Starting phenix.real_space_refine on Mon Mar 11 03:11:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga5_29890/03_2024/8ga5_29890.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga5_29890/03_2024/8ga5_29890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga5_29890/03_2024/8ga5_29890.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga5_29890/03_2024/8ga5_29890.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga5_29890/03_2024/8ga5_29890.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga5_29890/03_2024/8ga5_29890.pdb" } resolution = 2.6 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= 0.002 sd= 0.091 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: 5 Type Number sf(0) Gaussians S 42 5.16 5 Cl 6 4.86 5 C 4432 2.51 5 N 1140 2.21 5 O 1169 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ASP 73": "OD1" <-> "OD2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B ASP 171": "OD1" <-> "OD2" Residue "B ASP 240": "OD1" <-> "OD2" Residue "B GLU 377": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6789 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3377 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 19, 'TRANS': 430} Chain: "B" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3377 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 19, 'TRANS': 430} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 4.37, per 1000 atoms: 0.64 Number of scatterers: 6789 At special positions: 0 Unit cell: (75.9, 71.775, 112.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 6 17.00 S 42 16.00 O 1169 8.00 N 1140 7.00 C 4432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS B 450 " distance=2.02 Simple disulfide: pdb=" SG CYS A 450 " - pdb=" SG CYS B 25 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.67 Conformation dependent library (CDL) restraints added in 1.4 seconds 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 81.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 14 through 26 removed outlier: 3.635A pdb=" N CYS A 25 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 71 removed outlier: 3.964A pdb=" N LEU A 36 " --> pdb=" O PRO A 32 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 100 removed outlier: 3.594A pdb=" N ALA A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 126 through 141 Processing helix chain 'A' and resid 147 through 166 Processing helix chain 'A' and resid 170 through 190 removed outlier: 3.584A pdb=" N ARG A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 202 removed outlier: 3.571A pdb=" N ILE A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 233 removed outlier: 4.121A pdb=" N PHE A 232 " --> pdb=" O MET A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 251 through 285 removed outlier: 4.000A pdb=" N TYR A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Proline residue: A 267 - end of helix removed outlier: 3.966A pdb=" N VAL A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.826A pdb=" N LEU A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 313 removed outlier: 3.571A pdb=" N SER A 313 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 325 removed outlier: 3.576A pdb=" N ALA A 325 " --> pdb=" O PRO A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 349 Processing helix chain 'A' and resid 356 through 379 Processing helix chain 'A' and resid 386 through 401 removed outlier: 3.520A pdb=" N ALA A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 392 " --> pdb=" O THR A 388 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU A 398 " --> pdb=" O MET A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 417 removed outlier: 3.519A pdb=" N LEU A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 421 through 439 Processing helix chain 'A' and resid 443 through 457 Processing helix chain 'B' and resid 14 through 24 Processing helix chain 'B' and resid 33 through 71 removed outlier: 3.531A pdb=" N VAL B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 68 " --> pdb=" O ARG B 64 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS B 70 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 101 removed