Starting phenix.real_space_refine on Wed Feb 12 03:16:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9blt_44676/02_2025/9blt_44676.cif Found real_map, /net/cci-nas-00/data/ceres_data/9blt_44676/02_2025/9blt_44676.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/9blt_44676/02_2025/9blt_44676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9blt_44676/02_2025/9blt_44676.map" model { file = "/net/cci-nas-00/data/ceres_data/9blt_44676/02_2025/9blt_44676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9blt_44676/02_2025/9blt_44676.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 27 5.16 5 C 4459 2.51 5 N 1229 2.21 5 O 1383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 7098 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4516 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 21, 'TRANS': 572} 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} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 53 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Time building chain proxies: 5.54, per 1000 atoms: 0.78 Number of scatterers: 7098 At special positions: 0 Unit cell: (74.97, 122.745, 120.54, 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 27 16.00 O 1383 8.00 N 1229 7.00 C 4459 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: 1.67 Conformation dependent library (CDL) restraints added in 947.8 milliseconds 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 13 sheets defined 45.3% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 108 through 111 Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 130 through 140 removed outlier: 4.318A pdb=" N LYS A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 183 removed outlier: 3.609A pdb=" N GLY A 167 " --> pdb=" O PRO A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 274 through 294 removed outlier: 4.001A pdb=" N PHE A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 3.633A 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 387 through 391 removed outlier: 4.257A pdb=" N ARG A 391 " --> pdb=" O GLY A 388 " (cutoff:3.500A) 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 430 removed outlier: 3.712A pdb=" N ILE A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 556 through 568 removed outlier: 4.098A pdb=" N VAL A 562 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 566 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 597 Processing helix chain 'A' and resid 609 through 619 removed outlier: 4.104A pdb=" N GLU A 613 " --> pdb=" O ASN A 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 102 removed outlier: 3.622A pdb=" N GLU B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 125 removed outlier: 4.960A pdb=" N GLU B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 114 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 158 removed outlier: 3.834A pdb=" N HIS B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 124 removed outlier: 3.764A pdb=" N LYS C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU C 113 " --> pdb=" O LYS C 109 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 158 Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 77 removed outlier: 3.912A 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: 3.912A pdb=" N GLN A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N MET A 70 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL A 55 " --> pdb=" O MET A 70 " (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 192 through 193 Processing sheet with id=AA6, first strand: chain 'A' and resid 263 through 268 removed outlier: 5.600A pdb=" N VAL A 264 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLU A 256 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU A 382 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 333 removed outlier: 4.122A pdb=" N TYR A 331 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS A 340 " --> pdb=" O TYR A 331 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 454 through 458 removed outlier: 5.774A pdb=" N LYS A 456 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ILE A 447 " --> pdb=" O LYS A 456 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE A 458 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LYS A 485 " --> pdb=" O GLU A 448 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 468 through 472 Processing sheet with id=AB1, first strand: chain 'B' and resid 160 through 163 removed outlier: 6.556A pdb=" N TYR B 199 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 191 through 196 removed outlier: 6.735A pdb=" N GLY B 212 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N VAL B 194 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU B 210 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 160 through 163 removed