Starting phenix.real_space_refine on Thu Mar 6 09:52:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gb3_29912/03_2025/8gb3_29912.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gb3_29912/03_2025/8gb3_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/cci-nas-00/data/ceres_data/8gb3_29912/03_2025/8gb3_29912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gb3_29912/03_2025/8gb3_29912.map" model { file = "/net/cci-nas-00/data/ceres_data/8gb3_29912/03_2025/8gb3_29912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gb3_29912/03_2025/8gb3_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-5624/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: 4.16, per 1000 atoms: 0.75 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: 1.23 Conformation dependent library (CDL) restraints added in 673.6 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: 1.38 Time building geometry restraints manager: 1.50 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.960 Find NCS groups from input model: 0.050 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.360 ------------------------------------------------------------------------------- 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 : 0.522 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: 0.2278 time to fit residues: 38.2542 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 : 0.600 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.192226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.161940 restraints weight = 8820.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.166655 restraints weight = 5327.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.169799 restraints weight = 3569.561| |-----------------------------------------------------------------------------| r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 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 : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 ASN cc_start: 0.6631 (m-40) cc_final: 0.6321 (m-40) REVERT: D 49 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.7000 (mp) REVERT: D 166 ILE cc_start: 0.7453 (tp) cc_final: 0.7211 (tp) REVERT: D 182 GLU cc_start: 0.4594 (mt-10) cc_final: 0.4093 (mt-10) REVERT: D 229 MET cc_start: 0.5950 (tpt) cc_final: 0.5728 (tpt) REVERT: D 283 GLN cc_start: 0.6200 (tp-100) cc_final: 0.5723 (tp-100) REVERT: D 333 LYS cc_start: 0.7160 (ttmt) cc_final: 0.6828 (ttmt) REVERT: D 356 LEU cc_start: 0.8064 (mm) cc_final: 0.7697 (mm) REVERT: D 359 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6549 (mm-30) REVERT: D 395 LYS cc_start: 0.7687 (tmtt) cc_final: 0.7371 (tmtt) REVERT: D 416 GLN cc_start: 0.7793 (pm20) cc_final: 0.7577 (pm20) REVERT: E 63 GLN cc_start: 0.6679 (pm20) cc_final: 0.6450 (pm20) REVERT: F 69 PHE cc_start: 0.7384 (t80) cc_final: 0.6519 (t80) REVERT: F 75 ARG cc_start: 0.7021 (ttp-110) cc_final: 0.6707 (ttp-110) REVERT: F 78 ARG cc_start: 0.6956 (mmm160) cc_final: 0.6398 (mmm160) REVERT: F 102 LEU cc_start: 0.6084 (OUTLIER) cc_final: 0.5745 (pp) REVERT: F 117 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7212 (tppp) outliers start: 32 outliers final: 19 residues processed: 132 average time/residue: 0.2240 time to fit residues: 36.3306 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 : 0.552 ------------------------------------------------------------------------------- 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 11 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 33 optimal weight: 0.0970 chunk 61 optimal weight: 3.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.194741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.163831 restraints weight = 8648.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.168965 restraints weight = 5125.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.172657 restraints weight = 3374.890| |-----------------------------------------------------------------------------| r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6015 moved from start: 0.1529 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= 0.274 Angle : 0.624 12.069 7569 Z= 0.325 Chirality : 0.045 0.165 889 Planarity : 0.004 0.039 1008 Dihedral : 7.136 59.528 804 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 5.52 % Allowed : 14.83 % Favored : 79.66 % 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: -0.83 (0.32), residues: 723 helix: 0.57 (0.29), residues: 315 sheet: -0.56 (0.55), residues: 99 loop : -1.74 (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 0.018 0.002 PHE D 122 TYR 0.009 0.001 TYR D 155 ARG 0.007 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 