Starting phenix.real_space_refine on Fri Nov 15 08:41:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isz_35701/11_2024/8isz_35701.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isz_35701/11_2024/8isz_35701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isz_35701/11_2024/8isz_35701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isz_35701/11_2024/8isz_35701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isz_35701/11_2024/8isz_35701.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isz_35701/11_2024/8isz_35701.cif" } resolution = 3.27 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= 0.014 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 P 45 5.49 5 S 23 5.16 5 C 5301 2.51 5 N 1418 2.21 5 O 1674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8461 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3771 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 438} Chain breaks: 1 Chain: "B" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3754 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 435} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 482 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 454 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 8, 'rna3p_pur': 2} Link IDs: {'rna2p': 18, 'rna3p': 2} Time building chain proxies: 5.42, per 1000 atoms: 0.64 Number of scatterers: 8461 At special positions: 0 Unit cell: (83.2, 91.52, 141.44, 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) S 23 16.00 P 45 15.00 O 1674 8.00 N 1418 7.00 C 5301 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: 2.51 Conformation dependent library (CDL) restraints added in 963.7 milliseconds 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1742 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 9 sheets defined 37.4% alpha, 13.3% beta 6 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain 'A' and resid 22 through 30 Processing helix chain 'A' and resid 46 through 62 removed outlier: 3.565A pdb=" N LYS A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 98 through 106 removed outlier: 3.991A pdb=" N PHE A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 132 removed outlier: 3.752A pdb=" N ASP A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 151 removed outlier: 3.581A pdb=" N TYR A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.711A pdb=" N GLN A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 248 through 264 removed outlier: 4.148A pdb=" N LEU A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 366 through 375 removed outlier: 3.687A 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 490 Processing helix chain 'A' and resid 491 through 493 No H-bonds generated for 'chain 'A' and resid 491 through 493' Processing helix chain 'B' and resid 14 through 28 removed outlier: 3.726A pdb=" N THR B 18 " --> pdb=" O ASP B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 71 through 89 removed outlier: 3.567A pdb=" N LEU B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 138 Processing helix chain 'B' and resid 147 through 158 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 257 through 280 Processing helix chain 'B' and resid 300 through 304 removed outlier: 3.518A pdb=" N ASP B 303 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 368 removed outlier: 3.592A pdb=" N GLN B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 367 " --> pdb=" O LYS B 363 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 384 Processing helix chain 'B' and resid 421 through 438 removed outlier: 3.518A pdb=" N GLU B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU B 438 " --> pdb=" O ASN B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 448 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 removed outlier: 6.621A pdb=" N VAL A 357 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL A 386 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ILE A 359 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE A 388 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA A 361 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N CYS A 279 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N HIS A 360 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A 281 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 304 " --> pdb=" O TYR A 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 20 removed outlier: 3.800A pdb=" N GLN A 18 " --> pdb=" O PHE A 14 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.134A pdb=" N GLY