outlier: 6.656A pdb=" N TYR C 199 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 175 through 180 removed outlier: 7.464A pdb=" N VAL C 213 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N HIS C 180 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU C 210 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU C 193 " --> pdb=" O GLY C 212 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1086 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: 2.25 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2400 1.34 - 1.46: 693 1.46 - 1.57: 4053 1.57 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 7191 Sorted by residual: bond pdb=" N THR A 474 " pdb=" CA THR A 474 " ideal model delta sigma weight residual 1.454 1.488 -0.035 1.34e-02 5.57e+03 6.82e+00 bond pdb=" N SER A 473 " pdb=" CA SER A 473 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.36e-02 5.41e+03 5.86e+00 bond pdb=" N ALA A 475 " pdb=" CA ALA A 475 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.18e-02 7.18e+03 3.37e+00 bond pdb=" N ARG B 207 " pdb=" CA ARG B 207 " ideal model delta sigma weight residual 1.457 1.435 0.022 1.41e-02 5.03e+03 2.41e+00 bond pdb=" CA SER A 473 " pdb=" CB SER A 473 " ideal model delta sigma weight residual 1.530 1.507 0.023 1.52e-02 4.33e+03 2.33e+00 ... (remaining 7186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 9491 1.42 - 2.83: 157 2.83 - 4.25: 39 4.25 - 5.66: 11 5.66 - 7.08: 2 Bond angle restraints: 9700 Sorted by residual: angle pdb=" CA THR A 474 " pdb=" C THR A 474 " pdb=" O THR A 474 " ideal model delta sigma weight residual 121.87 118.35 3.52 1.16e+00 7.43e-01 9.20e+00 angle pdb=" CA ALA A 475 " pdb=" C ALA A 475 " pdb=" O ALA A 475 " ideal model delta sigma weight residual 120.90 117.88 3.02 1.03e+00 9.43e-01 8.61e+00 angle pdb=" CB GLU B 97 " pdb=" CG GLU B 97 " pdb=" CD GLU B 97 " ideal model delta sigma weight residual 112.60 117.30 -4.70 1.70e+00 3.46e-01 7.65e+00 angle pdb=" CA VAL A 546 " pdb=" CB VAL A 546 " pdb=" CG1 VAL A 546 " ideal model delta sigma weight residual 110.40 115.04 -4.64 1.70e+00 3.46e-01 7.45e+00 angle pdb=" N ILE B 130 " pdb=" CA ILE B 130 " pdb=" C ILE B 130 " ideal model delta sigma weight residual 106.21 109.02 -2.81 1.07e+00 8.73e-01 6.88e+00 ... (remaining 9695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 3728 17.89 - 35.77: 521 35.77 - 53.66: 168 53.66 - 71.54: 34 71.54 - 89.42: 10 Dihedral angle restraints: 4461 sinusoidal: 1819 harmonic: 2642 Sorted by residual: dihedral pdb=" CB GLU B 113 " pdb=" CG GLU B 113 " pdb=" CD GLU B 113 " pdb=" OE1 GLU B 113 " ideal model delta sinusoidal sigma weight residual 0.00 89.42 -89.42 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG A 309 " pdb=" CD ARG A 309 " pdb=" NE ARG A 309 " pdb=" CZ ARG A 309 " ideal model delta sinusoidal sigma weight residual -180.00 -136.02 -43.98 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CB GLU A 382 " pdb=" CG GLU A 382 " pdb=" CD GLU A 382 " pdb=" OE1 GLU A 382 " ideal model delta sinusoidal sigma weight residual 0.00 -86.54 86.54 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 4458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 669 0.028 - 0.055: 290 0.055 - 0.083: 90 0.083 - 0.111: 67 0.111 - 0.138: 16 Chirality restraints: 1132 Sorted by residual: chirality pdb=" CA ASN A 560 " pdb=" N ASN A 560 " pdb=" C ASN A 560 " pdb=" CB ASN A 560 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CB ILE A 633 " pdb=" CA ILE A 633 " pdb=" CG1 ILE A 633 " pdb=" CG2 ILE A 633 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE A 252 " pdb=" N ILE A 252 " pdb=" C ILE A 252 " pdb=" CB ILE A 252 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 1129 not shown) Planarity restraints: 1263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 103 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+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=" CA GLN A 108 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.31e+00 pdb=" C GLN A 108 " 0.020 2.00e-02 2.50e+03 pdb=" O GLN A 108 " -0.007 2.00e-02 2.50e+03 pdb=" N ALA A 109 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 130 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO A 131 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " 0.015 5.00e-02 4.00e+02 ... (remaining 1260 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 962 2.75 - 3.29: 6776 3.29 - 3.83: 11519 3.83 - 4.36: 12565 4.36 - 4.90: 23058 Nonbonded interactions: 54880 Sorted by model distance: nonbonded pdb=" OG SER A 444 " pdb=" O GLY A 489 " model vdw 2.218 3.040 nonbonded pdb=" NH2 ARG A 391 " pdb=" OD2 ASP A 414 " model vdw 2.230 3.120 nonbonded pdb=" OD2 ASP A 536 " pdb=" OG1 THR A 539 " model vdw 2.237 3.040 nonbonded pdb=" O GLY A 528 " pdb=" OG SER A 550 " model vdw 2.260 3.040 nonbonded pdb=" OD2 ASP A 556 " pdb=" ND2 ASN A 560 " model vdw 2.267 3.120 ... (remaining 54875 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: 3.240 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.420 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 0.036 7191 Z= 0.192 Angle : 0.513 7.078 9700 Z= 0.277 Chirality : 0.040 0.138 1132 Planarity : 0.003 0.041 1263 Dihedral : 18.586 89.425 2753 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.72 % Allowed : 32.77 % Favored : 64.