Starting phenix.real_space_refine on Thu Nov 14 22:01:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j84_36059/11_2024/8j84_36059.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j84_36059/11_2024/8j84_36059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j84_36059/11_2024/8j84_36059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j84_36059/11_2024/8j84_36059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j84_36059/11_2024/8j84_36059.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j84_36059/11_2024/8j84_36059.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.016 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 23 5.16 5 C 4818 2.51 5 N 1240 2.21 5 O 1367 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7448 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3689 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 26, 'TRANS': 429} Chain breaks: 1 Chain: "B" Number of atoms: 3759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3759 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Time building chain proxies: 4.46, per 1000 atoms: 0.60 Number of scatterers: 7448 At special positions: 0 Unit cell: (77.7, 84, 132.3, 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 23 16.00 O 1367 8.00 N 1240 7.00 C 4818 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: 1.89 Conformation dependent library (CDL) restraints added in 1.0 seconds 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 12 sheets defined 41.7% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 46 through 62 removed outlier: 3.776A pdb=" N GLN A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 97 through 105 removed outlier: 4.151A pdb=" N ILE A 101 " --> pdb=" O THR A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 132 removed outlier: 4.107A pdb=" N ASP A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 150 Processing helix chain 'A' and resid 205 through 217 removed outlier: 4.416A pdb=" N GLN A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 248 through 264 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 366 through 377 removed outlier: 3.598A pdb=" N TRP A 370 " --> pdb=" O ASN A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 464 Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.788A pdb=" N PHE A 482 " --> pdb=" O VAL A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 493 Processing helix chain 'B' and resid 14 through 29 removed outlier: 4.033A pdb=" N THR B 18 " --> pdb=" O ASP B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.541A pdb=" N LEU B 37 " --> pdb=" O CYS B 34 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 39 " --> pdb=" O ILE B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 56 Processing helix chain 'B' and resid 65 through 70 removed outlier: 4.257A pdb=" N LYS B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 88 Processing helix chain 'B' and resid 109 through 114 removed outlier: 4.371A pdb=" N ARG B 114 " --> pdb=" O ILE B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 138 Processing helix chain 'B' and resid 146 through 158 removed outlier: 4.021A pdb=" N SER B 150 " --> pdb=" O ASP B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 194 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 221 through 226 removed outlier: 3.695A pdb=" N ILE B 224 " --> pdb=" O TYR B 221 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS B 225 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN B 226 " --> pdb=" O PHE B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 226' Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 257 through 277 removed outlier: 3.527A pdb=" N CYS B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG B 263 " --> pdb=" O TYR B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 353 through 366 removed outlier: 3.588A pdb=" N GLN B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG B 362 " --> pdb=" O HIS B 358 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS B 363 " --> pdb=" O SER B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 385 removed outlier: 4.604A pdb=" N LYS B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 425 through 434 removed outlier: 3.683A pdb=" N ALA B 431 " --> pdb=" O GLU B 427 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 448 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 removed outlier: 6.659A pdb=" N GLY A 385 " --> pdb=" O ASN A 446 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL A 357 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL A 386 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE A 359 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE A 388 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ALA