Starting phenix.real_space_refine on Tue Feb 11 17:35:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9blu_44677/02_2025/9blu_44677.cif Found real_map, /net/cci-nas-00/data/ceres_data/9blu_44677/02_2025/9blu_44677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9blu_44677/02_2025/9blu_44677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9blu_44677/02_2025/9blu_44677.map" model { file = "/net/cci-nas-00/data/ceres_data/9blu_44677/02_2025/9blu_44677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9blu_44677/02_2025/9blu_44677.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 4020 2.51 5 N 1102 2.21 5 O 1233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6377 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3848 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 20, 'TRANS': 490} Chain breaks: 1 Chain: "B" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1270 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "C" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1259 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 7, 'TRANS': 151} Time building chain proxies: 4.61, per 1000 atoms: 0.72 Number of scatterers: 6377 At special positions: 0 Unit cell: (76.44, 120.54, 111.72, 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 22 16.00 O 1233 8.00 N 1102 7.00 C 4020 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: 1.53 Conformation dependent library (CDL) restraints added in 937.2 milliseconds 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1532 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 12 sheets defined 43.3% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 120 through 124 removed outlier: 3.885A pdb=" N ILE A 124 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 140 removed outlier: 4.392A pdb=" N LYS A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 183 removed outlier: 3.536A pdb=" N ILE A 166 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A 167 " --> pdb=" O PRO A 163 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 removed outlier: 3.603A pdb=" N SER A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 274 through 294 removed outlier: 4.173A pdb=" N PHE A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 319 Processing helix chain 'A' and resid 348 through 355 Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 363 through 373 Processing helix chain 'A' and resid 392 through 404 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.562A pdb=" N ILE A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 437 removed outlier: 4.046A pdb=" N LEU A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 102 Processing helix chain 'B' and resid 104 through 125 removed outlier: 5.056A pdb=" N GLU B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL B 114 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 158 removed outlier: 3.549A pdb=" N ASN B 139 " --> pdb=" O PRO B 135 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 125 removed outlier: 3.581A pdb=" N VAL C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLU C 113 " --> pdb=" O LYS C 109 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL C 125 " --> pdb=" O ALA C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 158 removed outlier: 3.728A pdb=" N ASN C 139 " --> pdb=" O PRO C 135 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU C 140 " --> pdb=" O HIS C 136 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 77 removed outlier: 3.703A pdb=" N GLN A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 77 removed outlier: 3.703A pdb=" N GLN A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N MET A 70 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL A 55 " --> pdb=" O MET A 70 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL A 56 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N THR A 192 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE A 58 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA A 189 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL A 219 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE A 191 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASN A 221 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL A 193 " --> pdb=" O ASN A 221 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 146 Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 270 Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 335 removed outlier: 4.015A pdb=" N TYR A 331 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS A 340 " --> pdb=" O TYR A 331 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR A 333 " --> pdb=" O GLY A 338 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLY A 338 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 445 through 447 Processing sheet with id=AA8, first