A 42 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE A 142 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL A 44 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP A 139 " --> pdb=" O GLN A 222 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU A 224 " --> pdb=" O TRP A 139 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL A 141 " --> pdb=" O LEU A 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 397 through 398 removed outlier: 3.512A pdb=" N GLU B 169 " --> pdb=" O GLY B 412 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 425 through 426 Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.518A pdb=" N LYS B 4 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU B 61 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N PHE B 6 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 63 " --> pdb=" O PHE B 6 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N SER B 8 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.701A pdb=" N MET B 336 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS B 328 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 334 " --> pdb=" O LYS B 328 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU B 402 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 401 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 403 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 207 through 210 Processing sheet with id=AA9, first strand: chain 'B' and resid 283 through 286 283 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1522 1.33 - 1.45: 2415 1.45 - 1.57: 4698 1.57 - 1.69: 88 1.69 - 1.81: 35 Bond restraints: 8758 Sorted by residual: bond pdb=" C TYR B 330 " pdb=" N PRO B 331 " ideal model delta sigma weight residual 1.336 1.365 -0.030 1.23e-02 6.61e+03 5.77e+00 bond pdb=" O5' A C 10 " pdb=" C5' A C 10 " ideal model delta sigma weight residual 1.420 1.452 -0.032 1.50e-02 4.44e+03 4.64e+00 bond pdb=" C2 U C 14 " pdb=" N3 U C 14 " ideal model delta sigma weight residual 1.373 1.334 0.039 2.00e-02 2.50e+03 3.76e+00 bond pdb=" O5' G C 11 " pdb=" C5' G C 11 " ideal model delta sigma weight residual 1.424 1.452 -0.028 1.50e-02 4.44e+03 3.55e+00 bond pdb=" O5' G C 8 " pdb=" C5' G C 8 " ideal model delta sigma weight residual 1.420 1.448 -0.028 1.50e-02 4.44e+03 3.45e+00 ... (remaining 8753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 11783 2.40 - 4.81: 202 4.81 - 7.21: 38 7.21 - 9.62: 11 9.62 - 12.02: 6 Bond angle restraints: 12040 Sorted by residual: angle pdb=" O3' U C 9 " pdb=" C3' U C 9 " pdb=" C2' U C 9 " ideal model delta sigma weight residual 109.50 118.15 -8.65 1.50e+00 4.44e-01 3.32e+01 angle pdb=" C3' A C 7 " pdb=" C2' A C 7 " pdb=" C1' A C 7 " ideal model delta sigma weight residual 101.50 97.02 4.48 1.00e+00 1.00e+00 2.00e+01 angle pdb=" C3' U C 9 " pdb=" O3' U C 9 " pdb=" P A C 10 " ideal model delta sigma weight residual 120.20 126.05 -5.85 1.50e+00 4.44e-01 1.52e+01 angle pdb=" CA LYS B 302 " pdb=" CB LYS B 302 " pdb=" CG LYS B 302 " ideal model delta sigma weight residual 114.10 121.72 -7.62 2.00e+00 2.50e-01 1.45e+01 angle pdb=" CB MET B 336 " pdb=" CG MET B 336 " pdb=" SD MET B 336 " ideal model delta sigma weight residual 112.70 123.83 -11.13 3.00e+00 1.11e-01 1.38e+01 ... (remaining 12035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 4875 35.40 - 70.81: 357 70.81 - 106.21: 10 106.21 - 141.61: 0 141.61 - 177.01: 2 Dihedral angle restraints: 5244 sinusoidal: 2549 harmonic: 2695 Sorted by residual: dihedral pdb=" O4' U C 9 " pdb=" C1' U C 9 " pdb=" N1 U C 9 " pdb=" C2 U C 9 " ideal model delta sinusoidal sigma weight residual 232.00 54.99 177.01 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' A C 10 " pdb=" C2' A C 10 " pdb=" C1' A C 10 " pdb=" C3' A C 10 " ideal model delta sinusoidal sigma weight residual 25.00 -21.92 46.92 1 8.00e+00 1.56e-02 4.75e+01 dihedral pdb=" C4' A C 10 " pdb=" C3' A C 10 " pdb=" C2' A C 10 " pdb=" C1' A C 10 " ideal model delta sinusoidal sigma weight residual 36.00 -7.55 43.55 1 8.00e+00 1.56e-02 4.13e+01 ... (remaining 5241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1258 0.111 - 0.223: 55 0.223 - 0.334: 0 0.334 - 0.446: 4 0.446 - 0.557: 2 Chirality restraints: 1319 Sorted by residual: chirality pdb=" P A C 10 " pdb=" OP1 A C 10 " pdb=" OP2 A C 10 " pdb=" O5' A C 10 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.76e+00 chirality pdb=" P A C 7 " pdb=" OP1 A C 7 " pdb=" OP2 A C 7 " pdb=" O5' A C 7 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" P G