A 361 " --> pdb=" O ILE A 388 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 20 removed outlier: 3.540A pdb=" N GLN A 18 " --> pdb=" O PHE A 14 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 95 removed outlier: 7.089A pdb=" N VAL A 43 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY A 42 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE A 142 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL A 44 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 280 through 287 Processing sheet with id=AA5, first strand: chain 'A' and resid 280 through 287 removed outlier: 4.044A pdb=" N LEU A 501 " --> pdb=" O VAL A 312 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AA7, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.826A pdb=" N SER A 431 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 5 through 6 removed outlier: 7.082A pdb=" N ILE B 5 " --> pdb=" O TRP B 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 62 through 63 removed outlier: 6.573A pdb=" N ILE B 62 " --> pdb=" O LEU B 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 283 through 286 removed outlier: 6.203A pdb=" N PHE B 291 " --> pdb=" O ALA B 325 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA B 325 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 283 through 286 removed outlier: 6.203A pdb=" N PHE B 291 " --> pdb=" O ALA B 325 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA B 325 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU B 402 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 208 through 210 removed outlier: 3.944A pdb=" N ILE B 208 " --> pdb=" O CYS B 215 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS B 215 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR B 210 " --> pdb=" O TYR B 213 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 864 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: 2.19 Time building geometry restraints manager: 2.17 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: 2361 1.34 - 1.46: 1367 1.46 - 1.57: 3869 1.57 - 1.69: 0 1.69 - 1.81: 35 Bond restraints: 7632 Sorted by residual: bond pdb=" CB LYS A 290 " pdb=" CG LYS A 290 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.07e+00 bond pdb=" CA PHE B 60 " pdb=" CB PHE B 60 " ideal model delta sigma weight residual 1.538 1.562 -0.024 2.12e-02 2.22e+03 1.30e+00 bond pdb=" CA THR A 218 " pdb=" CB THR A 218 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.51e-02 4.39e+03 9.65e-01 bond pdb=" CG ARG A 103 " pdb=" CD ARG A 103 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.32e-01 bond pdb=" CB GLU B 306 " pdb=" CG GLU B 306 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.85e-01 ... (remaining 7627 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 10152 1.85 - 3.70: 122 3.70 - 5.55: 25 5.55 - 7.40: 9 7.40 - 9.25: 4 Bond angle restraints: 10312 Sorted by residual: angle pdb=" N VAL B 43 " pdb=" CA VAL B 43 " pdb=" C VAL B 43 " ideal model delta sigma weight residual 111.62 107.05 4.57 7.90e-01 1.60e+00 3.35e+01 angle pdb=" CB LYS A 290 " pdb=" CG LYS A 290 " pdb=" CD LYS A 290 " ideal model delta sigma weight residual 111.30 120.55 -9.25 2.30e+00 1.89e-01 1.62e+01 angle pdb=" CA LYS A 290 " pdb=" CB LYS A 290 " pdb=" CG LYS A 290 " ideal model delta sigma weight residual 114.10 121.45 -7.35 2.00e+00 2.50e-01 1.35e+01 angle pdb=" CA GLU B 306 " pdb=" CB GLU B 306 " pdb=" CG GLU B 306 " ideal model delta sigma weight residual 114.10 120.01 -5.91 2.00e+00 2.50e-01 8.72e+00 angle pdb=" CA LEU A 462 " pdb=" CB LEU A 462 " pdb=" CG LEU A 462 " ideal model delta sigma weight residual 116.30 125.03 -8.73 3.50e+00 8.16e-02 6.21e+00 ... (remaining 10307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3875 17.70 - 35.39: 562 35.39 - 53.09: 117 53.09 - 70.79: 28 70.79 - 88.49: 10 Dihedral angle restraints: 4592 sinusoidal: 1927 harmonic: 2665 Sorted by residual: dihedral pdb=" CA LYS B 137 " pdb=" C LYS B 137 " pdb=" N GLN B 138 " pdb=" CA GLN B 138 " ideal model delta harmonic sigma weight residual 180.00 161.52 18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASP B 222 " pdb=" CB ASP B 222 " pdb=" CG ASP B 222 " pdb=" OD1 ASP B 222 " ideal model delta sinusoidal sigma weight residual -30.00 -88.68 58.68 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA MET A 406 " pdb=" C MET A 406 " pdb=" N ARG A 407 " pdb=" CA ARG A 407 " ideal model delta harmonic sigma weight residual 180.00 163.92 16.08 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 4589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 693 0.034 - 0.068: 283 0.068 - 0.102: 83 0.102 - 0.136: 45 0.136 - 0.170: 2 Chirality restraints: 1106 Sorted by residual: chirality pdb=" CB THR A 119 " pdb=" CA THR A 119 " pdb=" OG1 THR A 119 " pdb=" CG2 THR A 119 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CB THR A 463 " pdb=" CA THR A 463 " pdb=" OG1 THR A 463 " pdb=" CG2 THR A 463 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CG LEU A 423 " pdb=" CB LEU A 423 " pdb=" CD1 LEU A 423 " pdb=" CD2 LEU A 423 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 1103 not shown) Planarity restraints: 1312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 60 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.94e+00 pdb=" C PHE B 60 " -0.038 2.00e-02 2.50e+03 pdb=" O PHE B 60 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU B 61 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 60 " 0.009 2.00e-02 2.50e+03 1.14e-02 2.26e+00 pdb=" CG PHE B 60 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE B 60 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 60 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 60 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 60 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 60 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 285 " 0.007 2.00e-02 2.50e+03 8.65e-03 1.50e+00 pdb=" CG TYR A 285 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 285 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 285 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 285 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 285 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 285 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 285 " 0.004 2.00e-02 2.50e+03 ... (remaining 1309 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 331 2.71 - 3.26: 7812 3.26 - 3.81: 12917 3.81 - 4.35: 15474 4.35 - 4.90: 25397 Nonbonded interactions: 61931 Sorted by model distance: nonbonded pdb=" O TRP A 269 " pdb=" OH TYR A 467 " model vdw 2.166 3.040 nonbonded pdb=" NE2 GLN A 205 " pdb=" O ASP B 439 " model vdw 2.205 3.120 nonbonded pdb=" OG1 THR B 57 " pdb=" O LYS B 59 " model vdw 2.223 3.040 nonbonded pdb=" O SER A 88 " pdb=" OG SER A 88 " model vdw 2.227 3.040 nonbonded pdb=" N GLN A 295 " pdb=" OE1 GLN A 295 " model vdw 2.230 3.120 ... (remaining 61926 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.840 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: 0.060 Set scattering table: 0.080 Process input model: 19.990 Find NCS groups from input model: 0.090 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 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 : 0.002 0.043 7632 Z= 0.151 Angle : 0.581 9.248 10312 Z= 0.298 Chirality : 0.043 0.170 1106 Planarity : 0.003 0.032 1312 Dihedral : 17.270 88.487 2868 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.31 % Allowed : 27.59 % Favored : 68.10 % 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: -1.01 (0.28), residues: 900 helix: 0.61 (0.30), residues: 314 sheet: -1.26 (0.42), residues: 139 loop : -1.40 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 370 HIS 0.005 0.001 HIS B 358 PHE 0.024 0.001 PHE B 60 TYR 0.018 0.001 TYR A 285 ARG 0.007 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 89 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 HIS cc_start: 0.8814 (m-70) cc_final: 0.8344 (t-170) REVERT: A 295 GLN cc_start: 0.9062 (pm20) cc_final: 0.8649 (pm20) REVERT: A 348 GLU cc_start: 0.9408 (pp20) cc_final: 0.9091 (pp20) REVERT: A 474 ASP cc_start: 0.7047 (OUTLIER) cc_final: 0.6491 (p0) REVERT: B 75 LEU cc_start: 0.9178 (mm) cc_final: 0.8928 (mm) REVERT: B 172 ASP cc_start: 0.8126 (t0) cc_final: 0.7822 (t0) REVERT: B 345 MET cc_start: 0.8793 (mtm) cc_final: 0.8412 (mtm) REVERT: B 348 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8624 (mp) REVERT: B 369 TRP cc_start: 0.7515 (m-90) cc_final: 0.6825 (m-90) REVERT: B 371 ASP cc_start: 0.8002 (p0) cc_final: 0.6950 (m-30) REVERT: B 375 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6843 (mp0) outliers start: 35 outliers final: 29 residues processed: 116 average time/residue: 0.1805 time to fit residues: 29.2563 Evaluate side-chains 119 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 438 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 0.0970 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.0040 chunk 52 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 205 GLN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7632 Z= 0.254 Angle : 0.574 6.804 10312 Z= 0.300 Chirality : 0.044 0.174 1106 Planarity : 0.003 0.031 1312 Dihedral : 8.388 59.321 1040 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 6.03 % Allowed : 24.51 % Favored : 69.46 % 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: -1.12 (0.28), residues: 900 helix: 0.60 (0.30), residues: 318 sheet: -1.47 (0.42), residues: 128 loop : -1.50 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 369 HIS 0.006 0.001 HIS B 358 PHE 0.016 0.002 PHE B 60 TYR 0.012 0.001 TYR B 330 ARG 0.004 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 96 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 ASP cc_start: 0.8436 (t0) cc_final: 0.8104 (t0) REVERT: B 223 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.8992 (t80) REVERT: B 345 MET cc_start: 0.8742 (mtm) cc_final: 0.8342 (mtm) REVERT: B 371 ASP cc_start: 0.7969 (p0) cc_final: 0.7521 (m-30) outliers start: 49 outliers final: 29 residues processed: 131 average time/residue: 0.1908 time to fit residues: 34.7380 Evaluate side-chains 117 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 88 optimal weight: 0.0980 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 7632 Z= 0.374 Angle : 0.639 8.106 10312 Z= 0.334 Chirality : 0.046 0.186 1106 Planarity : 0.004 0.032 1312 Dihedral : 7.413 58.427 1005 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 7.51 % Allowed : 22.78 % Favored : 69.70 % 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: -1.26 (0.27), residues: 900 helix: 0.39 (0.29), residues: 310 sheet: -1.56 (0.43), residues: 126 loop : -1.47 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 86 HIS 0.006 0.001 HIS B 358 PHE 0.020 0.002 PHE B 60 TYR 0.020 0.002 TYR B 330 ARG 0.009 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 94 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8084 (p0) REVERT: B 172 ASP cc_start: 0.8442 (t0) cc_final: 0.8034 (t0) REVERT: B 345 MET cc_start: 0.8725 (mtm) cc_final: 0.8319 (mtm) REVERT: B 430 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8159 (mp) outliers start: 61 outliers final: 41 residues processed: 133 average time/residue: 0.1850 time to fit residues: 34.0212 Evaluate side-chains 127 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 84 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 430 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7632 Z= 0.197 Angle : 0.571 7.793 10312 Z= 0.293 Chirality : 0.044 0.179 1106 Planarity : 0.003 0.031 1312 Dihedral : 6.483 57.326 999 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 5.79 % Allowed : 24.75 % Favored : 69.46 % 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: -1.23 (0.27), residues: 900 helix: 0.42 (0.30), residues: 319 sheet: -1.47 (0.42), residues: 128 loop : -1.52 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 231 HIS 0.005 0.001 HIS B 358 PHE 0.020 0.001 PHE B 60 TYR 0.017 0.001 TYR B 330 ARG 0.002 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 93 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.9781 (tppt) cc_final: 0.9524 (tppt) REVERT: A 356 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6617 (mp0) REVERT: B 16 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8093 (p0) REVERT: B 138 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7992 (tm-30) REVERT: B 172 ASP cc_start: 0.8418 (t0) cc_final: 0.7940 (t0) REVERT: B 345 MET cc_start: 0.8706 (mtm) cc_final: 0.8292 (mtm) REVERT: B 348 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8636 (mp) REVERT: B 371 ASP cc_start: 0.8105 (p0) cc_final: 0.7731 (m-30) outliers start: 47 outliers final: 31 residues processed: 125 average time/residue: 0.1666 time to fit residues: 29.7954 Evaluate side-chains 118 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 84 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7632 Z= 0.239 Angle : 0.583 7.691 10312 Z= 0.299 Chirality : 0.045 0.196 1106 Planarity : 0.003 0.031 1312 Dihedral : 6.542 57.186 999 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 6.40 % Allowed : 24.88 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.28), residues: 900 helix: 0.53 (0.30), residues: 313 sheet: -1.47 (0.42), residues: 128 loop : -1.45 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 231 HIS 0.006 0.001 HIS B 358 PHE 0.033 0.002 PHE A 78 TYR 0.015 0.001 TYR B 330 ARG 0.002 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 91 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.9784 (tppt) cc_final: 0.9528 (tppt) REVERT: A 356 GLU cc_start: 0.7321 (mm-30) cc_final: 0.6785 (mm-30) REVERT: A 368 GLU cc_start: 0.9339 (OUTLIER) cc_final: 0.8379 (pm20) REVERT: B 16 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8052 (p0) REVERT: B 138 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7982 (tm-30) REVERT: B 172 ASP cc_start: 0.8423 (t0) cc_final: 0.7984 (t0) REVERT: B 345 MET cc_start: 0.8712 (mtm) cc_final: 0.7900 (ptt) REVERT: B 371 ASP cc_start: 0.8129 (p0) cc_final: 0.7777 (m-30) REVERT: B 421 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8297 (tp30) outliers start: 52 outliers final: 38 residues processed: 