Starting phenix.real_space_refine on Wed Feb 14 02:42:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isz_35701/02_2024/8isz_35701.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isz_35701/02_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_35701/02_2024/8isz_35701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isz_35701/02_2024/8isz_35701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isz_35701/02_2024/8isz_35701.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isz_35701/02_2024/8isz_35701.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.10, per 1000 atoms: 0.60 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 - 3.50 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: 3.89 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 2.70 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: 2.45 Time building geometry restraints manager: 3.99 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: 96.85 - 104.72: 260 104.72 - 112.58: 4520 112.58 - 120.45: 3796 120.45 - 128.31: 3336 128.31 - 136.17: 128 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 2.440 nonbonded pdb=" O ASN A 34 " pdb=" OH TYR A 261 " model vdw 2.242 2.440 nonbonded pdb=" OG SER B 104 " pdb=" OD1 ASP B 106 " model vdw 2.248 2.440 nonbonded pdb=" O PRO B 182 " pdb=" OG1 THR B 243 " model vdw 2.256 2.440 ... (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 ========== 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: 1.030 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: 2.990 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.040 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.360 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 0.982 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: 0.2389 time to fit residues: 51.1815 Evaluate side-chains 135 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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: 2.9990 chunk 24 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.0070 chunk 55 optimal weight: 7.9990 chunk 86 optimal weight: 0.0030 overall best weight: 1.6014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 8758 Z= 0.264 Angle : 0.708 9.745 12040 Z= 0.369 Chirality : 0.045 0.347 1319 Planarity : 0.005 0.070 1372 Dihedral : 19.517 175.069 1597 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.54 % Allowed : 31.71 % Favored : 64.76 % 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: -1.62 (0.27), residues: 909 helix: 0.25 (0.29), residues: 310 sheet: -1.02 (0.45), residues: 133 loop : -2.07 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 421 HIS 0.007 0.001 HIS A 329 PHE 0.024 0.002 PHE B 223 TYR 0.019 0.002 TYR A 285 ARG 0.004 0.001 ARG B 114 *********************** 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 176 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 147 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 TYR cc_start: 0.5595 (m-80) cc_final: 0.5257 (m-10) REVERT: A 462 LEU cc_start: 0.6658 (tt) cc_final: 0.6397 (tp) REVERT: B 386 ASP cc_start: 0.6127 (p0) cc_final: 0.5880 (p0) outliers start: 29 outliers final: 14 residues processed: 165 average time/residue: 0.2409 time to fit residues: 52.5892 Evaluate side-chains 149 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 207 HIS 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 A residue 474 ASP Chi-restraints excluded: chain B residue 62 ILE 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 266 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 433 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8758 Z= 0.248 Angle : 0.679 10.719 12040 Z= 0.355 Chirality : 0.044 0.178 1319 Planarity : 0.005 0.052 1372 Dihedral : 19.585 177.190 1597 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 5.00 % Allowed : 30.61 % 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: -1.48 (0.27), residues: 909 helix: 0.38 (0.30), residues: 310 sheet: -0.96 (0.43), residues: 120 loop : -1.97 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 368 HIS 0.005 0.001 HIS A 329 PHE 0.021 0.002 PHE A 75 TYR 0.023 0.002 TYR A 285 ARG 0.004 0.001 ARG A 407 *********************** 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 187 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 146 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ASN cc_start: 0.5459 (OUTLIER) cc_final: 0.5205 (p0) REVERT: A 200 TYR cc_start: 0.4331 (OUTLIER) cc_final: 0.3998 (m-80) REVERT: A 380 ASN cc_start: 0.7760 (p0) cc_final: 0.7472 (p0) REVERT: A 397 TYR cc_start: 0.5877 (m-80) cc_final: 0.5531 (m-10) REVERT: B 287 MET cc_start: 0.5344 (tpt) cc_final: 0.4118 (tpt) REVERT: B 336 MET cc_start: 0.6905 (ppp) cc_final: 0.6668 (ppp) REVERT: B 386 ASP cc_start: 0.6230 (p0) cc_final: 0.5972 (p0) outliers start: 41 outliers final: 24 residues processed: 172 average time/residue: 0.2428 time to fit residues: 54.9287 Evaluate side-chains 