C 11 " pdb=" OP1 G C 11 " pdb=" OP2 G C 11 " pdb=" O5' G C 11 " both_signs ideal model delta sigma weight residual True 2.41 -2.85 -0.44 2.00e-01 2.50e+01 4.92e+00 ... (remaining 1316 not shown) Planarity restraints: 1372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 331 " 0.054 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO A 332 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 322 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO A 323 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 323 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 323 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U C 14 " 0.012 2.00e-02 2.50e+03 1.53e-02 5.29e+00 pdb=" N1 U C 14 " 0.002 2.00e-02 2.50e+03 pdb=" C2 U C 14 " -0.030 2.00e-02 2.50e+03 pdb=" O2 U C 14 " -0.005 2.00e-02 2.50e+03 pdb=" N3 U C 14 " 0.031 2.00e-02 2.50e+03 pdb=" C4 U C 14 " 0.001 2.00e-02 2.50e+03 pdb=" O4 U C 14 " -0.006 2.00e-02 2.50e+03 pdb=" C5 U C 14 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U C 14 " -0.007 2.00e-02 2.50e+03 ... (remaining 1369 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 60 2.51 - 3.11: 5821 3.11 - 3.71: 14313 3.71 - 4.30: 18986 4.30 - 4.90: 29453 Nonbonded interactions: 68633 Sorted by model distance: nonbonded pdb=" C2 DA D 31 " pdb=" N1 G C 15 " model vdw 1.918 3.420 nonbonded pdb=" OD1 ASP B 44 " pdb=" OG SER B 47 " model vdw 2.233 3.040 nonbonded pdb=" O ASN A 34 " pdb=" OH TYR A 261 " model vdw 2.242 3.040 nonbonded pdb=" OG SER B 104 " pdb=" OD1 ASP B 106 " model vdw 2.248 3.040 nonbonded pdb=" O PRO B 182 " pdb=" OG1 THR B 243 " model vdw 2.256 3.040 ... (remaining 68628 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: 1.160 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.980 Find NCS groups from input model: 0.130 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 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 : 0.004 0.039 8758 Z= 0.228 Angle : 0.850 12.022 12040 Z= 0.436 Chirality : 0.057 0.557 1319 Planarity : 0.006 0.082 1372 Dihedral : 20.885 177.013 3502 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.12 % Allowed : 31.95 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -2.32 (0.25), residues: 909 helix: -0.54 (0.28), residues: 306 sheet: -1.04 (0.46), residues: 130 loop : -2.43 (0.24), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 369 HIS 0.005 0.001 HIS B 358 PHE 0.013 0.001 PHE A 403 TYR 0.021 0.001 TYR A 285 ARG 0.007 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 ASN cc_start: 0.7139 (p0) cc_final: 0.6823 (p0) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.2568 time to fit residues: 54.9070 Evaluate side-chains 135 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.1980 chunk 55 optimal weight: 7.9990 chunk 86 optimal weight: 0.0010 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8758 Z= 0.226 Angle : 0.717 10.226 12040 Z= 0.375 Chirality : 0.046 0.292 1319 Planarity : 0.005 0.067 1372 Dihedral : 19.396 177.825 1597 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.17 % Allowed : 29.76 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.77 (0.26), residues: 909 helix: 0.10 (0.29), residues: 310 sheet: -1.43 (0.40), residues: 158 loop : -2.03 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 421 HIS 0.006 0.001 HIS A 329 PHE 0.030 0.001 PHE A 503 TYR 0.020 0.001 TYR A 285 ARG 0.004 0.001 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 TYR cc_start: 0.5699 (m-10) cc_final: 0.5311 (m-10) outliers start: 26 outliers final: 10 residues processed: 164 average time/residue: 0.2597 time to fit residues: 55.5735 Evaluate side-chains 138 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 266 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 23 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 307 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8758 Z= 0.243 Angle : 0.697 10.559 12040 Z= 0.365 Chirality : 0.046 0.211 1319 Planarity : 0.005 0.060 1372 Dihedral : 19.535 174.754 1597 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 5.37 % Allowed : 28.90 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.56 (0.26), residues: 909 helix: 0.31 (0.29), residues: 309 sheet: -1.42 (0.41), residues: 139 loop : -1.87 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 421 HIS 0.004 0.001 HIS A 329 PHE 0.018 0.002 PHE B 223 TYR 0.020 0.002 TYR B 293 ARG 0.006 0.001 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 TYR cc_start: 0.5908 (m-80) cc_final: 0.5638 (m-10) REVERT: B 287 