Starting phenix.real_space_refine on Tue Mar 11 17:05:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9blu_44677/03_2025/9blu_44677.cif Found real_map, /net/cci-nas-00/data/ceres_data/9blu_44677/03_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_44677/03_2025/9blu_44677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9blu_44677/03_2025/9blu_44677.map" model { file = "/net/cci-nas-00/data/ceres_data/9blu_44677/03_2025/9blu_44677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9blu_44677/03_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-5624/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: 5.36, per 1000 atoms: 0.84 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: 1.46 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.73 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: 2.29 Time building geometry restraints manager: 1.76 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.390 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.730 ------------------------------------------------------------------------------- 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 : 0.847 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: 0.1842 time to fit residues: 17.0763 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 : 1.026 ------------------------------------------------------------------------------- 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 = 66)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.140560 restraints weight = 7051.117| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.59 r_work: 0.3516 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 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 : 0.746 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7786 (tp) REVERT: A 159 LYS cc_start: 0.8169 (mtpp) cc_final: 0.7909 (mtpp) REVERT: A 300 LYS cc_start: 0.7837 (pttm) cc_final: 0.7247 (pttm) REVERT: A 345 LYS cc_start: 0.7564 (tptp) cc_final: 0.7052 (mptt) REVERT: A 424 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6154 (tp-100) REVERT: C 90 GLN cc_start: 0.6270 (OUTLIER) cc_final: 0.5817 (mt0) outliers start: 26 outliers final: 13 residues processed: 68 average time/residue: 0.1668 time to fit residues: 16.3865 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 : 0.740 ------------------------------------------------------------------------------- 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 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: 0.0470 chunk 30 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- 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 = 0.4356 r_free = 0.4356 target = 0.206951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.147292 restraints weight = 7033.921| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.96 r_work: 0.3497 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.0797 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= 0.190 Angle : 0.453 7.331 8731 Z= 0.236 Chirality : 0.041 0.138 1022 Planarity : 0.003 0.040 1134 Dihedral : 4.614 40.890 886 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.77 % Allowed : 28.61 % Favored : 66.62 % 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: 1.40 (0.30), residues: 823 helix: 2.90 (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 A 360 *********************** 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 79 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 46 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7935 (tp) REVERT: A 191 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7706 (mt) REVERT: A 300 LYS cc_start: 0.7820 (pttm) cc_final: 0.7226 (pttm) REVERT: A 345 LYS cc_start: 0.7717 (tptp) cc_final: 0.7063 (mptt) REVERT: A 356 THR cc_start: 0.7458 (m) cc_final: 0.7120 (m) REVERT: B 201 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7970 (pt) REVERT: C 90 GLN cc_start: 0.6444 (OUTLIER) cc_final: 0.5945 (mt0) outliers start: 33 outliers final: 21 residues processed: 74 average time/residue: 0.1622 time to fit residues: 17.6973 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 : 0.789 ------------------------------------------------------------------------------- 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: 0.0570 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 = 0.4353 r_free = 0.4353 target = 0.206520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.148676 restraints weight = 7176.297| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 3.10 r_work: 0.3542 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.0927 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= 0.152 Angle : 0.436 7.089 8731 Z= 0.227 Chirality : 0.040 0.136 1022 Planarity : 0.003 0.038 1134 Dihedral : 4.530 40.709 886 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.62 % Allowed : 28.47 % 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: 1.49 (0.31), residues: 823 helix: 2.99 (0.27), residues: 325 sheet: 0.65 (0.51), residues: 113 loop : -0.71 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 