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.29), residues: 913 helix: 1.83 (0.27), residues: 382 sheet: -0.39 (0.53), residues: 111 loop : -0.90 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 126 HIS 0.002 0.001 HIS A 184 PHE 0.009 0.001 PHE A 197 TYR 0.016 0.001 TYR B 78 ARG 0.002 0.000 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.741 Fit side-chains REVERT: A 108 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.6933 (tt0) REVERT: A 252 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8162 (tp) REVERT: A 348 ARG cc_start: 0.6546 (OUTLIER) cc_final: 0.6066 (ttm-80) REVERT: B 127 LYS cc_start: 0.7619 (tttt) cc_final: 0.7055 (mptt) outliers start: 21 outliers final: 17 residues processed: 74 average time/residue: 0.1768 time to fit residues: 18.7451 Evaluate side-chains 74 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 0.0570 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.199170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.145742 restraints weight = 8696.570| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.36 r_work: 0.3594 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 7191 Z= 0.412 Angle : 0.638 10.029 9700 Z= 0.334 Chirality : 0.047 0.172 1132 Planarity : 0.004 0.044 1263 Dihedral : 6.226 48.030 1001 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 6.48 % Allowed : 29.15 % Favored : 64.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.28), residues: 913 helix: 1.34 (0.25), residues: 386 sheet: -0.48 (0.51), residues: 120 loop : -1.05 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 126 HIS 0.007 0.001 HIS A 341 PHE 0.015 0.002 PHE B 179 TYR 0.014 0.002 TYR B 102 ARG 0.003 0.000 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 59 time to evaluate : 0.774 Fit side-chains REVERT: A 108 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.6857 (pt0) REVERT: A 252 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8374 (tp) REVERT: A 573 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6926 (ptt90) REVERT: B 78 TYR cc_start: 0.7216 (t80) cc_final: 0.6887 (t80) REVERT: B 90 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7517 (mt0) REVERT: B 127 LYS cc_start: 0.7641 (tttt) cc_final: 0.6941 (mptt) REVERT: B 128 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6770 (mp0) REVERT: B 129 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7961 (mp0) outliers start: 50 outliers final: 24 residues processed: 103 average time/residue: 0.1878 time to fit residues: 26.7039 Evaluate side-chains 82 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 53 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 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 268 ASN B 136 HIS C 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.212518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.162012 restraints weight = 8919.457| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.17 r_work: 0.3777 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7191 Z= 0.192 Angle : 0.495 8.013 9700 Z= 0.259 Chirality : 0.041 0.151 1132 Planarity : 0.004 0.043 1263 Dihedral : 4.860 42.482 988 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.27 % Allowed : 31.35 % Favored : 64.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.28), residues: 913 helix: 1.86 (0.25), residues: 385 sheet: -0.45 (0.50), residues: 119 loop : -0.91 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 126 HIS 0.002 0.001 HIS A 184 PHE 0.023 0.001 PHE A 197 TYR 0.007 0.001 TYR A 243 ARG 0.002 0.000 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 55 time to evaluate : 0.759 Fit side-chains REVERT: A 108 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.6534 (pt0) REVERT: A 252 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8270 (tp) REVERT: A 334 MET cc_start: 0.8048 (mmt) cc_final: 0.7790 (mmt) REVERT: A 348 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.6174 (ttm-80) REVERT: A 556 ASP cc_start: 0.7222 (OUTLIER) cc_final: 0.6786 (t0) REVERT: B 78 TYR cc_start: 0.7132 (t80) cc_final: 0.6728 (t80) REVERT: B 90 GLN cc_start: 0.7744 (mt0) cc_final: 0.7270 (mt0) REVERT: B 127 LYS cc_start: 0.7697 (tttt) cc_final: 0.7060 (mptt) REVERT: B 129 