outlier: 3.813A pdb=" N SER B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 105 Processing helix chain 'B' and resid 108 through 117 Processing helix chain 'B' and resid 123 through 140 Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 147 through 166 Processing helix chain 'B' and resid 170 through 189 Processing helix chain 'B' and resid 192 through 202 removed outlier: 3.847A pdb=" N ILE B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 233 removed outlier: 3.722A pdb=" N LYS B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE B 232 " --> pdb=" O MET B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 251 through 285 removed outlier: 4.030A pdb=" N TYR B 255 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Proline residue: B 267 - end of helix removed outlier: 3.507A pdb=" N ARG B 282 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 305 Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.594A pdb=" N SER B 313 " --> pdb=" O PRO B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 325 removed outlier: 4.193A pdb=" N ILE B 322 " --> pdb=" O ASN B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 349 Processing helix chain 'B' and resid 356 through 379 removed outlier: 3.549A pdb=" N VAL B 376 " --> pdb=" O GLY B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 383 removed outlier: 3.556A pdb=" N HIS B 383 " --> pdb=" O PRO B 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 380 through 383' Processing helix chain 'B' and resid 387 through 395 removed outlier: 3.698A pdb=" N GLY B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 Processing helix chain 'B' and resid 404 through 417 Processing helix chain 'B' and resid 421 through 439 Processing helix chain 'B' and resid 443 through 460 508 hydrogen bonds defined for protein. 1509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1051 1.31 - 1.43: 1785 1.43 - 1.56: 3986 1.56 - 1.68: 0 1.68 - 1.81: 76 Bond restraints: 6898 Sorted by residual: bond pdb=" C LEU B 411 " pdb=" O LEU B 411 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.15e-02 7.56e+03 1.91e+01 bond pdb=" CA LEU B 411 " pdb=" C LEU B 411 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.27e-02 6.20e+03 1.66e+01 bond pdb=" C ILE B 410 " pdb=" N LEU B 411 " ideal model delta sigma weight residual 1.334 1.290 0.045 1.27e-02 6.20e+03 1.24e+01 bond pdb=" N LEU B 411 " pdb=" CA LEU B 411 " ideal model delta sigma weight residual 1.459 1.420 0.040 1.19e-02 7.06e+03 1.10e+01 bond pdb=" CA LEU B 411 " pdb=" CB LEU B 411 " ideal model delta sigma weight residual 1.529 1.505 0.024 1.55e-02 4.16e+03 2.37e+00 ... (remaining 6893 not shown) Histogram of bond angle deviations from ideal: 99.85 - 106.69: 213 106.69 - 113.52: 3737 113.52 - 120.36: 2788 120.36 - 127.19: 2555 127.19 - 134.02: 67 Bond angle restraints: 9360 Sorted by residual: angle pdb=" C LEU A 319 " pdb=" N ILE A 320 " pdb=" CA ILE A 320 " ideal model delta sigma weight residual 120.24 124.21 -3.97 6.30e-01 2.52e+00 3.96e+01 angle pdb=" N VAL B 241 " pdb=" CA VAL B 241 " pdb=" C VAL B 241 " ideal model delta sigma weight residual 110.05 106.92 3.13 1.09e+00 8.42e-01 8.24e+00 angle pdb=" CA LEU B 411 " pdb=" CB LEU B 411 " pdb=" CG LEU B 411 " ideal model delta sigma weight residual 116.30 126.27 -9.97 3.50e+00 8.16e-02 8.11e+00 angle pdb=" N TYR A 75 " pdb=" CA TYR A 75 " pdb=" C TYR A 75 " ideal model delta sigma weight residual 109.81 115.86 -6.05 2.21e+00 2.05e-01 7.50e+00 angle pdb=" N TYR B 75 " pdb=" CA TYR B 75 " pdb=" C TYR B 75 " ideal model delta sigma weight residual 109.81 115.59 -5.78 2.21e+00 2.05e-01 6.83e+00 ... (remaining 9355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 3606 17.66 - 35.31: 354 35.31 - 52.97: 44 52.97 - 70.63: 9 70.63 - 88.28: 3 Dihedral angle restraints: 4016 sinusoidal: 1528 harmonic: 2488 Sorted by residual: dihedral pdb=" CA ASP B 240 " pdb=" C ASP B 240 " pdb=" N VAL B 241 " pdb=" CA VAL B 241 " ideal model delta harmonic sigma weight residual 180.00 157.89 22.11 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ALA B 188 " pdb=" C ALA B 188 " pdb=" N ALA B 189 " pdb=" CA ALA B 189 " ideal model delta harmonic sigma weight residual 180.00 158.40 21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA ASP A 240 " pdb=" C ASP A 240 " pdb=" N VAL A 241 " pdb=" CA VAL A 241 " ideal model delta harmonic sigma weight residual 180.00 159.75 20.25 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 4013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 650 0.037 - 0.074: 346 0.074 - 0.111: 81 0.111 - 0.149: 20 0.149 - 0.186: 3 Chirality restraints: 1100 Sorted by residual: chirality pdb=" CB ILE A 356 " pdb=" CA ILE A 356 " pdb=" CG1 ILE A 356 " pdb=" CG2 ILE A 356 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.61e-01 chirality pdb=" CA LEU B 411 " pdb=" N LEU B 411 " pdb=" C LEU B 411 " pdb=" CB LEU B 411 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CB ILE B 356 " pdb=" CA ILE B 356 " pdb=" CG1 ILE B 356 " pdb=" CG2 ILE B 356 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 1097 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 149 " 0.050 5.00e-02 4.00e+02 7.60e-02 9.25e+00 pdb=" N PRO A 150 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 149 " 0.046 5.00e-02 4.00e+02 7.00e-02 7.84e+00 pdb=" N PRO B 150 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 150 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 150 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 358 " -0.045 5.00e-02 4.00e+02 6.67e-02 7.13e+00 pdb=" N PRO B 359 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 359 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 359 " -0.038 5.00e-02 4.00e+02 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1970 2.80 - 3.33: 6169 3.33 - 3.85: 12027 3.85 - 4.38: 15075 4.38 - 4.90: 24614 Nonbonded interactions: 59855 Sorted by model distance: nonbonded pdb=" OD2 ASP A 54 " pdb=" O HOH A 601 " model vdw 2.279 2.440 nonbonded pdb=" OH TYR A 94 " pdb=" OG SER A 350 " model vdw 2.315 2.440 nonbonded pdb=" O LEU A 397 " pdb=" OG SER A 401 " model vdw 2.317 2.440 nonbonded pdb=" OG1 THR B 344 " pdb=" O HOH B 601 " model vdw 2.324 2.440 nonbonded pdb=" O ARG A 147 " pdb=" OG1 THR A 151 " model vdw 2.325 2.440 ... (remaining 59850 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 6.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.900 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 22.900 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:11.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 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 : 0.005 0.071 6898 Z= 0.337 Angle : 0.803 9.965 9360 Z= 0.429 Chirality : 0.046 0.186 1100 Planarity : 0.008 0.076 1176 Dihedral : 13.672 88.284 2438 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % 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: -5.58 (0.17), residues: 896 helix: -3.85 (0.09), residues: 668 sheet: None (None), residues: 0 loop : -2.25 (0.34), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 253 HIS 0.002 0.001 HIS B 234 PHE 0.015 0.002 PHE B 357 TYR 0.011 0.002 TYR A 419 ARG 0.006 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.831 Fit side-chains REVERT: A 17 ARG cc_start: 0.7241 (ttp80) cc_final: 0.6374 (tpt-90) REVERT: B 19 ARG cc_start: 0.7478 (mtt-85) cc_final: 0.7243 (mtt-85) REVERT: B 172 GLU cc_start: 0.7017 (tm-30) cc_final: 0.6085 (tm-30) REVERT: B 174 ARG cc_start: 0.8239 (ttp-170) cc_final: 0.8015 (ttm170) REVERT: B 282 ARG cc_start: 0.7735 (mtp-110) cc_final: 0.7483 (mtt180) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 1.3775 time to fit residues: 184.3510 Evaluate side-chains 102 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 270 ASN A 284 HIS A 327 ASN A 418 ASN A 460 GLN B 157 ASN B 270 ASN B 284 HIS B 287 ASN B 327 ASN B 418 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6898 Z= 0.283 Angle : 0.590 5.620 9360 Z= 0.295 Chirality : 0.041 0.129 1100 Planarity : 0.006 0.063 1176 Dihedral : 4.718 20.562 960 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.62 % Allowed : 11.95 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.24), residues: 896 helix: -0.60 (0.17), residues: 676 sheet: None (None), residues: 