126 HIS 0.001 0.000 HIS A 341 PHE 0.006 0.001 PHE B 179 TYR 0.012 0.001 TYR A 243 ARG 0.001 0.000 ARG B 207 *********************** 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 79 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 47 time to evaluate : 0.780 Fit side-chains REVERT: A 300 LYS cc_start: 0.7830 (pttm) cc_final: 0.7244 (pttm) REVERT: A 345 LYS cc_start: 0.7713 (tptp) cc_final: 0.7083 (mptt) REVERT: A 356 THR cc_start: 0.7539 (m) cc_final: 0.7166 (m) REVERT: A 360 ARG cc_start: 0.7060 (tmm-80) cc_final: 0.6586 (ttp80) REVERT: B 201 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7839 (pp) REVERT: C 79 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6226 (pttt) REVERT: C 90 GLN cc_start: 0.6489 (OUTLIER) cc_final: 0.6014 (mt0) outliers start: 32 outliers final: 20 residues processed: 73 average time/residue: 0.1861 time to fit residues: 19.2713 Evaluate side-chains 69 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 46 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET 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 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 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: 0.9980 chunk 66 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 40 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 55 optimal weight: 0.0970 chunk 42 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.4335 r_free = 0.4335 target = 0.204738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.146685 restraints weight = 7024.964| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.95 r_work: 0.3483 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6466 Z= 0.180 Angle : 0.448 7.270 8731 Z= 0.233 Chirality : 0.041 0.163 1022 Planarity : 0.003 0.038 1134 Dihedral : 4.484 40.725 885 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.91 % Allowed : 28.47 % Favored : 66.62 % 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: 1.47 (0.30), residues: 823 helix: 2.96 (0.27), residues: 325 sheet: 0.63 (0.51), residues: 113 loop : -0.71 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 126 HIS 0.002 0.000 HIS A 341 PHE 0.007 0.001 PHE A 522 TYR 0.013 0.001 TYR A 243 ARG 0.001 0.000 ARG A 360 *********************** 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 80 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 46 time to evaluate : 0.754 Fit side-chains REVERT: A 60 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7827 (tp) REVERT: A 258 GLN cc_start: 0.6847 (OUTLIER) cc_final: 0.5517 (pm20) REVERT: A 300 LYS cc_start: 0.7835 (pttm) cc_final: 0.7260 (pttm) REVERT: A 345 LYS cc_start: 0.7654 (tptp) cc_final: 0.7019 (mptt) REVERT: A 356 THR cc_start: 0.7491 (m) cc_final: 0.7093 (m) REVERT: A 360 ARG cc_start: 0.6979 (tmm-80) cc_final: 0.6489 (ttp80) REVERT: B 201 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7808 (pt) REVERT: C 79 LYS cc_start: 0.6935 (OUTLIER) cc_final: 0.6185 (pttt) REVERT: C 90 GLN cc_start: 0.6340 (OUTLIER) cc_final: 0.5879 (mt0) outliers start: 34 outliers final: 20 residues processed: 74 average time/residue: 0.1594 time to fit residues: 16.8456 Evaluate side-chains 71 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 46 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 30.0000 chunk 56 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4338 r_free = 0.4338 target = 0.204806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.144173 restraints weight = 7114.002| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 3.03 r_work: 0.3481 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1068 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= 0.204 Angle : 0.463 7.464 8731 Z= 0.240 Chirality : 0.041 0.137 1022 Planarity : 0.003 0.038 1134 Dihedral : 4.449 40.964 884 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.62 % Allowed : 29.05 % Favored : 66.33 % 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: 1.40 (0.30), residues: 823 helix: 2.89 (0.27), residues: 325 sheet: 0.55 (0.51), residues: 113 loop : -0.72 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 126 HIS 0.003 0.001 HIS A 341 PHE 0.007 0.001 PHE B 179 TYR 0.015 0.001 TYR A 243 ARG 0.001 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 82 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 50 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7881 (tp) REVERT: A 300 LYS cc_start: 0.7910 (pttm) cc_final: 0.7331 (pttm) REVERT: A 345 LYS cc_start: 0.7691 (tptp) cc_final: 0.7067 (mptt) REVERT: A 356 THR cc_start: 0.7591 (m) cc_final: 0.7180 (m) REVERT: A 360 ARG cc_start: 0.6978 (tmm-80) cc_final: 0.6491 (ttp80) REVERT: B 157 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8256 (ttmt) REVERT: B 201 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7820 (pt) REVERT: C 79 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6203 (pttt) REVERT: C 90 GLN cc_start: 0.6331 (OUTLIER) cc_final: 0.5889 (mt0) outliers start: 32 outliers final: 22 residues processed: 76 average time/residue: 