MET cc_start: 0.5333 (tpt) cc_final: 0.4059 (tpt) REVERT: B 336 MET cc_start: 0.6929 (ppp) cc_final: 0.6639 (ppp) outliers start: 44 outliers final: 22 residues processed: 173 average time/residue: 0.2654 time to fit residues: 60.0406 Evaluate side-chains 154 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 433 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 6.9990 chunk 64 optimal weight: 0.0470 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 82 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 HIS ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8758 Z= 0.191 Angle : 0.694 11.794 12040 Z= 0.357 Chirality : 0.045 0.189 1319 Planarity : 0.005 0.056 1372 Dihedral : 19.471 171.975 1597 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.15 % Allowed : 30.98 % Favored : 64.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 909 helix: 0.29 (0.29), residues: 322 sheet: -1.13 (0.40), residues: 140 loop : -1.97 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 421 HIS 0.002 0.001 HIS A 251 PHE 0.018 0.001 PHE A 75 TYR 0.019 0.001 TYR B 293 ARG 0.005 0.000 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.874 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: A 262 TYR cc_start: 0.6391 (t80) cc_final: 0.6178 (t80) REVERT: A 355 LYS cc_start: 0.7440 (tppt) cc_final: 0.7099 (tppt) REVERT: A 380 ASN cc_start: 0.7619 (p0) cc_final: 0.7335 (p0) REVERT: A 397 TYR cc_start: 0.5885 (m-80) cc_final: 0.5672 (m-10) REVERT: B 287 MET cc_start: 0.5348 (tpt) cc_final: 0.4067 (tpt) outliers start: 34 outliers final: 22 residues processed: 163 average time/residue: 0.2656 time to fit residues: 56.5722 Evaluate side-chains 157 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 433 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 68 optimal weight: 0.1980 chunk 37 optimal weight: 0.0370 chunk 78 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8758 Z= 0.215 Angle : 0.687 11.110 12040 Z= 0.353 Chirality : 0.045 0.174 1319 Planarity : 0.005 0.054 1372 Dihedral : 19.313 171.349 1597 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.90 % Allowed : 32.32 % Favored : 63.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.27), residues: 909 helix: 0.53 (0.30), residues: 314 sheet: -1.15 (0.40), residues: 142 loop : -1.89 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 421 HIS 0.003 0.001 HIS B 9 PHE 0.017 0.001 PHE A 75 TYR 0.022 0.001 TYR B 293 ARG 0.005 0.001 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.851 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: A 355 LYS cc_start: 0.7543 (tppt) cc_final: 0.7248 (tppt) REVERT: A 380 ASN cc_start: 0.7664 (p0) cc_final: 0.7351 (p0) REVERT: B 287 MET cc_start: 0.5731 (tpt) cc_final: 0.4225 (tpt) outliers start: 32 outliers final: 20 residues processed: 157 average time/residue: 0.2598 time to fit residues: 53.4474 Evaluate side-chains 158 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 433 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 8758 Z= 0.369 Angle : 0.779 10.842 12040 Z= 0.402 Chirality : 0.046 0.172 1319 Planarity : 0.006 0.053 1372 Dihedral : 19.361 170.531 1597 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.88 % Allowed : 30.73 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.27), residues: 909 helix: 0.38 (0.30), residues: 308 sheet: -1.51 (0.41), residues: 136 loop : -1.84 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 369 HIS 0.004 0.001 HIS A 329 PHE 0.018 0.002 PHE A 403 TYR 0.023 0.002 TYR B 293 ARG 0.007 0.001 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 137 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7510 (tt0) REVERT: A 380 ASN cc_start: 0.7885 (p0) cc_final: 0.7606 (p0) REVERT: A 462 LEU cc_start: 0.6718 (tt) cc_final: 0.6380 (tp) REVERT: B 287 MET cc_start: 0.5993 (tpt) cc_final: 0.4202 (tpt) outliers start: 40 outliers final: 26 residues processed: 162 average time/residue: 0.2660 time to fit residues: 56.5727 Evaluate side-chains 156 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 433 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 8758 Z= 0.340 Angle : 0.790 11.842 12040 Z= 0.407 Chirality : 0.047 0.174 1319 Planarity : 0.006 0.055 1372 Dihedral : 19.430 170.654 1597 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 4.88 % Allowed : 31.22 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.27), residues: 909 helix: 0.23 (0.29), residues: 315 sheet: -1.38 (0.43), residues: 124 loop : -1.88 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 