139 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 45 ASN cc_start: 0.6606 (m-40) cc_final: 0.6244 (m-40) REVERT: D 166 ILE cc_start: 0.7435 (tp) cc_final: 0.7220 (tp) REVERT: D 182 GLU cc_start: 0.4633 (mt-10) cc_final: 0.4310 (mt-10) REVERT: D 229 MET cc_start: 0.5764 (tpt) cc_final: 0.5397 (tpt) REVERT: D 231 MET cc_start: 0.5315 (mmt) cc_final: 0.4648 (mmt) REVERT: D 283 GLN cc_start: 0.6240 (tp-100) cc_final: 0.5700 (tp-100) REVERT: D 297 ILE cc_start: 0.2893 (OUTLIER) cc_final: 0.2488 (tt) REVERT: D 356 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7619 (mm) REVERT: D 357 LYS cc_start: 0.7966 (pttm) cc_final: 0.7633 (pttm) REVERT: D 359 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6503 (mm-30) REVERT: D 395 LYS cc_start: 0.7736 (tmtt) cc_final: 0.7364 (tmtt) REVERT: D 416 GLN cc_start: 0.7819 (pm20) cc_final: 0.7612 (pm20) REVERT: E 63 GLN cc_start: 0.6827 (pm20) cc_final: 0.6497 (pm20) REVERT: F 69 PHE cc_start: 0.7253 (t80) cc_final: 0.6492 (t80) REVERT: F 78 ARG cc_start: 0.6897 (mmm160) cc_final: 0.6312 (mmm160) REVERT: F 102 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5844 (pp) REVERT: F 117 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7198 (tppp) outliers start: 32 outliers final: 17 residues processed: 128 average time/residue: 0.2233 time to fit residues: 35.2070 Evaluate side-chains 127 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 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 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 102 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 45 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 9 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 67 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 64 optimal weight: 20.0000 chunk 21 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 57 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.196653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.166491 restraints weight = 9046.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.171504 restraints weight = 5332.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.175284 restraints weight = 3481.089| |-----------------------------------------------------------------------------| r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5985 moved from start: 0.1777 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= 0.236 Angle : 0.610 12.276 7569 Z= 0.316 Chirality : 0.044 0.139 889 Planarity : 0.004 0.038 1008 Dihedral : 7.042 58.000 804 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 5.69 % Allowed : 14.31 % Favored : 80.00 % 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: -0.65 (0.32), residues: 723 helix: 0.82 (0.29), residues: 315 sheet: -0.50 (0.56), residues: 99 loop : -1.74 (0.36), residues: 309 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 0.014 0.001 PHE D 122 TYR 0.009 0.001 TYR D 155 ARG 0.007 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: 33 poor density : 108 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 45 ASN cc_start: 0.6536 (m-40) cc_final: 0.6194 (m-40) REVERT: D 166 ILE cc_start: 0.7403 (tp) cc_final: 0.7202 (tp) REVERT: D 182 GLU cc_start: 0.4490 (mt-10) cc_final: 0.3631 (mt-10) REVERT: D 215 LYS cc_start: 0.6710 (tptp) cc_final: 0.6434 (tptp) REVERT: D 229 MET cc_start: 0.5747 (tpt) cc_final: 0.5470 (tpt) REVERT: D 249 GLN cc_start: 0.7659 (pp30) cc_final: 0.7175 (pp30) REVERT: D 272 GLN cc_start: 0.6815 (OUTLIER) cc_final: 0.6601 (pm20) REVERT: D 283 GLN cc_start: 0.6110 (tp-100) cc_final: 0.5635 (tp-100) REVERT: D 297 ILE cc_start: 0.2954 (OUTLIER) cc_final: 0.2468 (tt) REVERT: D 356 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7590 (mm) REVERT: D 357 LYS cc_start: 0.7902 (pttm) cc_final: 0.7604 (pttm) REVERT: D 359 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6461 (mm-30) REVERT: D 395 LYS cc_start: 0.7686 (tmtt) cc_final: 0.7344 (tmtt) REVERT: E 63 GLN cc_start: 0.6807 (pm20) cc_final: 0.6540 (pm20) REVERT: F 69 PHE cc_start: 0.7193 (t80) cc_final: 0.6388 (t80) REVERT: F 78 ARG cc_start: 0.6846 (mmm160) cc_final: 0.6220 (mmm160) REVERT: F 117 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7229 (tppp) outliers start: 33 outliers final: 22 residues processed: 124 average time/residue: 0.2787 time to fit residues: 42.3886 Evaluate side-chains 131 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 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 377 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 E residue 96 LEU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 145 VAL 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 117 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 57 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 24 optimal weight: 0.0970 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.194547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.164535 restraints weight = 8893.