0.1695 time to fit residues: 18.0424 Evaluate side-chains 76 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 49 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 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 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: 6.9990 chunk 33 optimal weight: 0.0970 chunk 21 optimal weight: 0.0970 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 0.0010 chunk 61 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 46 optimal weight: 30.0000 chunk 42 optimal weight: 6.9990 overall best weight: 0.3182 ------------------------------------------------------------------------------- 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 = 0.4367 r_free = 0.4367 target = 0.207984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.148339 restraints weight = 7001.684| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 3.03 r_work: 0.3524 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6466 Z= 0.134 Angle : 0.440 6.894 8731 Z= 0.226 Chirality : 0.040 0.134 1022 Planarity : 0.003 0.037 1134 Dihedral : 4.298 39.992 884 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.47 % Allowed : 30.20 % Favored : 66.33 % 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: 1.59 (0.31), residues: 823 helix: 3.11 (0.27), residues: 325 sheet: 0.57 (0.51), residues: 113 loop : -0.65 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 126 HIS 0.001 0.000 HIS C 158 PHE 0.006 0.001 PHE B 179 TYR 0.010 0.001 TYR A 161 ARG 0.001 0.000 ARG B 207 *********************** 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 77 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 300 LYS cc_start: 0.7828 (pttm) cc_final: 0.7262 (pttm) REVERT: A 345 LYS cc_start: 0.7665 (tptp) cc_final: 0.7028 (mptt) REVERT: A 356 THR cc_start: 0.7397 (m) cc_final: 0.7005 (m) REVERT: A 360 ARG cc_start: 0.6954 (tmm-80) cc_final: 0.6512 (ttp80) REVERT: B 201 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7661 (pp) REVERT: C 90 GLN cc_start: 0.6278 (OUTLIER) cc_final: 0.5830 (mt0) outliers start: 24 outliers final: 20 residues processed: 72 average time/residue: 0.1539 time to fit residues: 15.9759 Evaluate side-chains 70 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 249 THR 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 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 544 GLN 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 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: 30.0000 chunk 53 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 0.0010 chunk 61 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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 = 0.4349 r_free = 0.4349 target = 0.206007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.146669 restraints weight = 7108.425| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.47 r_work: 0.3510 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1213 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= 0.184 Angle : 0.459 7.301 8731 Z= 0.237 Chirality : 0.041 0.136 1022 Planarity : 0.003 0.038 1134 Dihedral : 4.307 39.915 883 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.19 % Allowed : 30.06 % Favored : 65.75 % 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: 1.52 (0.31), residues: 823 helix: 3.00 (0.27), residues: 326 sheet: 0.57 (0.52), residues: 111 loop : -0.66 (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 A 341 PHE 0.006 0.001 PHE B 179 TYR 0.015 0.001 TYR A 243 ARG 0.001 0.000 ARG A 360 *********************** 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 75 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 46 time to evaluate : 0.730 Fit side-chains REVERT: A 300 LYS cc_start: 0.7892 (pttm) cc_final: 0.7320 (pttm) REVERT: A 345 LYS cc_start: 0.7624 (tptp) cc_final: 0.7079 (mptt) REVERT: A 356 THR cc_start: 0.7547 (m) cc_final: 0.7138 (m) REVERT: A 360 ARG cc_start: 0.6907 (tmm-80) cc_final: 0.6476 (ttp80) REVERT: A 424 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6243 (tp-100) REVERT: B 201 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7780 (pt) REVERT: C 90 GLN cc_start: 0.6329 (OUTLIER) cc_final: 0.5868 (mt0) outliers start: 29 outliers final: 20 residues processed: 71 average time/residue: 0.1510 time to fit residues: 15.5110 Evaluate side-chains 69 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 46 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 249 THR 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 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 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 201 LEU Chi-restraints excluded: chain C residue 90 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 43 optimal weight: 8.9990 chunk 23 optimal weight: 0.3980 chunk 47 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.204765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.144846 restraints weight = 7108.555| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.29 r_work: 0.3488 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6466 