Starting phenix.real_space_refine on Fri Dec 8 13:12:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isz_35701/12_2023/8isz_35701.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isz_35701/12_2023/8isz_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_35701/12_2023/8isz_35701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isz_35701/12_2023/8isz_35701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isz_35701/12_2023/8isz_35701.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isz_35701/12_2023/8isz_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 4.89, per 1000 atoms: 0.58 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: 3.55 Conformation dependent library (CDL) restraints added in 1.4 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: 2.84 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: 2.75 Time building geometry restraints manager: 3.76 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: 4855 35.40 - 70.81: 345 70.81 - 106.21: 10 106.21 - 141.61: 0 141.61 - 177.01: 2 Dihedral angle restraints: 5212 sinusoidal: 2517 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 5209 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: 0.660 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: 3.010 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 28.090 Find NCS groups from input model: 0.240 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 34.800 ------------------------------------------------------------------------------- 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 : 20.689 177.013 3470 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 : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.2422 time to fit residues: 51.8546 Evaluate side-chains 135 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2945 ------------------------------------------------------------------------------- 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: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8758 Z= 0.269 Angle : 0.711 9.867 12040 Z= 0.371 Chirality : 0.046 0.375 1319 Planarity : 0.005 0.068 1372 Dihedral : 19.003 175.865 1565 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.66 % Allowed : 31.34 % Favored : 65.00 % 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: -1.03 (0.45), residues: 133 loop : -2.07 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 421 HIS 0.007 0.001 HIS A 329 PHE 0.027 0.002 PHE B 223 TYR 0.021 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: 30 poor density : 146 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 165 average time/residue: 0.2402 time to fit residues: 52.9764 Evaluate side-chains 148 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 0.889 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0853 time to fit residues: 3.5729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 71 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 76 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8758 Z= 0.240 Angle : 0.674 10.560 12040 Z= 0.352 Chirality : 0.045 0.226 1319 Planarity : 0.005 0.053 1372 Dihedral : 19.083 177.793 1565 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.54 % Allowed : 31.46 % Favored : 65.00 % 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: 0.37 (0.30), residues: 310 sheet: -1.02 (0.43), residues: 122 loop : -1.93 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 368 HIS 0.003 0.001 HIS B 9 PHE 0.020 0.002 PHE B 60 TYR 0.019 0.002 TYR A 285 ARG 0.004 0.000 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 177 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 148 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 11 residues processed: 168 average time/residue: 0.2571 time to fit residues: 56.2582 Evaluate side-chains 146 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0831 time to fit residues: 2.9166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0670 chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 45 optimal weight: 0.0050 chunk 82 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 overall best weight: 0.9134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8758 Z= 0.214 Angle : 0.681 11.079 12040 Z= 0.348 Chirality : 0.044 0.176 1319 Planarity : 0.005 0.055 1372 Dihedral : 19.105 179.171 1565 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.68 % Allowed : 33.66 % Favored : 63.66 % 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: -1.49 (0.27), residues: 909 helix: 0.39 (0.30), residues: 321 sheet: -1.44 (0.41), residues: 148 loop : -1.89 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 421 HIS 0.003 0.001 HIS A 329 PHE 0.017 0.001 PHE B 223 TYR 0.012 0.001 TYR B 293 ARG 0.004 0.000 ARG A 275 *********************** 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 161 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 139 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 151 average time/residue: 0.2646 time to fit residues: 52.0176 Evaluate side-chains 145 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 0.836 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1397 time to fit residues: 4.1066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8758 Z= 0.206 Angle : 0.661 11.409 12040 Z= 0.340 Chirality : 0.044 0.173 1319 Planarity : 0.005 0.056 1372 Dihedral : 18.999 179.287 1565 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.68 % Allowed : 34.39 % 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: -1.43 (0.27), residues: 909 helix: 0.52 (0.30), residues: 321 sheet: -1.47 (0.41), residues: 