0 loop : -1.65 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 291 HIS 0.003 0.001 HIS B 284 PHE 0.023 0.002 PHE B 357 TYR 0.009 0.002 TYR A 210 ARG 0.002 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7122 (ttp80) cc_final: 0.6217 (tpt-90) REVERT: A 205 ARG cc_start: 0.7401 (ttp-110) cc_final: 0.6570 (ttm170) REVERT: A 276 MET cc_start: 0.8839 (mmm) cc_final: 0.8493 (mmm) REVERT: B 172 GLU cc_start: 0.6985 (tm-30) cc_final: 0.6079 (tm-30) REVERT: B 174 ARG cc_start: 0.8016 (ttp-170) cc_final: 0.7701 (ttm170) outliers start: 11 outliers final: 6 residues processed: 103 average time/residue: 1.5883 time to fit residues: 170.3114 Evaluate side-chains 97 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 293 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.0570 chunk 25 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6898 Z= 0.203 Angle : 0.516 5.457 9360 Z= 0.256 Chirality : 0.039 0.124 1100 Planarity : 0.005 0.056 1176 Dihedral : 4.401 19.617 960 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.77 % Allowed : 12.68 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.27), residues: 896 helix: 0.97 (0.19), residues: 682 sheet: None (None), residues: 0 loop : -1.55 (0.37), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 124 HIS 0.002 0.000 HIS B 234 PHE 0.020 0.001 PHE A 357 TYR 0.006 0.001 TYR B 94 ARG 0.002 0.000 ARG B 209 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7130 (ttp80) cc_final: 0.6287 (tpt-90) REVERT: A 20 GLN cc_start: 0.7545 (tm-30) cc_final: 0.6443 (tp40) REVERT: A 205 ARG cc_start: 0.7259 (ttp-110) cc_final: 0.6951 (ttp80) REVERT: A 276 MET cc_start: 0.8808 (mmm) cc_final: 0.8516 (mmm) REVERT: B 172 GLU cc_start: 0.7033 (tm-30) cc_final: 0.6208 (tm-30) REVERT: B 271 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7923 (ptpt) outliers start: 12 outliers final: 5 residues processed: 100 average time/residue: 1.4684 time to fit residues: 153.3985 Evaluate side-chains 92 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 313 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6898 Z= 0.240 Angle : 0.525 5.354 9360 Z= 0.260 Chirality : 0.040 0.129 1100 Planarity : 0.004 0.055 1176 Dihedral : 4.329 20.521 960 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.77 % Allowed : 13.72 % Favored : 84.51 % 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: 1.26 (0.27), residues: 896 helix: 1.51 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -1.42 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 124 HIS 0.002 0.001 HIS B 234 PHE 0.026 0.001 PHE B 357 TYR 0.007 0.001 TYR A 210 ARG 0.002 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7113 (ttp80) cc_final: 0.6294 (tpt-90) REVERT: A 20 GLN cc_start: 0.7565 (tm-30) cc_final: 0.6458 (tp40) REVERT: A 276 MET cc_start: 0.8811 (mmm) cc_final: 0.8483 (mmm) REVERT: B 19 ARG cc_start: 0.7397 (mtt-85) cc_final: 0.6959 (mtt-85) REVERT: B 172 GLU cc_start: 0.7031 (tm-30) cc_final: 0.6213 (tm-30) REVERT: B 271 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7926 (ptpt) outliers start: 12 outliers final: 6 residues processed: 97 average time/residue: 1.5577 time to fit residues: 157.8062 Evaluate side-chains 92 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 313 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6898 Z= 0.272 Angle : 0.540 5.311 9360 Z= 0.267 Chirality : 0.041 0.130 1100 Planarity : 0.004 0.055 1176 Dihedral : 4.352 20.847 960 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.51 % Allowed : 13.57 % Favored : 83.92 % 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: 1.51 (0.27), residues: 896 helix: 1.70 (0.19), residues: 686 sheet: None (None), residues: 0 loop : -1.32 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 124 HIS 0.003 0.001 HIS B 234 PHE 0.024 0.002 PHE B 357 TYR 0.009 0.001 TYR A 210 ARG 0.002 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7098 (ttp80) cc_final: 0.6071 (tpt-90) REVERT: A 20 GLN cc_start: 0.7587 (tm-30) cc_final: 0.6468 (tp40) REVERT: A 21 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7129 (mm) REVERT: A 30 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7170 (ptpp) REVERT: A 276 MET cc_start: 0.8809 (mmm) cc_final: 0.8438 (mmm) REVERT: B 19 ARG cc_start: 0.7406 (mtt-85) cc_final: 0.6999 (mtt-85) REVERT: B 172 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6272 (tm-30) REVERT: B 271 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7923 (ptpt) outliers start: 17 outliers final: 9 residues processed: 102 average time/residue: 1.4090 time to fit residues: 150.5485 Evaluate side-chains 97 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 313 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 72 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6898 Z= 0.236 Angle : 0.526 5.348 9360 Z= 0.260 Chirality : 0.040 0.127 1100 Planarity : 0.004 0.054 1176 Dihedral : 4.273 20.097 960 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.80 % Allowed : 13.72 % Favored : 83.48 % 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: 1.75 (0.27), residues: 896 helix: 1.87 (0.19), residues: 686 sheet: None (None), residues: 0 loop : -1.26 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 124 HIS 0.002 0.001 HIS A 175 PHE 0.025 0.001 PHE B 357 TYR 0.008 0.001 TYR A 210 ARG 0.003 0.000 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7066 (ttp80) cc_final: 0.6247 (tpt-90) REVERT: A 20 GLN cc_start: 0.7570 (tm-30) cc_final: 0.6470 (tp40) REVERT: A 30 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7122 (ptpp) REVERT: A 276 MET cc_start: 0.8799 (mmm) cc_final: 0.8447 (mmm) REVERT: B 19 ARG cc_start: 0.7404 (mtt-85) cc_final: 0.6987 (mtt-85) REVERT: B 172 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6286 (tm-30) REVERT: B 174 ARG cc_start: 0.7948 (ttp-170) cc_final: 0.7700 (ttp80) REVERT: B 271 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7915 (ptpt) outliers start: 19 outliers final: 6 residues processed: 103 average time/residue: 1.3871 time to fit residues: 149.6988 Evaluate side-chains 93 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 313 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.0060 chunk 49 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6898 Z= 0.207 Angle : 0.511 5.380 9360 Z= 0.253 Chirality : 0.039 0.125 1100 Planarity : 0.004 0.053 1176 Dihedral : 4.185 18.995 960 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.51 % Allowed : 14.01 % Favored : 83.48 % 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: 2.01 (0.28), residues: 896 helix: 2.06 (0.19), residues: 686 sheet: None (None), residues: 0 loop : -1.17 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 124 HIS 0.002 0.001 HIS B 234 PHE 0.028 0.001 PHE B 357 TYR 0.007 0.001 TYR A 210 ARG 0.003 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7078 (ttp80) cc_final: 0.6063 (tpt-90) REVERT: A 20 GLN cc_start: 0.7585 (tm-30) cc_final: 0.6470 (tp40) REVERT: A 21 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7134 (mm) REVERT: B 19 ARG cc_start: 0.7398 (mtt-85) cc_final: 0.6959 (mtt-85) REVERT: B 172 GLU cc_start: 0.7067 (tm-30) cc_final: 0.6264 (tm-30) REVERT: B 174 ARG cc_start: 0.7947 (ttp-170) cc_final: 0.7712 (ttp80) REVERT: B 209 ARG cc_start: 0.7356 (mtp-110) cc_final: 0.6301 (mmp80) outliers start: 17 outliers final: 7 residues processed: 102 average time/residue: 1.4845 time to fit residues: 158.0946 Evaluate side-chains 91 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 313 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 75 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6898 Z= 0.240 Angle : 0.529 5.242 9360 Z= 0.261 Chirality : 0.040 0.129 1100 Planarity : 0.004 0.053 1176 Dihedral : 4.224 19.619 960 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.92 % Allowed : 14.75 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.28), residues: 896 helix: 2.08 (0.19), residues: 686 sheet: None (None), residues: 0 loop : -1.15 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 124 HIS 0.002 0.001 HIS A 175 PHE 0.032 0.002 PHE B 357 TYR 0.008 0.001 TYR A 210 ARG 0.003 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7074 (ttp80) cc_final: 0.6052 (tpt-90) REVERT: A 20 GLN cc_start: 0.7594 (tm-30) cc_final: 