369 HIS 0.004 0.001 HIS B 9 PHE 0.035 0.002 PHE A 78 TYR 0.026 0.002 TYR B 293 ARG 0.008 0.001 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 287 MET cc_start: 0.6010 (tpt) cc_final: 0.4340 (tpt) outliers start: 40 outliers final: 28 residues processed: 165 average time/residue: 0.2480 time to fit residues: 54.2519 Evaluate side-chains 159 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 433 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 62 optimal weight: 0.0060 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 HIS ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8758 Z= 0.224 Angle : 0.786 13.353 12040 Z= 0.397 Chirality : 0.046 0.176 1319 Planarity : 0.005 0.055 1372 Dihedral : 19.331 170.181 1597 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.17 % Allowed : 32.93 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.46 (0.28), residues: 909 helix: 0.40 (0.30), residues: 317 sheet: -1.42 (0.43), residues: 136 loop : -1.84 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 421 HIS 0.004 0.001 HIS A 329 PHE 0.023 0.001 PHE A 78 TYR 0.021 0.001 TYR B 293 ARG 0.010 0.001 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 287 MET cc_start: 0.5971 (tpt) cc_final: 0.4435 (tpt) outliers start: 26 outliers final: 19 residues processed: 163 average time/residue: 0.2677 time to fit residues: 57.0694 Evaluate side-chains 152 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8758 Z= 0.246 Angle : 0.803 13.303 12040 Z= 0.406 Chirality : 0.046 0.178 1319 Planarity : 0.005 0.055 1372 Dihedral : 19.339 169.652 1597 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.05 % Allowed : 33.66 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.28), residues: 909 helix: 0.31 (0.29), residues: 318 sheet: -1.40 (0.43), residues: 136 loop : -1.86 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 421 HIS 0.005 0.001 HIS A 251 PHE 0.017 0.001 PHE A 78 TYR 0.024 0.002 TYR B 330 ARG 0.015 0.001 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 LEU cc_start: 0.6629 (tt) cc_final: 0.6221 (tt) REVERT: B 157 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7691 (tp) outliers start: 25 outliers final: 22 residues processed: 155 average time/residue: 0.2810 time to fit residues: 56.4542 Evaluate side-chains 155 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 chunk 80 optimal weight: 0.0570 chunk 23 optimal weight: 5.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 HIS ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8758 Z= 0.230 Angle : 0.801 13.798 12040 Z= 0.403 Chirality : 0.045 0.195 1319 Planarity : 0.006 0.109 1372 Dihedral : 19.306 169.036 1597 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.93 % Allowed : 33.05 % Favored : 64.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.28), residues: 909 helix: 0.35 (0.30), residues: 311 sheet: -1.40 (0.41), residues: 152 loop : -1.85 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 421 HIS 0.004 0.001 HIS B 340 PHE 0.016 0.001 PHE A 403 TYR 0.021 0.001 TYR B 330 ARG 0.015 0.001 ARG B 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 157 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7653 (tp) REVERT: B 287 MET cc_start: 0.6064 (tpt) cc_final: 0.4477 (tpt) outliers start: 24 outliers final: 21 residues processed: 154 average time/residue: 0.2727 time to fit residues: 55.0673 Evaluate side-chains 155 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 0.0010 chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 HIS ** A 222 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 = 0.4216 r_free = 0.4216 target = 0.141381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.115615 restraints weight = 24316.997| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 5.37 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8758 Z= 0.229 Angle : 0.808 13.597 12040 Z= 0.405 Chirality : 0.045 0.182 1319 Planarity : 0.006 0.065 1372 Dihedral : 19.298 168.895 1597 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.68 % Allowed : 33.78 % Favored : 63.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.48 (0.28), residues: 909 helix: 0.40 (0.29), residues: 311 sheet: -1.34 (0.41), residues: 151 loop : -1.87 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 421 HIS 0.003 0.001 HIS B 9 PHE 0.016 0.001 PHE A 403 TYR 0.021 0.001 TYR B 330 ARG 0.012 0.001 ARG A 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2096.25 seconds wall clock time: 39 minutes 10.98 seconds (2350.98 seconds total)