166 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN 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 200 TYR Chi-restraints excluded: chain A residue 210 LEU 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 367 ASP 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 15 ASP Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 62 ILE 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: 2.9990 chunk 64 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.6455 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8758 Z= 0.197 Angle : 0.679 11.570 12040 Z= 0.347 Chirality : 0.044 0.177 1319 Planarity : 0.005 0.054 1372 Dihedral : 19.612 178.811 1597 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 5.24 % Allowed : 32.44 % Favored : 62.32 % 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: -1.47 (0.27), residues: 909 helix: 0.39 (0.30), residues: 323 sheet: -1.12 (0.43), residues: 131 loop : -1.99 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 421 HIS 0.002 0.001 HIS A 329 PHE 0.016 0.001 PHE B 223 TYR 0.022 0.001 TYR B 293 ARG 0.006 0.000 ARG A 481 *********************** 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 185 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 142 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASN cc_start: 0.5214 (OUTLIER) cc_final: 0.4961 (p0) REVERT: A 200 TYR cc_start: 0.4296 (OUTLIER) cc_final: 0.3961 (m-80) REVERT: A 380 ASN cc_start: 0.7747 (p0) cc_final: 0.7282 (p0) REVERT: A 397 TYR cc_start: 0.5764 (m-80) cc_final: 0.5461 (m-10) REVERT: B 287 MET cc_start: 0.5358 (tpt) cc_final: 0.4058 (tpt) REVERT: B 386 ASP cc_start: 0.6093 (p0) cc_final: 0.5888 (p0) outliers start: 43 outliers final: 26 residues processed: 169 average time/residue: 0.2464 time to fit residues: 54.5466 Evaluate side-chains 164 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 136 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 229 LEU 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 363 THR Chi-restraints excluded: chain A residue 367 ASP 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 A residue 474 ASP Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 62 ILE 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 275 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 395 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 8758 Z= 0.261 Angle : 0.693 10.706 12040 Z= 0.357 Chirality : 0.045 0.176 1319 Planarity : 0.005 0.049 1372 Dihedral : 19.580 179.780 1597 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 5.73 % Allowed : 31.34 % Favored : 62.93 % 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: -1.34 (0.28), residues: 909 helix: 0.57 (0.30), residues: 316 sheet: -1.35 (0.41), residues: 143 loop : -1.83 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 369 HIS 0.003 0.001 HIS B 9 PHE 0.018 0.002 PHE A 75 TYR 0.023 0.002 TYR B 293 ARG 0.005 0.001 ARG A 481 *********************** 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 192 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 145 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASN cc_start: 0.5675 (OUTLIER) cc_final: 0.5442 (p0) REVERT: A 200 TYR cc_start: 0.4232 (OUTLIER) cc_final: 0.3808 (m-80) REVERT: A 303 MET cc_start: 0.6934 (mmm) cc_final: 0.6720 (tpp) REVERT: A 397 TYR cc_start: 0.5822 (m-80) cc_final: 0.5538 (m-10) REVERT: B 287 MET cc_start: 0.5512 (tpt) cc_final: 0.4033 (tpt) REVERT: B 386 ASP cc_start: 0.6161 (p0) cc_final: 0.5933 (p0) outliers start: 47 outliers final: 32 residues processed: 174 average time/residue: 0.2583 time to fit residues: 59.1582 Evaluate side-chains 169 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 200 TYR 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 243 ARG Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 367 ASP 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 A residue 437 VAL Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 109 ASN 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 232 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 0.2980 chunk 18 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 76 optimal weight: 0.0980 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN ** 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: 0.6485 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8758 Z= 0.206 Angle : 0.700 12.587 12040 Z= 0.355 Chirality : 0.044 0.171 1319 Planarity : 0.005 0.049 1372 Dihedral : 19.395 178.636 1597 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.88 % Allowed : 33.41 % Favored : 61.71 % 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: -1.39 (0.27), residues: 909 helix: 0.55 (0.30), residues: 322 sheet: -1.29 (0.42), residues: 136 loop : -1.93 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 369 HIS 0.003 0.001 HIS B 320 PHE 0.014 0.001 PHE A 403 TYR 0.019 0.001 TYR B 330 ARG 0.008 0.001 ARG A 407 *********************** 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 182 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 142 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASN cc_start: 0.5372 (OUTLIER) cc_final: 0.5128 (p0) REVERT: A 74 MET cc_start: 0.5981 (mpp) cc_final: 0.5753 (mpp) REVERT: A 200 TYR cc_start: 0.4251 (OUTLIER) cc_final: 0.3838 (m-80) REVERT: A 262 TYR cc_start: 0.6541 (t80) cc_final: 0.6341 (t80) REVERT: A 397 TYR cc_start: 0.5853 (m-80) cc_final: 0.5532 (m-10) REVERT: B 287 MET cc_start: 0.5659 (tpt) cc_final: 0.4101 (tpt) REVERT: B 364 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8045 (mp10) REVERT: B 386 ASP cc_start: 0.6102 (p0) cc_final: 0.5890 (p0) outliers start: 40 outliers final: 27 residues processed: 170 average time/residue: 0.2382 time to fit residues: 53.9757 Evaluate side-chains 164 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 134 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 406 MET 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 62 ILE Chi-restraints excluded: chain B residue 109 ASN 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 275 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 364 GLN 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 433 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 0.0030 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 overall best weight: 1.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 8758 Z= 0.266 Angle : 0.720 11.665 12040 Z= 0.366 Chirality : 0.044 0.172 1319 Planarity : 0.005 0.049 1372 Dihedral : 19.360 178.244 1597 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 5.24 % Allowed : 33.78 % Favored : 60.98 % 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: -1.42 (0.28), residues: 909 helix: 0.63 (0.30), residues: 314 sheet: -1.42 (0.41), residues: 146 loop : -1.96 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 421 HIS 0.004 0.001 HIS A 329 PHE 0.018 0.001 PHE A 75 TYR 0.021 0.002 TYR B 293 ARG 0.010 0.001 ARG B 54 *********************** 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 182 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 139 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASN cc_start: 0.5860 (OUTLIER) cc_final: 0.5627 (p0) REVERT: A 74 MET cc_start: 0.6229 (mpp) cc_final: 0.5953 (mpp) REVERT: A 200 TYR cc_start: 0.4346 (OUTLIER) cc_final: 0.3827 (m-80) REVERT: A 397 TYR cc_start: 0.5911 (m-80) cc_final: 0.5560 (m-10) REVERT: B 287 MET cc_start: 0.5411 (tpt) cc_final: 0.3691 (tpt) REVERT: B 364 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7160 (mp-120) REVERT: B 386 ASP cc_start: 0.6194 (p0) cc_final: 0.5984 (p0) outliers start: 43 outliers final: 28 residues processed: 166 average time/residue: 0.2457 time to fit residues: 54.0935 Evaluate side-chains 166 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 207 HIS 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 243 ARG 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 367 ASP Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 109 ASN 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 311 VAL Chi-restraints excluded: chain B residue 364 GLN 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 433 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.6515 moved from start: 0.3532 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= 0.223 Angle : 0.727 13.161 12040 Z= 0.365 Chirality : 0.044 0.172 1319 Planarity : 0.005 0.046 1372 Dihedral : 19.317 177.875 1597 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.27 % Allowed : 35.24 % Favored : 60.49 % 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: -1.33 (0.28), residues: 909 helix: 0.62 (0.30), residues: 319 sheet: -1.26 (0.43), residues: 137 loop : -1.90 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 86 HIS 0.003 0.001 HIS A 329 PHE 0.021 0.001 PHE A 78 TYR 0.018 0.001 TYR B 293 ARG 0.007 0.000 ARG A 275 *********************** 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 176 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 141 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASN cc_start: 0.5623 (OUTLIER) cc_final: 0.5375 (p0) REVERT: A 74 MET cc_start: 0.6005 (mpp) cc_final: 0.5784 (mpp) REVERT: A 200 TYR cc_start: 0.4333 (OUTLIER) cc_final: 0.3812 (m-80) REVERT: A 397 TYR cc_start: 0.5991 (m-80) cc_final: 0.5681 (m-10) REVERT: B 157 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7708 (tp) REVERT: B 287 MET cc_start: 0.5697 (tpt) cc_final: 0.3594 (tpt) REVERT: B 364 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8047 (mp10) outliers start: 35 outliers final: 25 residues processed: 169 average time/residue: 0.2343 time to fit residues: 52.3737 Evaluate side-chains 164 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 135 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 207 HIS 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 