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.169536 restraints weight = 5314.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.173218 restraints weight = 3501.297| |-----------------------------------------------------------------------------| r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6003 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 5597 Z= 0.263 Angle : 0.625 12.535 7569 Z= 0.326 Chirality : 0.044 0.137 889 Planarity : 0.004 0.041 1008 Dihedral : 7.081 58.273 804 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 6.03 % Allowed : 16.21 % Favored : 77.76 % 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: 309 sheet: -0.75 (0.58), residues: 92 loop : -1.69 (0.35), residues: 322 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 0.012 0.001 TYR D 155 ARG 0.009 0.000 ARG F 75 *********************** 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: 35 poor density : 104 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 229 MET cc_start: 0.5745 (tpt) cc_final: 0.5453 (tpt) REVERT: D 249 GLN cc_start: 0.7677 (pp30) cc_final: 0.7136 (pp30) REVERT: D 283 GLN cc_start: 0.6136 (tp-100) cc_final: 0.5689 (tp-100) REVERT: D 297 ILE cc_start: 0.3005 (OUTLIER) cc_final: 0.2563 (tt) REVERT: D 356 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7616 (mm) REVERT: D 357 LYS cc_start: 0.7929 (pttm) cc_final: 0.7627 (pttm) REVERT: D 359 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6449 (mm-30) REVERT: D 395 LYS cc_start: 0.7685 (tmtt) cc_final: 0.7142 (tmtt) REVERT: E 63 GLN cc_start: 0.6792 (pm20) cc_final: 0.6565 (pm20) REVERT: E 106 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7404 (ttp-170) REVERT: F 64 ARG cc_start: 0.7099 (mmm-85) cc_final: 0.6812 (mmm-85) REVERT: F 69 PHE cc_start: 0.7238 (t80) cc_final: 0.6448 (t80) REVERT: F 102 LEU cc_start: 0.6168 (OUTLIER) cc_final: 0.5781 (pp) REVERT: F 117 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7731 (tmmm) REVERT: F 122 LYS cc_start: 0.7962 (tptt) cc_final: 0.7635 (tptt) outliers start: 35 outliers final: 22 residues processed: 125 average time/residue: 0.2252 time to fit residues: 34.5127 Evaluate side-chains 130 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 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 377 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 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 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 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.0470 chunk 3 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 49 optimal weight: 20.0000 chunk 23 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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** E 80 GLN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.194670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.164194 restraints weight = 8892.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.169274 restraints weight = 5283.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.173083 restraints weight = 3449.026| |-----------------------------------------------------------------------------| r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5597 Z= 0.245 Angle : 0.611 11.132 7569 Z= 0.319 Chirality : 0.044 0.141 889 Planarity : 0.004 0.037 1008 Dihedral : 6.900 58.873 802 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 6.03 % Allowed : 14.83 % Favored : 79.14 % 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: -0.61 (0.32), residues: 723 helix: 1.02 (0.30), residues: 306 sheet: -0.74 (0.58), residues: 92 loop : -1.72 (0.34), residues: 325 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 0.016 0.001 PHE D 122 TYR 0.010 0.001 TYR D 155 ARG 0.007 0.000 ARG F 75 *********************** 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 144 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: D 107 LEU cc_start: 0.7482 (mp) cc_final: 0.6480 (mt) REVERT: D 215 LYS cc_start: 0.6738 (tptp) cc_final: 0.6433 (tptp) REVERT: D 229 MET cc_start: 0.5617 (tpt) cc_final: 0.5315 (tpt) REVERT: D 249 GLN cc_start: 0.7721 (pp30) cc_final: 0.7165 (pp30) REVERT: D 283 GLN cc_start: 0.6194 (tp-100) cc_final: 0.5749 (tp-100) REVERT: D 356 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7595 (mm) REVERT: D 357 LYS