0.6449 (tp40) REVERT: A 21 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7207 (mm) REVERT: B 19 ARG cc_start: 0.7393 (mtt-85) cc_final: 0.6965 (mtt-85) REVERT: B 172 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6275 (tm-30) outliers start: 13 outliers final: 7 residues processed: 96 average time/residue: 1.4179 time to fit residues: 142.5988 Evaluate side-chains 92 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 313 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 0.0040 chunk 73 optimal weight: 0.6980 chunk 76 optimal weight: 0.0970 chunk 53 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6898 Z= 0.189 Angle : 0.515 7.987 9360 Z= 0.254 Chirality : 0.039 0.124 1100 Planarity : 0.004 0.052 1176 Dihedral : 4.109 17.651 960 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.62 % Allowed : 15.78 % Favored : 82.60 % 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: 2.28 (0.28), residues: 896 helix: 2.26 (0.19), residues: 686 sheet: None (None), residues: 0 loop : -1.08 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 124 HIS 0.002 0.000 HIS B 234 PHE 0.032 0.001 PHE B 357 TYR 0.006 0.001 TYR B 94 ARG 0.002 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.7519 (tm-30) cc_final: 0.6388 (tp40) REVERT: A 21 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7163 (mm) REVERT: A 65 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.5982 (mpm) REVERT: B 19 ARG cc_start: 0.7383 (mtt-85) cc_final: 0.6948 (mtt-85) REVERT: B 20 GLN cc_start: 0.7011 (mm110) cc_final: 0.6575 (tp40) REVERT: B 172 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6230 (tm-30) REVERT: B 209 ARG cc_start: 0.7350 (mtp-110) cc_final: 0.6293 (mmp80) outliers start: 11 outliers final: 6 residues processed: 100 average time/residue: 1.3861 time to fit residues: 145.7179 Evaluate side-chains 94 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 313 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6898 Z= 0.222 Angle : 0.532 7.732 9360 Z= 0.262 Chirality : 0.040 0.127 1100 Planarity : 0.004 0.052 1176 Dihedral : 4.163 18.072 960 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.47 % Allowed : 16.37 % Favored : 82.15 % 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: 2.25 (0.28), residues: 896 helix: 2.23 (0.19), residues: 686 sheet: None (None), residues: 0 loop : -1.10 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 124 HIS 0.002 0.000 HIS B 234 PHE 0.037 0.001 PHE B 357 TYR 0.008 0.001 TYR A 210 ARG 0.002 0.000 ARG B 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7082 (ttp80) cc_final: 0.6037 (tpt-90) REVERT: A 20 GLN cc_start: 0.7549 (tm-30) cc_final: 0.6416 (tp40) REVERT: A 21 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7226 (mm) REVERT: A 65 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6012 (mpm) REVERT: B 19 ARG cc_start: 0.7385 (mtt-85) cc_final: 0.6954 (mtt-85) REVERT: B 172 GLU cc_start: 0.7050 (tm-30) cc_final: 0.6244 (tm-30) outliers start: 10 outliers final: 5 residues processed: 94 average time/residue: 1.5054 time to fit residues: 147.9960 Evaluate side-chains 94 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 313 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.127710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.100404 restraints weight = 6751.441| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.41 r_work: 0.3013 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6898 Z= 0.230 Angle : 0.541 8.125 9360 Z= 0.266 Chirality : 0.040 0.129 1100 Planarity : 0.004 0.052 1176 Dihedral : 4.194 18.230 960 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.77 % Allowed : 15.93 % Favored : 82.30 % 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: 2.25 (0.28), residues: 896 helix: 2.23 (0.19), residues: 686 sheet: None (None), residues: 0 loop : -1.09 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 124 HIS 0.002 0.001 HIS A 175 PHE 0.037 0.002 PHE B 357 TYR 0.009 0.001 TYR A 210 ARG 0.002 0.000 ARG A 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2997.29 seconds wall clock time: 54 minutes 19.75 seconds (3259.75 seconds total)