strand: chain 'A' and resid 468 through 473 removed outlier: 3.607A pdb=" N LYS A 468 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 533 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL A 532 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE A 545 " --> pdb=" O VAL A 532 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 175 through 179 removed outlier: 7.289A pdb=" N VAL B 213 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU B 210 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL B 194 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLY B 212 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 199 through 201 removed outlier: 6.553A pdb=" N TYR B 199 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 160 through 163 removed outlier: 3.563A pdb=" N GLY C 198 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR C 199 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 175 through 180 removed outlier: 7.299A pdb=" N VAL C 213 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N HIS C 180 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU C 193 " --> pdb=" O GLY C 212 " (cutoff:3.500A) 326 hydrogen bonds defined for protein. 942 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: 2.07 Time building geometry restraints manager: 1.79 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: 2149 1.34 - 1.46: 1031 1.46 - 1.58: 3250 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 6466 Sorted by residual: bond pdb=" SD MET A 174 " pdb=" CE MET A 174 " ideal model delta sigma weight residual 1.791 1.768 0.023 2.50e-02 1.60e+03 8.39e-01 bond pdb=" CB GLU A 155 " pdb=" CG GLU A 155 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.01e-01 bond pdb=" CB ARG A 360 " pdb=" CG ARG A 360 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 7.85e-01 bond pdb=" CA PRO B 165 " pdb=" C PRO B 165 " ideal model delta sigma weight residual 1.527 1.518 0.009 1.07e-02 8.73e+03 7.20e-01 bond pdb=" N PRO B 165 " pdb=" CA PRO B 165 " ideal model delta sigma weight residual 1.479 1.467 0.013 1.71e-02 3.42e+03 5.67e-01 ... (remaining 6461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 8630 1.61 - 3.21: 82 3.21 - 4.82: 14 4.82 - 6.43: 3 6.43 - 8.04: 2 Bond angle restraints: 8731 Sorted by residual: angle pdb=" CB MET A 46 " pdb=" CG MET A 46 " pdb=" SD MET A 46 " ideal model delta sigma weight residual 112.70 120.74 -8.04 3.00e+00 1.11e-01 7.18e+00 angle pdb=" CA ARG A 360 " pdb=" CB ARG A 360 " pdb=" CG ARG A 360 " ideal model delta sigma weight residual 114.10 119.03 -4.93 2.00e+00 2.50e-01 6.07e+00 angle pdb=" CB GLU A 155 " pdb=" CG GLU A 155 " pdb=" CD GLU A 155 " ideal model delta sigma weight residual 112.60 116.76 -4.16 1.70e+00 3.46e-01 6.00e+00 angle pdb=" CA GLU A 155 " pdb=" CB GLU A 155 " pdb=" CG GLU A 155 " ideal model delta sigma weight residual 114.10 118.71 -4.61 2.00e+00 2.50e-01 5.31e+00 angle pdb=" N MET A 174 " pdb=" CA MET A 174 " pdb=" CB MET A 174 " ideal model delta sigma weight residual 110.28 113.66 -3.38 1.55e+00 4.16e-01 4.76e+00 ... (remaining 8726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 3339 17.93 - 35.87: 445 35.87 - 53.80: 165 53.80 - 71.74: 30 71.74 - 89.67: 10 Dihedral angle restraints: 3989 sinusoidal: 1614 harmonic: 2375 Sorted by residual: dihedral pdb=" CB GLU C 63 " pdb=" CG GLU C 63 " pdb=" CD GLU C 63 " pdb=" OE1 GLU C 63 " ideal model delta sinusoidal sigma weight residual 0.00 -89.67 89.67 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG A 513 " pdb=" CD ARG A 513 " pdb=" NE ARG A 513 " pdb=" CZ ARG A 513 " ideal model delta sinusoidal sigma weight residual 180.00 135.25 44.75 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA ASP A 556 " pdb=" CB ASP A 556 " pdb=" CG ASP A 556 " pdb=" OD1 ASP A 556 " ideal model delta sinusoidal sigma weight residual -30.00 -83.43 53.43 1 2.00e+01 2.50e-03 9.70e+00 ... (remaining 3986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 612 0.027 - 0.054: 249 0.054 - 0.080: 81 0.080 - 0.107: 58 0.107 - 0.134: 22 Chirality restraints: 1022 Sorted by residual: chirality pdb=" CB ILE A 524 " pdb=" CA ILE A 524 " pdb=" CG1 ILE A 524 " pdb=" CG2 ILE A 524 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE A 144 " pdb=" N ILE A 144 " pdb=" C ILE A 144 " pdb=" CB ILE A 144 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA ILE A 508 " pdb=" N ILE A 508 " pdb=" C ILE A 508 " pdb=" CB ILE A 508 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 1019 not shown) Planarity restraints: 1134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 103 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO A 104 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 125 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO C 126 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 