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7936 (mp0) outliers start: 33 outliers final: 20 residues processed: 80 average time/residue: 0.1803 time to fit residues: 20.2221 Evaluate side-chains 76 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 60 optimal weight: 0.4980 chunk 78 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 30.0000 chunk 42 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN C 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.213805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.166037 restraints weight = 9018.961| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 2.38 r_work: 0.3763 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7191 Z= 0.176 Angle : 0.475 7.832 9700 Z= 0.248 Chirality : 0.041 0.144 1132 Planarity : 0.003 0.039 1263 Dihedral : 4.621 41.492 986 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.05 % Allowed : 29.79 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.28), residues: 913 helix: 2.01 (0.25), residues: 386 sheet: -0.53 (0.50), residues: 120 loop : -0.85 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 126 HIS 0.002 0.001 HIS C 175 PHE 0.015 0.001 PHE A 197 TYR 0.009 0.001 TYR A 243 ARG 0.005 0.000 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 52 time to evaluate : 0.762 Fit side-chains REVERT: A 108 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.6509 (pt0) REVERT: A 252 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8297 (tp) REVERT: A 348 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6206 (ttm-80) REVERT: A 556 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6751 (t0) REVERT: B 78 TYR cc_start: 0.7219 (t80) cc_final: 0.6822 (t80) REVERT: B 90 GLN cc_start: 0.7741 (mt0) cc_final: 0.7263 (mt0) REVERT: B 127 LYS cc_start: 0.7700 (tttt) cc_final: 0.7082 (mptt) REVERT: B 128 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: B 129 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7973 (mp0) REVERT: B 201 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7512 (pp) outliers start: 39 outliers final: 22 residues processed: 83 average time/residue: 0.1616 time to fit residues: 19.5431 Evaluate side-chains 78 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 50 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 56 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 82 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN B 180 HIS C 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.199100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.145082 restraints weight = 8768.560| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.69 r_work: 0.3566 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7191 Z= 0.256 Angle : 0.515 8.437 9700 Z= 0.268 Chirality : 0.042 0.153 1132 Planarity : 0.004 0.039 1263 Dihedral : 4.772 42.265 985 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.53 % Allowed : 30.05 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.28), residues: 913 helix: 1.88 (0.25), residues: 386 sheet: -0.64 (0.49), residues: 119 loop : -0.90 (0.31), residues: 408 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 0.030 0.002 PHE A 197 TYR 0.014 0.001 TYR A 243 ARG 0.003 0.000 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 54 time to evaluate : 0.777 Fit side-chains REVERT: A 108 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.6492 (pt0) REVERT: A 252 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8258 (tp) REVERT: A 348 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.6431 (ttp-170) REVERT: A 556 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.6834 (t0) REVERT: B 78 TYR cc_start: 0.7158 (t80) cc_final: 0.6811 (t80) REVERT: B 90 GLN cc_start: 0.7771 (mt0) cc_final: 0.7348 (mt0) REVERT: B 127 LYS cc_start: 0.7676 (tttt) cc_final: 0.6961 (mptt) REVERT: B 128 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: B 129 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8014 (mp0) REVERT: B 201 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7433 (pp) outliers start: 35 outliers final: 23 residues processed: 81 average time/residue: 0.1638 time to fit residues: 19.1064 Evaluate side-chains 82 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 53 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 180 HIS Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 17 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 9 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 40.0000 chunk 10 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN C 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.200476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.146305 restraints weight = 8728.202| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.33 r_work: 0.3618 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7191 Z= 0.176 Angle : 0.488 7.803 9700 Z= 0.250 Chirality : 0.041 0.146 1132 Planarity : 0.003 0.039 1263 Dihedral : 4.572 41.340 985 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.27 % Allowed : 30.18 % Favored : 65.