: 723 helix: 1.06 (0.30), residues: 306 sheet: -0.62 (0.60), residues: 89 loop : -1.76 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 204 HIS 0.005 0.001 HIS D 459 PHE 0.012 0.001 PHE D 122 TYR 0.008 0.001 TYR D 155 ARG 0.010 0.001 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 182 GLU cc_start: 0.4454 (mt-10) cc_final: 0.3835 (mt-10) REVERT: D 229 MET cc_start: 0.5709 (tpt) cc_final: 0.5391 (tpt) REVERT: D 272 GLN cc_start: 0.6858 (OUTLIER) cc_final: 0.6472 (pp30) REVERT: D 283 GLN cc_start: 0.6199 (tp-100) cc_final: 0.5748 (tp-100) REVERT: D 356 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7576 (mm) REVERT: D 357 LYS cc_start: 0.7989 (pttm) cc_final: 0.7669 (pttm) REVERT: D 359 GLU cc_start: 0.6896 (mm-30) cc_final: 0.6406 (mm-30) REVERT: D 395 LYS cc_start: 0.7726 (tmtt) cc_final: 0.7147 (tmtt) REVERT: E 63 GLN cc_start: 0.6844 (pm20) cc_final: 0.6600 (pm20) REVERT: E 106 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7476 (ttp-170) REVERT: F 64 ARG cc_start: 0.7099 (mmm-85) cc_final: 0.6874 (mmm-85) REVERT: F 69 PHE cc_start: 0.7152 (t80) cc_final: 0.6401 (t80) REVERT: F 102 LEU cc_start: 0.6250 (OUTLIER) cc_final: 0.5850 (pp) REVERT: F 117 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7775 (tmmm) REVERT: F 122 LYS cc_start: 0.8004 (tptt) cc_final: 0.7611 (tptt) outliers start: 35 outliers final: 22 residues processed: 126 average time/residue: 0.2345 time to fit residues: 36.5321 Evaluate side-chains 132 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 78 ARG Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 32 optimal weight: 0.0070 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN ** D 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5597 Z= 0.247 Angle : 0.612 11.636 7569 Z= 0.319 Chirality : 0.045 0.273 889 Planarity : 0.005 0.053 1008 Dihedral : 7.119 57.844 804 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 5.86 % Allowed : 17.59 % Favored : 76.55 % 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: -0.58 (0.32), residues: 723 helix: 1.06 (0.30), residues: 306 sheet: -0.61 (0.59), residues: 89 loop : -1.77 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 204 HIS 0.005 0.001 HIS D 459 PHE 0.015 0.001 PHE D 122 TYR 0.010 0.001 TYR D 155 ARG 0.011 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 90 GLU cc_start: 0.7752 (mp0) cc_final: 0.7212 (mp0) REVERT: D 182 GLU cc_start: 0.4339 (mt-10) cc_final: 0.3849 (mt-10) REVERT: D 215 LYS cc_start: 0.6735 (tptp) cc_final: 0.6421 (tptp) REVERT: D 229 MET cc_start: 0.5761 (tpt) cc_final: 0.5467 (tpt) REVERT: D 249 GLN cc_start: 0.7617 (pp30) cc_final: 0.7210 (pp30) REVERT: D 272 GLN cc_start: 0.6886 (OUTLIER) cc_final: 0.6479 (pp30) REVERT: D 283 GLN cc_start: 0.6247 (tp-100) cc_final: 0.5748 (tp-100) REVERT: D 356 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7579 (mm) REVERT: D 357 LYS cc_start: 0.7994 (pttm) cc_final: 0.7672 (pttm) REVERT: D 359 GLU cc_start: 0.6881 (mm-30) cc_final: 0.6397 (mm-30) REVERT: D 395 LYS cc_start: 0.7745 (tmtt) cc_final: 0.7130 (tmtt) REVERT: D 416 GLN cc_start: 0.8527 (pp30) cc_final: 0.8305 (pm20) REVERT: D 453 ASP cc_start: 0.7234 (t0) cc_final: 0.6886 (t0) REVERT: E 63 GLN cc_start: 0.6827 (pm20) cc_final: 0.6600 (pm20) REVERT: E 95 LEU cc_start: 0.8456 (mt) cc_final: 0.8235 (mp) REVERT: E 106 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7517 (ttp-170) REVERT: F 64 ARG cc_start: 0.7117 (mmm-85) cc_final: 0.6891 (mmm-85) REVERT: F 69 PHE cc_start: 0.7197 (t80) cc_final: 0.6431 (t80) REVERT: F 102 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5851 (pp) REVERT: F 117 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7846 (tmmm) REVERT: F 122 LYS cc_start: 0.8014 (tptt) cc_final: 0.7584 (tptt) outliers start: 34 outliers final: 24 residues processed: 130 average time/residue: 