243 ARG Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 109 ASN 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 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 364 GLN 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 433 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8758 Z= 0.224 Angle : 0.728 13.046 12040 Z= 0.366 Chirality : 0.044 0.174 1319 Planarity : 0.005 0.046 1372 Dihedral : 19.301 178.037 1597 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 4.88 % Allowed : 34.02 % Favored : 61.10 % 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: -1.37 (0.28), residues: 909 helix: 0.52 (0.30), residues: 325 sheet: -1.12 (0.46), residues: 122 loop : -1.95 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 421 HIS 0.003 0.001 HIS A 329 PHE 0.019 0.001 PHE A 78 TYR 0.028 0.001 TYR B 392 ARG 0.009 0.001 ARG A 275 *********************** 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 179 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 139 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASN cc_start: 0.5481 (OUTLIER) cc_final: 0.5267 (p0) REVERT: A 99 GLU cc_start: 0.6754 (tp30) cc_final: 0.6484 (tp30) REVERT: A 200 TYR cc_start: 0.4241 (OUTLIER) cc_final: 0.3627 (m-80) REVERT: A 262 TYR cc_start: 0.6602 (t80) cc_final: 0.6373 (t80) REVERT: A 397 TYR cc_start: 0.5991 (m-80) cc_final: 0.5675 (m-10) REVERT: B 157 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7686 (tp) REVERT: B 287 MET cc_start: 0.5701 (tpt) cc_final: 0.3613 (tpt) REVERT: B 364 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8029 (mp10) outliers start: 40 outliers final: 28 residues processed: 168 average time/residue: 0.2563 time to fit residues: 56.6148 Evaluate side-chains 166 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 134 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 207 HIS 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 243 ARG Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 109 ASN 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 157 ILE 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 364 GLN 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 433 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8758 Z= 0.260 Angle : 0.768 13.358 12040 Z= 0.386 Chirality : 0.044 0.176 1319 Planarity : 0.005 0.070 1372 Dihedral : 19.368 178.083 1597 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 4.15 % Allowed : 35.24 % Favored : 60.61 % 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 (0.27), residues: 909 helix: 0.46 (0.29), residues: 320 sheet: -1.09 (0.46), residues: 119 loop : -2.02 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 421 HIS 0.003 0.001 HIS B 9 PHE 0.019 0.001 PHE A 75 TYR 0.016 0.001 TYR B 293 ARG 0.011 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 172 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 138 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASN cc_start: 0.5882 (OUTLIER) cc_final: 0.5638 (p0) REVERT: A 200 TYR cc_start: 0.4275 (OUTLIER) cc_final: 0.3646 (m-80) REVERT: A 262 TYR cc_start: 0.6650 (t80) cc_final: 0.6433 (t80) REVERT: A 397 TYR cc_start: 0.6000 (m-80) cc_final: 0.5617 (m-10) REVERT: B 287 MET cc_start: 0.5830 (tpt) cc_final: 0.3833 (tpt) REVERT: B 364 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7060 (mp-120) outliers start: 34 outliers final: 26 residues processed: 162 average time/residue: 0.2530 time to fit residues: 53.6891 Evaluate side-chains 166 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 207 HIS 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 243 ARG Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 116 ASN 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 266 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 433 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 chunk 75 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** ** B 234 ASN ** 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 = 0.4154 r_free = 0.4154 target = 0.134548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.107583 restraints weight = 22529.128| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 5.41 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8758 Z= 0.220 Angle : 0.751 13.643 12040 Z= 0.378 Chirality : 0.044 0.176 1319 Planarity : 0.005 0.041 1372 Dihedral : 19.343 178.382 1597 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.54 % Allowed : 36.22 % Favored : 60.24 % 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: -1.47 (0.28), residues: 909 helix: 0.46 (0.30), residues: 322 sheet: -1.11 (0.47), residues: 120 loop : -2.04 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 421 HIS 0.003 0.001 HIS A 329 PHE 0.020 0.001 PHE A 75 TYR 0.042 0.001 TYR B 392 ARG 0.016 0.001 ARG B 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2030.91 seconds wall clock time: 37 minutes 50.34 seconds (2270.34 seconds total)