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.28), residues: 913 helix: 2.07 (0.25), residues: 386 sheet: -0.62 (0.50), residues: 119 loop : -0.87 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 126 HIS 0.002 0.001 HIS B 180 PHE 0.023 0.001 PHE A 197 TYR 0.010 0.001 TYR A 243 ARG 0.002 0.000 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 55 time to evaluate : 0.809 Fit side-chains REVERT: A 108 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.6724 (tt0) REVERT: A 252 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8223 (tp) REVERT: A 348 ARG cc_start: 0.6724 (OUTLIER) cc_final: 0.6367 (ttp-170) REVERT: A 556 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.6777 (t0) REVERT: B 78 TYR cc_start: 0.7037 (t80) cc_final: 0.6675 (t80) REVERT: B 90 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7276 (mt0) REVERT: B 91 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7405 (ttm170) REVERT: B 127 LYS cc_start: 0.7595 (tttt) cc_final: 0.6940 (mptt) REVERT: B 128 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6771 (mp0) REVERT: B 129 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7957 (mp0) REVERT: B 201 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7332 (pp) outliers start: 33 outliers final: 21 residues processed: 81 average time/residue: 0.1912 time to fit residues: 21.9321 Evaluate side-chains 80 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 51 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 2 optimal weight: 0.0470 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.202750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.146819 restraints weight = 8803.437| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 3.26 r_work: 0.3579 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7191 Z= 0.141 Angle : 0.465 7.275 9700 Z= 0.238 Chirality : 0.040 0.137 1132 Planarity : 0.003 0.045 1263 Dihedral : 4.354 39.416 985 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.37 % Allowed : 30.83 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.29), residues: 913 helix: 2.20 (0.26), residues: 393 sheet: -0.55 (0.50), residues: 119 loop : -0.87 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 126 HIS 0.002 0.000 HIS C 175 PHE 0.018 0.001 PHE A 197 TYR 0.008 0.001 TYR A 243 ARG 0.002 0.000 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 55 time to evaluate : 0.728 Fit side-chains REVERT: A 108 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.6756 (tt0) REVERT: A 348 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6383 (ttp-170) REVERT: A 556 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.6830 (t0) REVERT: B 127 LYS cc_start: 0.7624 (tttt) cc_final: 0.7030 (mptt) REVERT: B 128 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: B 129 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7963 (mp0) REVERT: B 201 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7300 (pp) outliers start: 26 outliers final: 16 residues processed: 76 average time/residue: 0.1620 time to fit residues: 17.7943 Evaluate side-chains 72 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.200861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.148011 restraints weight = 8822.064| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.56 r_work: 0.3604 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7191 Z= 0.189 Angle : 0.506 10.281 9700 Z= 0.260 Chirality : 0.041 0.151 1132 Planarity : 0.003 0.037 1263 Dihedral : 4.370 40.386 982 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.37 % Allowed : 30.57 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.28), residues: 913 helix: 2.20 (0.25), residues: 390 sheet: -0.59 (0.49), residues: 119 loop : -0.85 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 126 HIS 0.002 0.001 HIS A 341 PHE 0.020 0.001 PHE A 197 TYR 0.014 0.001 TYR A 243 ARG 0.003 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 0.724 Fit side-chains REVERT: A 108 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.6828 (tt0) REVERT: A 348 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.6406 (ttp-170) REVERT: B 91 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7391 (ttm170) REVERT: B 127 LYS cc_start: 0.7605 (tttt) cc_final: 0.7060 (mptt) REVERT: B 128 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: B 129 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8008 (mp0) REVERT: B 201 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7313 (pp) outliers start: 26 outliers final: 18 residues