126 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 126 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 392 " -0.016 5.00e-02 4.00e+02 2.43e-02 9.43e-01 pdb=" N PRO A 393 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 393 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 393 " -0.014 5.00e-02 4.00e+02 ... (remaining 1131 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 746 2.75 - 3.29: 5959 3.29 - 3.83: 10368 3.83 - 4.36: 11124 4.36 - 4.90: 20498 Nonbonded interactions: 48695 Sorted by model distance: nonbonded pdb=" O GLU A 352 " pdb=" OG1 THR A 356 " model vdw 2.214 3.040 nonbonded pdb=" OD2 ASP B 110 " pdb=" NE2 HIS C 158 " model vdw 2.257 3.120 nonbonded pdb=" NH2 ARG A 391 " pdb=" OD2 ASP A 414 " model vdw 2.300 3.120 nonbonded pdb=" OH TYR A 230 " pdb=" O LEU A 385 " model vdw 2.328 3.040 nonbonded pdb=" NH2 ARG A 202 " pdb=" OD1 ASN A 221 " model vdw 2.331 3.120 ... (remaining 48690 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 Found NCS groups: ncs_group { reference = (chain 'B' and resid 59 through 217) selection = chain 'C' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.670 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 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 0.027 6466 Z= 0.180 Angle : 0.453 8.036 8731 Z= 0.233 Chirality : 0.040 0.134 1022 Planarity : 0.003 0.041 1134 Dihedral : 18.948 89.669 2457 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.18 % Allowed : 29.91 % Favored : 66.91 % 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: 1.22 (0.31), residues: 823 helix: 2.54 (0.28), residues: 328 sheet: 0.69 (0.57), residues: 104 loop : -0.70 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 126 HIS 0.003 0.001 HIS A 341 PHE 0.007 0.001 PHE B 179 TYR 0.012 0.001 TYR C 78 ARG 0.001 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 69 VAL cc_start: 0.8449 (OUTLIER) cc_final: 0.8067 (m) REVERT: A 254 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7519 (mm) REVERT: A 345 LYS cc_start: 0.7831 (tptp) cc_final: 0.6998 (mmtt) REVERT: A 508 ILE cc_start: -0.1736 (OUTLIER) cc_final: -0.2409 (tt) REVERT: B 201 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7747 (pp) REVERT: C 90 GLN cc_start: 0.6396 (OUTLIER) cc_final: 0.5915 (mt0) outliers start: 22 outliers final: 16 residues processed: 62 average time/residue: 0.1480 time to fit residues: 13.4817 Evaluate side-chains 64 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 211 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 34 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 33 optimal weight: 0.0070 chunk 64 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 74 optimal weight: 0.4980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.206098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.140566 restraints weight = 7051.113| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.59 r_work: 0.3515 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6466 Z= 0.156 Angle : 0.453 6.947 8731 Z= 0.238 Chirality : 0.041 0.141 1022 Planarity : 0.003 0.039 1134 Dihedral : 5.198 41.230 902 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.76 % Allowed : 28.90 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.31), residues: 823 helix: 2.94 (0.28), residues: 325 sheet: 0.65 (0.52), residues: 113 loop : -0.74 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 126 HIS 0.001 0.000 HIS A 184 PHE 0.007 0.001 PHE B 179 TYR 0.011 0.001 TYR A 243 ARG 0.002 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 45 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7873 (tp) REVERT: A 159 LYS cc_start: 0.8066 (mtpp) cc_final: 0.7809 (mtpp) REVERT: A 300 LYS cc_start: 0.7802 (pttm) cc_final: 0.7203 (pttm) REVERT: A 345 LYS cc_start: 0.7657 (tptp) cc_final: 0.7071 (mptt) REVERT: A 424 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6339 (tp-100) REVERT: C 90 GLN cc_start: 0.6460 (OUTLIER) cc_final: 0.5946 (mt0) outliers start: 26 outliers final: 13 residues processed: 68 average time/residue: 0.1545 time to fit residues: 14.8774 Evaluate side-chains 61 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 32 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 74 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.207094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.141632 restraints weight = 7041.012| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.57 r_work: 0.3497 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6466 Z= 0.184 Angle : 0.450 7.311 8731 Z= 0.235 Chirality : 0.041 0.138 1022 Planarity : 0.003 0.039 1134 Dihedral : 4.604 40.849 886 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.62 % Allowed : 28.61 % Favored : 66.76 % 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: 1.41 (0.30), residues: 823 