cc_start: 0.7935 (pttm) cc_final: 0.7664 (pttm) REVERT: D 359 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6427 (mm-30) REVERT: D 395 LYS cc_start: 0.7692 (tmtt) cc_final: 0.7113 (tmtt) REVERT: D 455 ASN cc_start: 0.6983 (m-40) cc_final: 0.6779 (p0) REVERT: E 63 GLN cc_start: 0.6792 (pm20) cc_final: 0.6587 (pm20) REVERT: E 106 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7391 (ttp-170) REVERT: F 64 ARG cc_start: 0.7102 (mmm-85) cc_final: 0.6857 (mmm-85) REVERT: F 69 PHE cc_start: 0.7231 (t80) cc_final: 0.6437 (t80) REVERT: F 102 LEU cc_start: 0.6191 (OUTLIER) cc_final: 0.5831 (pp) REVERT: F 111 LEU cc_start: 0.4843 (OUTLIER) cc_final: 0.3523 (mm) REVERT: F 117 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7320 (ttmm) REVERT: F 122 LYS cc_start: 0.7908 (tptt) cc_final: 0.7590 (tptt) outliers start: 35 outliers final: 22 residues processed: 129 average time/residue: 0.2394 time to fit residues: 37.7538 Evaluate side-chains 134 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 145 VAL 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 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 377 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 102 LEU Chi-restraints excluded: chain F residue 111 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 59 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 21 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 7 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 61 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.195789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.165528 restraints weight = 8825.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.170561 restraints weight = 5284.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.173978 restraints weight = 3477.739| |-----------------------------------------------------------------------------| r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5988 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5597 Z= 0.236 Angle : 0.622 11.500 7569 Z= 0.329 Chirality : 0.045 0.190 889 Planarity : 0.005 0.109 1008 Dihedral : 6.883 59.048 802 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 6.21 % Allowed : 16.38 % Favored : 77.41 % 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: -0.59 (0.32), residues: 723 helix: 1.04 (0.30), residues: 306 sheet: -0.73 (0.58), residues: 92 loop : -1.72 (0.35), residues: 325 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 0.018 0.001 PHE D 122 TYR 0.008 0.001 TYR D 415 ARG 0.005 0.000 ARG F 75 *********************** 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 145 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: D 90 GLU cc_start: 0.7753 (mp0) cc_final: 0.7236 (mp0) REVERT: D 215 LYS cc_start: 0.6726 (tptp) cc_final: 0.6418 (tptp) REVERT: D 229 MET cc_start: 0.5622 (tpt) cc_final: 0.5328 (tpt) REVERT: D 283 GLN cc_start: 0.6191 (tp-100) cc_final: 0.5690 (tp-100) REVERT: D 356 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7594 (mm) REVERT: D 357 LYS cc_start: 0.7923 (pttm) cc_final: 0.7651 (pttm) REVERT: D 359 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6452 (mm-30) REVERT: D 382 MET cc_start: 0.6384 (OUTLIER) cc_final: 0.6083 (ttp) REVERT: D 395 LYS cc_start: 0.7672 (tmtt) cc_final: 0.7044 (tmtt) REVERT: D 416 GLN cc_start: 0.8532 (pp30) cc_final: 0.8320 (pm20) REVERT: E 106 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7356 (ttp-170) REVERT: F 69 PHE cc_start: 0.7272 (t80) cc_final: 0.6465 (t80) REVERT: F 102 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.5874 (pp) REVERT: F 111 LEU cc_start: 0.4843 (OUTLIER) cc_final: 0.3518 (mm) REVERT: F 117 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7336 (ttmm) REVERT: F 122 LYS cc_start: 0.7891 (tptt) cc_final: 0.7566 (tptt) outliers start: 36 outliers final: 22 residues processed: 128 average time/residue: 0.2214 time to fit residues: 34.9591 Evaluate side-chains 135 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 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 377 THR Chi-restraints excluded: chain D residue 382 MET 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 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 111 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 4 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 10 optimal weight: 0.0000 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 61 ASN ** D 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.195974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.166243 restraints weight = 8856.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.171095 restraints weight = 5387.