Z= 0.223 Angle : 0.484 7.502 8731 Z= 0.250 Chirality : 0.042 0.138 1022 Planarity : 0.003 0.038 1134 Dihedral : 4.393 39.815 883 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.90 % Allowed : 29.91 % 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: 1.41 (0.30), residues: 823 helix: 2.87 (0.27), residues: 326 sheet: 0.54 (0.52), residues: 111 loop : -0.68 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 126 HIS 0.004 0.001 HIS A 341 PHE 0.007 0.001 PHE B 179 TYR 0.016 0.001 TYR A 243 ARG 0.001 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 76 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 49 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 345 LYS cc_start: 0.7620 (tptp) cc_final: 0.7028 (mptt) REVERT: A 356 THR cc_start: 0.7576 (m) cc_final: 0.7161 (m) REVERT: A 360 ARG cc_start: 0.6938 (tmm-80) cc_final: 0.6517 (ttp80) REVERT: A 508 ILE cc_start: -0.2083 (OUTLIER) cc_final: -0.2697 (tt) REVERT: B 157 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8254 (ttmt) REVERT: B 201 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7805 (pt) REVERT: C 79 LYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6253 (pttt) REVERT: C 90 GLN cc_start: 0.6362 (OUTLIER) cc_final: 0.5902 (mt0) outliers start: 27 outliers final: 21 residues processed: 71 average time/residue: 0.1807 time to fit residues: 18.1790 Evaluate side-chains 73 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 47 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 60 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 14 optimal weight: 0.0970 chunk 47 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.4342 r_free = 0.4342 target = 0.205084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.144277 restraints weight = 7107.153| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.96 r_work: 0.3498 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1305 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= 0.193 Angle : 0.473 7.323 8731 Z= 0.245 Chirality : 0.041 0.135 1022 Planarity : 0.003 0.039 1134 Dihedral : 4.379 39.441 883 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.76 % Allowed : 30.20 % Favored : 66.04 % 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: 1.45 (0.30), residues: 823 helix: 2.92 (0.27), residues: 326 sheet: 0.56 (0.52), residues: 111 loop : -0.68 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 126 HIS 0.003 0.001 HIS A 341 PHE 0.007 0.001 PHE B 179 TYR 0.026 0.002 TYR C 78 ARG 0.001 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 70 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 44 time to evaluate : 0.696 Fit side-chains REVERT: A 300 LYS cc_start: 0.7930 (pttm) cc_final: 0.7351 (pttm) REVERT: A 344 MET cc_start: 0.7756 (tpp) cc_final: 0.7285 (ttm) REVERT: A 345 LYS cc_start: 0.7645 (tptp) cc_final: 0.7063 (mptt) REVERT: A 356 THR cc_start: 0.7550 (m) cc_final: 0.7131 (m) REVERT: A 360 ARG cc_start: 0.6883 (tmm-80) cc_final: 0.6463 (ttp80) REVERT: A 389 MET cc_start: 0.7488 (mmp) cc_final: 0.7256 (mmp) REVERT: A 508 ILE cc_start: -0.1871 (OUTLIER) cc_final: -0.2528 (tt) REVERT: B 157 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8228 (ttmt) REVERT: B 201 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7810 (pt) REVERT: C 90 GLN cc_start: 0.6365 (OUTLIER) cc_final: 0.5912 (mt0) outliers start: 26 outliers final: 20 residues processed: 65 average time/residue: 0.1706 time to fit residues: 15.9209 Evaluate side-chains 68 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 44 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 249 THR 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 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 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 90 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 19 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 72 optimal weight: 0.0770 chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 8 optimal weight: 0.0030 chunk 52 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 overall best weight: 0.3548 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.207467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.150519 restraints weight = 7206.094| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.92 r_work: 0.3552 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6466 Z= 0.143 Angle : 0.452 6.892 8731 Z= 0.233 Chirality : 0.040 0.134 1022 Planarity : 0.003 0.038 1134 Dihedral : 4.263 38.657 883 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.47 % Allowed : 30.35 % 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: 1.60 (0.31), residues: 823 helix: 3.09 (0.27), residues: 326 sheet: 0.61 (0.52), residues: 111 loop : -0.64 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 126 HIS 0.001 0.000 HIS C 158 PHE 0.006 0.001 PHE B 179 TYR 0.010 0.001 TYR A 243 ARG 0.001 0.000 ARG B 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3961.50 seconds wall clock time: 68 minutes 24.45 seconds (4104.45 seconds total)