processed: 72 average time/residue: 0.1747 time to fit residues: 17.8455 Evaluate side-chains 73 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 HIS C 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.198074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.145063 restraints weight = 8904.150| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.49 r_work: 0.3564 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7191 Z= 0.291 Angle : 0.563 8.966 9700 Z= 0.290 Chirality : 0.043 0.159 1132 Planarity : 0.004 0.036 1263 Dihedral : 4.722 43.345 982 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.50 % Allowed : 30.44 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.28), residues: 913 helix: 1.86 (0.25), residues: 390 sheet: -0.69 (0.49), residues: 122 loop : -0.91 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 126 HIS 0.004 0.001 HIS A 341 PHE 0.025 0.002 PHE A 197 TYR 0.017 0.002 TYR A 243 ARG 0.003 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 53 time to evaluate : 0.744 Fit side-chains REVERT: A 108 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.6602 (pt0) REVERT: A 348 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6461 (ttp-170) REVERT: B 90 GLN cc_start: 0.7781 (mt0) cc_final: 0.7348 (mt0) REVERT: B 91 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7655 (ttm170) REVERT: B 127 LYS cc_start: 0.7628 (tttt) cc_final: 0.6992 (mptt) REVERT: B 128 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: B 129 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8049 (mp0) REVERT: B 201 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7489 (pp) outliers start: 27 outliers final: 20 residues processed: 76 average time/residue: 0.1911 time to fit residues: 20.2694 Evaluate side-chains 78 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 180 HIS Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 74 optimal weight: 0.2980 chunk 81 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** 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 = 0.4381 r_free = 0.4381 target = 0.200542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.147288 restraints weight = 9027.317| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.69 r_work: 0.3604 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7191 Z= 0.175 Angle : 0.517 8.783 9700 Z= 0.267 Chirality : 0.041 0.147 1132 Planarity : 0.003 0.036 1263 Dihedral : 4.449 41.726 982 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.98 % Allowed : 31.22 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.28), residues: 913 helix: 2.11 (0.25), residues: 390 sheet: -0.67 (0.49), residues: 119 loop : -0.91 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 126 HIS 0.002 0.001 HIS B 180 PHE 0.021 0.001 PHE A 197 TYR 0.012 0.001 TYR B 78 ARG 0.002 0.000 ARG A 405 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 54 time to evaluate : 0.818 Fit side-chains REVERT: A 108 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.6617 (tt0) REVERT: A 348 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.6379 (ttp-170) REVERT: B 90 GLN cc_start: 0.7710 (mt0) cc_final: 0.7275 (mt0) REVERT: B 91 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7385 (ttm170) REVERT: B 127 LYS cc_start: 0.7590 (tttt) cc_final: 0.7043 (mptt) REVERT: B 128 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: B 129 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8014 (mp0) REVERT: B 201 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7301 (pp) outliers start: 23 outliers final: 18 residues processed: 74 average time/residue: 0.1958 time to fit residues: 20.1743 Evaluate side-chains 76 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 82 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 81 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 0.0370 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.203778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.148843 restraints weight = 8859.931| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.42 r_work: 0.3650 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7191 Z= 0.155 Angle : 0.492 8.075 9700 Z= 0.253 Chirality : 0.040 0.143 1132 Planarity : 0.003 0.036 1263 Dihedral : 4.260 39.353 982 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.11 % Allowed : 31.09 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.28), residues: 913 helix: 2.30 (0.26), residues: 392 sheet: -0.61 (0.49), residues: 119 loop : -0.93 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 126 HIS 0.002 0.001 HIS B 180 PHE 0.018 0.001 PHE A 197 TYR 0.011 0.001 TYR B 78 ARG 0.002 0.000 ARG B 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4467.41 seconds wall clock time: 79 minutes 49.90 seconds (4789.90 seconds total)