helix: 2.92 (0.27), residues: 325 sheet: 0.61 (0.51), residues: 113 loop : -0.76 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 126 HIS 0.003 0.001 HIS A 341 PHE 0.007 0.001 PHE B 179 TYR 0.013 0.001 TYR A 243 ARG 0.001 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 46 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7917 (tp) REVERT: A 191 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7693 (mt) REVERT: A 345 LYS cc_start: 0.7698 (tptp) cc_final: 0.7065 (mptt) REVERT: A 356 THR cc_start: 0.7474 (m) cc_final: 0.7132 (m) REVERT: C 90 GLN cc_start: 0.6419 (OUTLIER) cc_final: 0.5927 (mt0) outliers start: 32 outliers final: 22 residues processed: 73 average time/residue: 0.1377 time to fit residues: 14.8894 Evaluate side-chains 70 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 45 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 211 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.204903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.145722 restraints weight = 7175.776| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.90 r_work: 0.3498 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6466 Z= 0.244 Angle : 0.478 7.658 8731 Z= 0.249 Chirality : 0.042 0.138 1022 Planarity : 0.003 0.041 1134 Dihedral : 4.695 41.398 886 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.64 % Allowed : 27.89 % Favored : 66.47 % 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: 1.30 (0.30), residues: 823 helix: 2.77 (0.27), residues: 325 sheet: 0.59 (0.51), residues: 113 loop : -0.78 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 126 HIS 0.004 0.001 HIS A 341 PHE 0.007 0.001 PHE B 179 TYR 0.016 0.001 TYR A 243 ARG 0.002 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 48 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7908 (tp) REVERT: A 258 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.5740 (pm20) REVERT: A 300 LYS cc_start: 0.7869 (pttm) cc_final: 0.7242 (pttm) REVERT: A 345 LYS cc_start: 0.7785 (tptp) cc_final: 0.7100 (mptt) REVERT: A 356 THR cc_start: 0.7563 (m) cc_final: 0.7191 (m) REVERT: A 360 ARG cc_start: 0.7074 (tmm-80) cc_final: 0.6583 (ttp80) REVERT: B 201 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7975 (pt) REVERT: C 79 LYS cc_start: 0.7002 (OUTLIER) cc_final: 0.6233 (pttt) REVERT: C 90 GLN cc_start: 0.6524 (OUTLIER) cc_final: 0.5994 (mt0) outliers start: 39 outliers final: 22 residues processed: 80 average time/residue: 0.1534 time to fit residues: 17.5425 Evaluate side-chains 74 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 47 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 211 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.204154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.146835 restraints weight = 7145.714| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.70 r_work: 0.3510 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6466 Z= 0.206 Angle : 0.468 7.500 8731 Z= 0.244 Chirality : 0.042 0.167 1022 Planarity : 0.003 0.041 1134 Dihedral : 4.688 41.475 886 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.91 % Allowed : 28.90 % Favored : 66.18 % 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: 1.28 (0.30), residues: 823 helix: 2.80 (0.27), residues: 325 sheet: 0.54 (0.51), residues: 113 loop : -0.82 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 126 HIS 0.002 0.001 HIS A 341 PHE 0.007 0.001 PHE B 179 TYR 0.014 0.001 TYR A 243 ARG 0.001 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 49 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7896 (tp) REVERT: A 258 GLN cc_start: 0.6927 (OUTLIER) cc_final: 0.5689 (pm20) REVERT: A 300 LYS cc_start: 0.7869 (pttm) cc_final: 0.7255 (pttm) REVERT: A 345 LYS cc_start: 0.7789 (tptp) cc_final: 0.7099 (mptt) REVERT: A 356 THR cc_start: 0.7588 (m) cc_final: 0.7182 (m) REVERT: A 360 ARG cc_start: 0.7117 (tmm-80) cc_final: 0.6635 (ttp80) REVERT: B 157 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8370 (ttmt) REVERT: B 201 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7992 (pt) REVERT: C 79 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6258 (pttt) REVERT: C 90 GLN cc_start: 0.6539 (OUTLIER) cc_final: 0.6013 (mt0) outliers start: 34 outliers final: 21 residues processed: 78 average time/residue: 0.1526 time to fit residues: 16.9379 Evaluate side-chains 73 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 46 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 211 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 chunk 56 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 424 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.203185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.142605 restraints weight = 7143.414| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 3.22 r_work: 0.3486 