129 average time/residue: 0.1781 time to fit residues: 32.0875 Evaluate side-chains 126 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 84 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 421 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7632 Z= 0.199 Angle : 0.579 8.245 10312 Z= 0.295 Chirality : 0.045 0.197 1106 Planarity : 0.003 0.031 1312 Dihedral : 6.343 56.427 998 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 6.03 % Allowed : 25.00 % Favored : 68.97 % 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: -1.10 (0.28), residues: 900 helix: 0.62 (0.30), residues: 310 sheet: -1.62 (0.43), residues: 122 loop : -1.42 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 231 HIS 0.006 0.001 HIS B 358 PHE 0.027 0.001 PHE A 78 TYR 0.014 0.001 TYR B 330 ARG 0.002 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 92 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.9792 (tppt) cc_final: 0.9537 (tppt) REVERT: A 356 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6996 (mp0) REVERT: B 16 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8120 (p0) REVERT: B 138 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7949 (tm-30) REVERT: B 172 ASP cc_start: 0.8404 (t0) cc_final: 0.7904 (t0) REVERT: B 345 MET cc_start: 0.8676 (mtm) cc_final: 0.7887 (ptt) REVERT: B 371 ASP cc_start: 0.8055 (p0) cc_final: 0.7788 (m-30) outliers start: 49 outliers final: 38 residues processed: 127 average time/residue: 0.1683 time to fit residues: 30.5597 Evaluate side-chains 127 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 87 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 73 optimal weight: 0.0270 chunk 48 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7632 Z= 0.210 Angle : 0.578 7.417 10312 Z= 0.297 Chirality : 0.045 0.207 1106 Planarity : 0.003 0.031 1312 Dihedral : 6.333 55.996 998 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 6.90 % Allowed : 24.14 % Favored : 68.97 % 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: -1.02 (0.28), residues: 900 helix: 0.71 (0.30), residues: 304 sheet: -1.36 (0.43), residues: 128 loop : -1.42 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.006 0.001 HIS B 358 PHE 0.024 0.001 PHE B 60 TYR 0.016 0.001 TYR B 330 ARG 0.001 0.000 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 93 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8527 (mmtt) cc_final: 0.8317 (mmmt) REVERT: A 112 LYS cc_start: 0.9795 (tppt) cc_final: 0.9543 (tppt) REVERT: A 356 GLU cc_start: 0.7317 (mm-30) cc_final: 0.7016 (mp0) REVERT: A 368 GLU cc_start: 0.9321 (OUTLIER) cc_final: 0.8357 (pm20) REVERT: B 16 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8040 (p0) REVERT: B 138 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7952 (tm-30) REVERT: B 172 ASP cc_start: 0.8389 (t0) cc_final: 0.7862 (t0) REVERT: B 223 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8728 (t80) REVERT: B 274 GLU cc_start: 0.8307 (tm-30) cc_final: 0.8098 (tm-30) REVERT: B 345 MET cc_start: 0.8679 (mtm) cc_final: 0.7902 (ptt) REVERT: B 371 ASP cc_start: 0.8118 (p0) cc_final: 0.7797 (m-30) REVERT: B 425 GLU cc_start: 0.9175 (pm20) cc_final: 0.8934 (pm20) outliers start: 56 outliers final: 43 residues processed: 134 average time/residue: 0.1755 time to fit residues: 33.1902 Evaluate side-chains 131 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 84 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 0.0870 chunk 59 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7632 Z= 0.191 Angle : 0.591 8.421 10312 Z= 0.302 Chirality : 0.045 0.210 1106 Planarity : 0.003 0.031 1312 Dihedral : 6.242 54.779 998 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 6.28 % Allowed : 25.12 % Favored : 68.60 % 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: -0.99 (0.28), residues: 900 helix: 0.65 (0.30), residues: 310 sheet: -1.08 (0.42), residues: 138 loop : -1.45 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.006 0.001 HIS B 358 PHE 0.031 0.001 PHE B 60 TYR 0.021 0.001 TYR A 285 ARG 0.002 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 89 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8525 (mmtt) cc_final: 0.8322 (mmmt) REVERT: A 112 LYS cc_start: 0.9796 (tppt) cc_final: 0.9537 (tppt) REVERT: A 356 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6946 (mp0) REVERT: A 368 GLU cc_start: 0.9313 (OUTLIER) cc_final: 0.8336 (pm20) REVERT: A 435 MET cc_start: 0.7762 (tpt) cc_final: 0.7533 (tpt) REVERT: A 486 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7453 (tt) REVERT: B 16 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8044 (p0) REVERT: B 138 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7929 (tm-30) REVERT: B 172 ASP cc_start: 0.8403 (t0) cc_final: 0.7864 (t0) REVERT: B 223 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8759 (t80) REVERT: B 345 MET cc_start: 0.8674 (mtm) cc_final: 0.7896 (ptt) REVERT: B 371 ASP cc_start: 0.8147 (p0) cc_final: 0.7867 (m-30) outliers start: 51 outliers final: 41 residues processed: 126 average time/residue: 0.1785 time to fit residues: 31.6813 Evaluate side-chains 129 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 83 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 63 optimal weight: 0.0870 chunk 24 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7632 Z= 0.198 Angle : 0.599 8.150 10312 Z= 0.306 Chirality : 0.045 0.207 1106 Planarity : 0.003 0.031 1312 Dihedral : 6.231 54.198 998 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 6.03 % Allowed : 25.62 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.28), residues: 900 helix: 0.64 (0.30), residues: 310 sheet: -1.03 (0.43), residues: 138 loop : -1.44 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.006 0.001 HIS B 358 PHE 0.028 0.001 PHE B 60 TYR 0.013 0.001 TYR A 353 ARG 0.004 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 86 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.9094 (ptt-90) cc_final: 0.8737 (ptp90) REVERT: A 112 LYS cc_start: 0.9797 (tppt) cc_final: 0.9535 (tppt) REVERT: A 356 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6911 (mp0) REVERT: A 368 GLU cc_start: 0.9316 (OUTLIER) cc_final: 0.8927 (pm20) REVERT: B 16 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8080 (p0) REVERT: B 138 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: B 172 ASP cc_start: 0.8399 (t0) cc_final: 0.7856 (t0) REVERT: B 223 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8796 (t80) REVERT: B 345 MET cc_start: 0.8654 (mtm) cc_final: 0.7894 (ptt) REVERT: B 371 ASP cc_start: 0.8115 (p0) cc_final: 0.7885 (m-30) outliers start: 49 outliers final: 40 residues processed: 121 average time/residue: 0.1841 time to fit residues: 31.0619 Evaluate side-chains 126 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 82 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7632 Z= 0.211 Angle : 0.605 8.294 10312 Z= 0.310 Chirality : 0.045 0.205 1106 Planarity : 0.003 0.031 1312 Dihedral : 6.243 53.469 998 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.42 % Allowed : 26.35 % Favored : 68.23 % 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: -1.03 (0.28), residues: 900 helix: 0.54 (0.30), residues: 315 sheet: -1.13 (0.44), residues: 128 loop : -1.42 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 231 HIS 0.005 0.001 HIS B 358 PHE 0.027 0.001 PHE B 60 TYR 0.031 0.001 TYR A 285 ARG 0.003 0.000 ARG A 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 85 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.9790 (tppt) cc_final: 0.9526 (tppt) REVERT: A 356 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7012 (mp0) REVERT: A 368 GLU cc_start: 0.9319 (OUTLIER) cc_final: 0.8931 (pm20) REVERT: B 16 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8080 (p0) REVERT: B 44 ASP cc_start: 0.8854 (p0) cc_final: 0.8325 (p0) REVERT: B 138 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7962 (tm-30) REVERT: B 172 ASP cc_start: 0.8371 (t0) cc_final: 0.7827 (t0) REVERT: B 223 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8852 (t80) REVERT: B 345 MET cc_start: 0.8645 (mtm) cc_final: 0.7899 (ptt) REVERT: B 371 ASP cc_start: 0.8110 (p0) cc_final: 0.7888 (m-30) outliers start: 44 outliers final: 40 residues processed: 115 average time/residue: 0.1777 time to fit residues: 29.1797 Evaluate side-chains 126 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 82 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.0060 chunk 10 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 0.0370 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.105855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.083242 restraints weight = 18508.462| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 4.74 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7632 Z= 0.175 Angle : 0.598 8.397 10312 Z= 0.304 Chirality : 0.045 0.199 1106 Planarity : 0.003 0.032 1312 Dihedral : 6.113 51.962 998 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.93 % Allowed : 26.85 % Favored : 68.23 % 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: -0.98 (0.28), residues: 900 helix: 0.61 (0.30), residues: 315 sheet: -1.06 (0.42), residues: 142 loop : -1.43 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.005 0.001 HIS B 358 PHE 0.027 0.001 PHE B 60 TYR 0.055 0.001 TYR A 285 ARG 0.003 0.000 ARG A 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1746.90 seconds wall clock time: 32 minutes 52.60 seconds (1972.60 seconds total)