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.174426 restraints weight = 3552.332| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5985 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 : 0.004 0.045 5597 Z= 0.248 Angle : 0.642 11.526 7569 Z= 0.337 Chirality : 0.045 0.167 889 Planarity : 0.004 0.036 1008 Dihedral : 6.880 58.970 802 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 5.52 % Allowed : 17.76 % Favored : 76.72 % 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: -0.64 (0.32), residues: 723 helix: 0.94 (0.30), residues: 307 sheet: -0.51 (0.59), residues: 89 loop : -1.77 (0.34), residues: 327 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 0.001 PHE D 122 TYR 0.010 0.001 TYR D 155 ARG 0.004 0.000 ARG F 75 *********************** 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 134 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 90 GLU cc_start: 0.7731 (mp0) cc_final: 0.7235 (mp0) REVERT: D 215 LYS cc_start: 0.6733 (tptp) cc_final: 0.6430 (tptp) REVERT: D 229 MET cc_start: 0.5669 (tpt) cc_final: 0.5390 (tpt) REVERT: D 249 GLN cc_start: 0.7576 (pp30) cc_final: 0.7198 (pp30) REVERT: D 283 GLN cc_start: 0.6121 (tp-100) cc_final: 0.5707 (tp-100) REVERT: D 356 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7586 (mm) REVERT: D 357 LYS cc_start: 0.7929 (pttm) cc_final: 0.7664 (pttm) REVERT: D 359 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6443 (mm-30) REVERT: D 384 ARG cc_start: 0.6996 (tpp80) cc_final: 0.6792 (tpp80) REVERT: D 395 LYS cc_start: 0.7617 (tmtt) cc_final: 0.7250 (tmtt) REVERT: E 106 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7377 (ttp-170) REVERT: F 69 PHE cc_start: 0.7281 (t80) cc_final: 0.6480 (t80) REVERT: F 102 LEU cc_start: 0.6257 (OUTLIER) cc_final: 0.5885 (pp) REVERT: F 111 LEU cc_start: 0.4865 (OUTLIER) cc_final: 0.3534 (mm) REVERT: F 117 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7334 (ttmm) REVERT: F 122 LYS cc_start: 0.7785 (tptt) cc_final: 0.7545 (tptt) outliers start: 32 outliers final: 22 residues processed: 121 average time/residue: 0.2903 time to fit residues: 43.4782 Evaluate side-chains 127 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 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 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 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 377 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 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 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 51 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 6 optimal weight: 0.0970 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.0970 chunk 9 optimal weight: 0.1980 chunk 66 optimal weight: 0.5980 chunk 40 optimal weight: 0.0060 overall best weight: 0.1392 ------------------------------------------------------------------------------- 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 61 ASN D 389 ASN D 455 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.200060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.170433 restraints weight = 8879.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.175474 restraints weight = 5323.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.179196 restraints weight = 3480.440| |-----------------------------------------------------------------------------| r_work (final): 0.4320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5887 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5597 Z= 0.182 Angle : 0.630 11.585 7569 Z= 0.328 Chirality : 0.043 0.188 889 Planarity : 0.004 0.038 1008 Dihedral : 6.660 58.563 802 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.66 % Allowed : 18.62 % Favored : 76.72 % 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: -0.43 (0.32), residues: 723 helix: 1.13 (0.29), residues: 313 sheet: 0.21 (0.59), residues: 88 loop : -1.94 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 77 HIS 0.004 0.001 HIS D 459 PHE 0.016 0.001 PHE D 122 TYR 0.010 0.001 TYR F 72 ARG 0.004 0.000 ARG F 75 *********************** 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 132 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 215 LYS cc_start: 0.6698 (tptp) cc_final: 0.6348 (tptp) REVERT: D 229 MET cc_start: 0.5485 (tpt) cc_final: 0.5214 (tpt) REVERT: D 249 GLN cc_start: 0.7508 (pp30) cc_final: 0.7095 (pp30) REVERT: D 283 GLN cc_start: 0.6070 (tp-100) cc_final: 0.5672 (tp-100) REVERT: D 356 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7571 (mm) REVERT: D 359 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6582 (mm-30) REVERT: D 395 LYS cc_start: 0.7573 (tmtt) cc_final: 0.7204 (tmtt) REVERT: D 396 ARG cc_start: 0.6974 (tpt170) cc_final: 0.6715 (tpt170) REVERT: D 416 GLN cc_start: 0.8660 (pp30) cc_final: 0.7982 (pm20) REVERT: D 418 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.5246 (mm-30) REVERT: E 106 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7359 (ttp-170) REVERT: F 69 PHE cc_start: 0.7191 (t80) cc_final: 0.6420 (t80) REVERT: F 102 LEU cc_start: 0.6223 (OUTLIER) cc_final: 0.5866 (pp) outliers start: 27 outliers final: 15 residues processed: 118 average time/residue: 0.2740 time to fit residues: 39.5855 Evaluate side-chains 122 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 145 VAL 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 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 106 ARG Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 102 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 50 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 0.0270 chunk 60 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 389 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.198839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.168589 restraints weight = 8873.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.173704 restraints weight = 5306.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.177475 restraints weight = 3474.666| |-----------------------------------------------------------------------------| r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5956 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5597 Z= 0.253 Angle : 0.669 13.657 7569 Z= 0.349 Chirality : 0.046 0.194 889 Planarity : 0.004 0.035 1008 Dihedral : 6.435 53.124 798 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 4.14 % Allowed : 19.31 % 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: -0.52 (0.32), residues: 723 helix: 1.06 (0.29), residues: 310 sheet: -0.24 (0.55), residues: 97 loop : -1.86 (0.35), residues: 316 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 0.001 PHE D 122 TYR 0.010 0.001 TYR D 155 ARG 0.004 0.000 ARG F 75 ********************** 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 128 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 215 LYS cc_start: 0.6684 (tptp) cc_final: 0.6351 (tptm) REVERT: D 229 MET cc_start: 0.5614 (tpt) cc_final: 0.5254 (tpt) REVERT: D 231 MET cc_start: 0.5224 (mmt) cc_final: 0.4654 (mmt) REVERT: D 249 GLN cc_start: 0.7586 (pp30) cc_final: 0.7196 (pp30) REVERT: D 283 GLN cc_start: 0.6171 (tp-100) cc_final: 0.5773 (tp-100) REVERT: D 356 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7558 (mm) REVERT: D 359 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6481 (mm-30) REVERT: D 384 ARG cc_start: 0.7132 (tpp80) cc_final: 0.6809 (ttm-80) REVERT: D 395 LYS cc_start: 0.7606 (tmtt) cc_final: 0.7235 (tmtt) REVERT: D 396 ARG cc_start: 0.6989 (tpt170) cc_final: 0.6677 (tpt170) REVERT: D 416 GLN cc_start: 0.8693 (pp30) cc_final: 0.8064 (pm20) REVERT: F 102 LEU cc_start: 0.6311 (OUTLIER) cc_final: 0.5952 (pp) outliers start: 24 outliers final: 18 residues processed: 119 average time/residue: 0.2693 time to fit residues: 38.9353 Evaluate side-chains 122 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 145 VAL 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 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 14 optimal weight: 0.5980 chunk 44 optimal weight: 0.0570 chunk 60 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.199936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.167773 restraints weight = 9005.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.173122 restraints weight = 5416.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.176703 restraints weight = 3581.412| |-----------------------------------------------------------------------------| r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5977 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5597 Z= 0.231 Angle : 0.676 13.865 7569 Z= 0.352 Chirality : 0.045 0.175 889 Planarity : 0.004 0.036 1008 Dihedral : 6.432 52.892 798 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.14 % Allowed : 20.17 % Favored : 75.69 % 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 (0.31), residues: 723 helix: 0.88 (0.29), residues: 311 sheet: -0.19 (0.56), residues: 97 loop : -1.86 (0.35), residues: 315 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 0.001 PHE D 122 TYR 0.006 0.001 TYR D 155 ARG 0.004 0.000 ARG D 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2313.06 seconds wall clock time: 42 minutes 15.40 seconds (2535.40 seconds total)