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6466 Z= 0.233 Angle : 0.485 7.635 8731 Z= 0.251 Chirality : 0.043 0.256 1022 Planarity : 0.003 0.042 1134 Dihedral : 4.695 41.850 885 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.91 % Allowed : 29.91 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.30), residues: 823 helix: 2.69 (0.27), residues: 325 sheet: 0.44 (0.51), residues: 113 loop : -0.87 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 126 HIS 0.002 0.001 HIS C 158 PHE 0.008 0.001 PHE B 179 TYR 0.022 0.002 TYR C 78 ARG 0.002 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 47 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7932 (tp) REVERT: A 345 LYS cc_start: 0.7765 (tptp) cc_final: 0.7087 (mptt) REVERT: A 356 THR cc_start: 0.7511 (m) cc_final: 0.7069 (m) REVERT: A 360 ARG cc_start: 0.7072 (tmm-80) cc_final: 0.6610 (ttp80) REVERT: B 157 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8308 (ttmt) REVERT: B 201 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7945 (pt) REVERT: C 79 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6189 (pttt) REVERT: C 90 GLN cc_start: 0.6502 (OUTLIER) cc_final: 0.5991 (mt0) outliers start: 34 outliers final: 24 residues processed: 75 average time/residue: 0.1795 time to fit residues: 18.7261 Evaluate side-chains 75 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 46 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 211 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 68 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 0.0030 chunk 61 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.204327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.145873 restraints weight = 7056.783| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 3.16 r_work: 0.3518 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6466 Z= 0.188 Angle : 0.474 7.364 8731 Z= 0.244 Chirality : 0.042 0.286 1022 Planarity : 0.003 0.043 1134 Dihedral : 4.644 41.637 885 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.91 % Allowed : 30.06 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.30), residues: 823 helix: 2.80 (0.27), residues: 325 sheet: 0.41 (0.51), residues: 113 loop : -0.84 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 126 HIS 0.002 0.000 HIS C 158 PHE 0.008 0.001 PHE B 179 TYR 0.017 0.002 TYR C 78 ARG 0.001 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 48 time to evaluate : 0.700 Fit side-chains REVERT: A 60 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7916 (tp) REVERT: A 258 GLN cc_start: 0.6922 (OUTLIER) cc_final: 0.5709 (pm20) REVERT: A 300 LYS cc_start: 0.7897 (pttm) cc_final: 0.7301 (pttm) REVERT: A 345 LYS cc_start: 0.7780 (tptp) cc_final: 0.7125 (mptt) REVERT: A 356 THR cc_start: 0.7578 (m) cc_final: 0.7145 (m) REVERT: A 360 ARG cc_start: 0.7101 (tmm-80) cc_final: 0.6661 (ttp80) REVERT: A 508 ILE cc_start: -0.2004 (OUTLIER) cc_final: -0.2657 (tt) REVERT: B 157 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8312 (ttmt) REVERT: C 79 LYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6233 (pttt) REVERT: C 90 GLN cc_start: 0.6509 (OUTLIER) cc_final: 0.6003 (mt0) outliers start: 34 outliers final: 23 residues processed: 78 average time/residue: 0.1667 time to fit residues: 18.2902 Evaluate side-chains 76 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 47 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 211 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 48 optimal weight: 40.0000 chunk 53 optimal weight: 4.9990 chunk 64 optimal weight: 0.0470 chunk 5 optimal weight: 0.2980 chunk 76 optimal weight: 0.6980 chunk 58 optimal weight: 0.0980 chunk 55 optimal weight: 0.0470 chunk 44 optimal weight: 30.0000 chunk 61 optimal weight: 0.3980 chunk 68 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 overall best weight: 0.1776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.209017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.153107 restraints weight = 7074.348| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.80 r_work: 0.3576 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6466 Z= 0.130 Angle : 0.446 6.104 8731 Z= 0.231 Chirality : 0.041 0.283 1022 Planarity : 0.003 0.040 1134 Dihedral : 4.351 40.185 884 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.18 % Allowed : 31.79 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.31), residues: 823 helix: 3.17 (0.27), residues: 324 sheet: 0.47 (0.51), residues: 113 loop : -0.68 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 126 HIS 0.003 0.000 HIS A 341 PHE 0.006 0.001 PHE B 179 TYR 0.017 0.001 TYR C 78 ARG 0.001 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 266 SER cc_start: 0.7108 (t) cc_final: 0.6814 (m) REVERT: A 345 LYS cc_start: 0.7779 (tptp) cc_final: 0.7172 (mptt) REVERT: A 356 