0.2339 time to fit residues: 37.4815 Evaluate side-chains 138 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 78 ARG Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 0.5980 chunk 21 optimal weight: 0.0060 chunk 13 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 0.0770 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.0570 chunk 55 optimal weight: 0.8980 chunk 64 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.2872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5597 Z= 0.185 Angle : 0.592 11.501 7569 Z= 0.307 Chirality : 0.044 0.237 889 Planarity : 0.004 0.037 1008 Dihedral : 6.983 57.319 804 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 5.69 % Allowed : 18.28 % Favored : 76.03 % 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 (0.32), residues: 723 helix: 1.20 (0.30), residues: 307 sheet: -0.35 (0.56), residues: 97 loop : -1.74 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 204 HIS 0.005 0.001 HIS D 459 PHE 0.014 0.001 PHE D 122 TYR 0.007 0.001 TYR F 72 ARG 0.007 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 90 GLU cc_start: 0.7676 (mp0) cc_final: 0.7147 (mp0) REVERT: D 215 LYS cc_start: 0.6694 (tptp) cc_final: 0.6400 (tptp) REVERT: D 229 MET cc_start: 0.5672 (tpt) cc_final: 0.5366 (tpt) REVERT: D 249 GLN cc_start: 0.7589 (pp30) cc_final: 0.7132 (pp30) REVERT: D 272 GLN cc_start: 0.6812 (OUTLIER) cc_final: 0.6422 (pp30) REVERT: D 283 GLN cc_start: 0.6140 (tp-100) cc_final: 0.5724 (tp-100) REVERT: D 356 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7538 (mm) REVERT: D 357 LYS cc_start: 0.7968 (pttm) cc_final: 0.7641 (pttm) REVERT: D 359 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6434 (mm-30) REVERT: D 395 LYS cc_start: 0.7733 (tmtt) cc_final: 0.7160 (tmtt) REVERT: F 69 PHE cc_start: 0.7142 (t80) cc_final: 0.6393 (t80) REVERT: F 102 LEU cc_start: 0.6192 (OUTLIER) cc_final: 0.5815 (pp) REVERT: F 111 LEU cc_start: 0.4905 (OUTLIER) cc_final: 0.3578 (mm) REVERT: F 117 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7415 (ttmm) REVERT: F 122 LYS cc_start: 0.8011 (tptt) cc_final: 0.7584 (tptt) outliers start: 33 outliers final: 20 residues processed: 125 average time/residue: 0.2185 time to fit residues: 33.8315 Evaluate side-chains 128 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 78 ARG Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 39 optimal weight: 0.0670 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5954 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5597 Z= 0.243 Angle : 0.625 11.312 7569 Z= 0.326 Chirality : 0.044 0.217 889 Planarity : 0.004 0.039 1008 Dihedral : 7.031 57.445 804 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 5.17 % Allowed : 18.97 % Favored : 75.86 % 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: -0.54 (0.32), residues: 723 helix: 1.04 (0.29), residues: 310 sheet: -0.48 (0.58), residues: 89 loop : -1.75 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 204 HIS 0.005 0.001 HIS D 459 PHE 0.015 0.001 PHE D 122 TYR 0.009 0.001 TYR D 155 ARG 0.008 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 90 GLU cc_start: 0.7703 (mp0) cc_final: 0.7168 (mp0) REVERT: D 215 LYS cc_start: 0.6747 (tptp) cc_final: 0.6432 (tptp) REVERT: D 229 MET cc_start: 0.5639 (tpt) cc_final: 0.5334 (tpt) REVERT: D 249 GLN cc_start: 0.7628 (pp30) cc_final: 0.7174 (pp30) REVERT: D 272 GLN cc_start: 0.6880 (OUTLIER) cc_final: 0.6485 (pp30) REVERT: D 283 GLN cc_start: 0.6187 (tp-100) cc_final: 0.5766 (tp-100) REVERT: D 356 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7574 (mm) REVERT: D 357 LYS cc_start: 0.7969 (pttm) cc_final: 0.7605 (pttm) REVERT: D 359 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6441 (mm-30) REVERT: D 395 LYS cc_start: 0.7704 (tmtt) cc_final: 0.7475 (tmtt) REVERT: F 69 PHE cc_start: 0.7182 (t80) cc_final: 0.6433 (t80) REVERT: F 102 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5809 (pp) REVERT: F 117 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7865 (tmmm) REVERT: F 122 LYS cc_start: 0.8042 (tptt) cc_final: 0.7608 (tptt) outliers start: 30 outliers final: 21 residues processed: 126 average time/residue: 0.2263 time to fit residues: 35.3193 Evaluate side-chains 128 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 72 optimal weight: 0.0870 chunk 66 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5970 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5597 Z= 0.269 Angle : 0.661 11.457 7569 Z= 0.344 Chirality : 0.045 0.219 889 Planarity : 0.005 0.081 1008 Dihedral : 7.000 58.462 802 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.66 % Allowed : 20.00 % Favored : 75.34 % 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: 723 helix: 0.99 (0.30), residues: 310 sheet: -0.53 (0.58), residues: 89 loop : -1.78 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 204 HIS 0.005 0.001 HIS D 459 PHE 0.016 0.001 PHE D 122 TYR 0.016 0.002 TYR D 415 ARG 0.008 0.001 ARG E 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 90 GLU cc_start: 0.7721 (mp0) cc_final: 0.7186 (mp0) REVERT: D 215 LYS cc_start: 0.6722 (tptp) cc_final: 0.6408 (tptp) REVERT: D 229 MET cc_start: 0.5673 (tpt) cc_final: 0.5369 (tpt) REVERT: D 249 GLN cc_start: 0.7672 (pp30) cc_final: 0.7250 (pp30) REVERT: D 272 GLN cc_start: 0.6903 (OUTLIER) cc_final: 0.6651 (pm20) REVERT: D 283 GLN cc_start: 0.6195 (tp-100) cc_final: 0.5785 (tp-100) REVERT: D 356 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7548 (mm) REVERT: D 357 LYS cc_start: 0.7997 (pttm) cc_final: 0.7651 (pttm) REVERT: D 359 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6437 (mm-30) REVERT: D 395 LYS cc_start: 0.7919 (tmtt) cc_final: 0.7558 (tmtt) REVERT: D 396 ARG cc_start: 0.7151 (tpt170) cc_final: 0.6914 (tpt170) REVERT: E 95 LEU cc_start: 0.8378 (mm) cc_final: 0.8163 (mt) REVERT: F 69 PHE cc_start: 0.7197 (t80) cc_final: 0.6460 (t80) REVERT: F 102 LEU cc_start: 0.6148 (OUTLIER) cc_final: 0.5765 (pp) REVERT: F 122 LYS cc_start: 0.8065 (tptt) cc_final: 0.7621 (tptt) outliers start: 27 outliers final: 22 residues processed: 117 average time/residue: 0.2365 time to fit residues: 34.0481 Evaluate side-chains 124 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 0.0040 chunk 24 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 3 optimal weight: 0.0670 chunk 41 optimal weight: 7.9990 overall best weight: 0.5132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 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 = 0.4524 r_free = 0.4524 target = 0.196082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.165684 restraints weight = 8761.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.170684 restraints weight = 5297.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.174458 restraints weight = 3499.246| |-----------------------------------------------------------------------------| r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5981 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5597 Z= 0.241 Angle : 0.656 11.401 7569 Z= 0.338 Chirality : 0.044 0.213 889 Planarity : 0.005 0.067 1008 Dihedral : 6.984 59.316 802 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.83 % Allowed : 20.00 % Favored : 75.17 % 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: -0.56 (0.32), residues: 723 helix: 1.06 (0.30), residues: 310 sheet: -0.54 (0.58), residues: 89 loop : -1.79 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 204 HIS 0.005 0.001 HIS D 459 PHE 0.015 0.001 PHE D 122 TYR 0.014 0.002 TYR D 415 ARG 0.011 0.000 ARG F 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1598.86 seconds wall clock time: 29 minutes 35.91 seconds (1775.91 seconds total)