THR cc_start: 0.7436 (m) cc_final: 0.7028 (m) REVERT: A 360 ARG cc_start: 0.7069 (tmm-80) cc_final: 0.6659 (ttp80) REVERT: A 508 ILE cc_start: -0.2045 (OUTLIER) cc_final: -0.2657 (tt) REVERT: C 90 GLN cc_start: 0.6455 (OUTLIER) cc_final: 0.6000 (mt0) outliers start: 22 outliers final: 15 residues processed: 70 average time/residue: 0.1598 time to fit residues: 16.2371 Evaluate side-chains 64 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 211 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 43 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 5 optimal weight: 0.0470 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 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 = 0.4335 r_free = 0.4335 target = 0.204252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.144306 restraints weight = 7078.101| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 3.28 r_work: 0.3495 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6466 Z= 0.232 Angle : 0.498 6.766 8731 Z= 0.257 Chirality : 0.043 0.295 1022 Planarity : 0.003 0.039 1134 Dihedral : 4.435 40.675 883 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.89 % Allowed : 32.08 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.30), residues: 823 helix: 2.91 (0.27), residues: 326 sheet: 0.50 (0.51), residues: 111 loop : -0.75 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 126 HIS 0.003 0.001 HIS C 158 PHE 0.007 0.001 PHE B 179 TYR 0.015 0.002 TYR A 243 ARG 0.002 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 345 LYS cc_start: 0.7652 (tptp) cc_final: 0.7070 (mptt) REVERT: A 356 THR cc_start: 0.7548 (m) cc_final: 0.7128 (m) REVERT: A 508 ILE cc_start: -0.2022 (OUTLIER) cc_final: -0.2679 (tt) REVERT: C 90 GLN cc_start: 0.6349 (OUTLIER) cc_final: 0.5877 (mt0) outliers start: 20 outliers final: 18 residues processed: 64 average time/residue: 0.1527 time to fit residues: 14.2187 Evaluate side-chains 67 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 211 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 60 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 47 optimal weight: 20.0000 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.204871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.147716 restraints weight = 7143.729| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.92 r_work: 0.3520 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6466 Z= 0.202 Angle : 0.486 6.447 8731 Z= 0.251 Chirality : 0.042 0.285 1022 Planarity : 0.003 0.040 1134 Dihedral : 4.425 40.227 883 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.18 % Allowed : 32.08 % Favored : 64.74 % 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: 1.36 (0.30), residues: 823 helix: 2.89 (0.27), residues: 326 sheet: 0.47 (0.51), residues: 111 loop : -0.77 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 126 HIS 0.002 0.001 HIS C 158 PHE 0.007 0.001 PHE B 179 TYR 0.017 0.002 TYR C 78 ARG 0.002 0.000 ARG A 360 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 0.673 Fit side-chains REVERT: A 300 LYS cc_start: 0.7926 (pttm) cc_final: 0.7328 (pttm) REVERT: A 345 LYS cc_start: 0.7764 (tptp) cc_final: 0.7128 (mptt) REVERT: A 356 THR cc_start: 0.7612 (m) cc_final: 0.7196 (m) REVERT: A 424 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.6440 (tp-100) REVERT: A 508 ILE cc_start: -0.1979 (OUTLIER) cc_final: -0.2626 (tt) REVERT: C 90 GLN cc_start: 0.6547 (OUTLIER) cc_final: 0.6043 (mt0) outliers start: 22 outliers final: 19 residues processed: 62 average time/residue: 0.1432 time to fit residues: 13.2463 Evaluate side-chains 65 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 43 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 211 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 72 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 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 = 0.4341 r_free = 0.4341 target = 0.204991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.147466 restraints weight = 7233.979| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.97 r_work: 0.3524 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6466 Z= 0.185 Angle : 0.485 6.444 8731 Z= 0.250 Chirality : 0.042 0.285 1022 Planarity : 0.003 0.039 1134 Dihedral : 4.404 39.995 883 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.32 % Allowed : 31.94 % Favored : 64.74 % 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: 1.38 (0.30), residues: 823 helix: 2.91 (0.27), residues: 326 sheet: 0.48 (0.51), residues: 111 loop : -0.76 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 126 HIS 0.002 0.000 HIS C 158 PHE 0.007 0.001 PHE B 179 TYR 0.013 0.001 TYR A 243 ARG 0.001 0.000 ARG A 360 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4048.04 seconds wall clock time: 72 minutes 20.02 seconds (4340.02 seconds total)