146 loop : -1.89 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 369 HIS 0.003 0.001 HIS A 329 PHE 0.019 0.001 PHE A 75 TYR 0.012 0.001 TYR B 392 ARG 0.004 0.000 ARG A 407 *********************** 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 168 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 156 average time/residue: 0.2542 time to fit residues: 52.6921 Evaluate side-chains 150 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 0.896 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0962 time to fit residues: 3.1637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 18 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 76 optimal weight: 0.0670 chunk 42 optimal weight: 0.0670 chunk 7 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8758 Z= 0.211 Angle : 0.689 12.242 12040 Z= 0.349 Chirality : 0.044 0.170 1319 Planarity : 0.005 0.054 1372 Dihedral : 18.855 178.362 1565 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.32 % Allowed : 34.63 % Favored : 63.05 % 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: 0.45 (0.30), residues: 324 sheet: -1.18 (0.43), residues: 134 loop : -1.90 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 369 HIS 0.002 0.001 HIS A 329 PHE 0.015 0.001 PHE A 75 TYR 0.019 0.001 TYR B 293 ARG 0.006 0.000 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 163 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 155 average time/residue: 0.2491 time to fit residues: 50.9238 Evaluate side-chains 145 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 0.844 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0870 time to fit residues: 2.3856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 91 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 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 A 302 GLN ** 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: 0.6466 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8758 Z= 0.199 Angle : 0.695 12.697 12040 Z= 0.352 Chirality : 0.043 0.170 1319 Planarity : 0.005 0.058 1372 Dihedral : 18.796 177.539 1565 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.71 % Allowed : 36.71 % Favored : 61.59 % 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: 0.56 (0.30), residues: 325 sheet: -1.32 (0.42), residues: 143 loop : -1.88 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 421 HIS 0.003 0.001 HIS B 9 PHE 0.021 0.001 PHE A 75 TYR 0.019 0.001 TYR B 293 ARG 0.007 0.000 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 159 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 145 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 152 average time/residue: 0.2933 time to fit residues: 59.2817 Evaluate side-chains 142 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 137 time to evaluate : 0.908 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0954 time to fit residues: 2.1053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 62 optimal weight: 0.0770 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6459 moved from start: 0.3272 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= 0.210 Angle : 0.732 12.916 12040 Z= 0.366 Chirality : 0.044 0.171 1319 Planarity : 0.005 0.057 1372 Dihedral : 18.806 177.317 1565 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.85 % Allowed : 38.17 % 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: -1.31 (0.28), residues: 909 helix: 0.57 (0.30), residues: 323 sheet: -1.26 (0.43), residues: 140 loop : -1.86 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 421 HIS 0.003 0.001 HIS B 320 PHE 0.022 0.001 PHE A 75 TYR 0.019 0.001 TYR B 293 ARG 0.007 0.001 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 147 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 141 average time/residue: 0.2577 time to fit residues: 47.6666 Evaluate side-chains 136 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 0.851 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1165 time to fit residues: 1.5241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS ** 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 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8758 Z= 0.257 Angle : 0.754 12.815 12040 Z= 0.380 Chirality : 0.044 0.174 1319 Planarity : 0.005 0.057 1372 Dihedral : 18.896 177.444 1565 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.61 % Allowed : 37.93 % Favored : 61.46 % 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 (0.28), residues: 909 helix: 0.58 (0.30), residues: 316 sheet: -1.31 (0.43), residues: 141 loop : -1.88 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 369 HIS 0.003 0.001 HIS A 329 PHE 0.026 0.002 PHE A 75 TYR 0.022 0.002 TYR B 293 ARG 0.015 0.001 ARG B 54 *********************** 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 140 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 137 average time/residue: 0.2623 time to fit residues: 47.5010 Evaluate side-chains 136 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0940 time to fit residues: 1.5532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.0670 chunk 62 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 80 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8758 Z= 0.214 Angle : 0.746 13.748 12040 Z= 0.375 Chirality : 0.044 0.174 1319 Planarity : 0.005 0.058 1372 Dihedral : 18.886 177.593 1565 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.61 % Allowed : 37.68 % 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: -1.35 (0.28), residues: 909 helix: 0.54 (0.30), residues: 324 sheet: -1.16 (0.45), residues: 128 loop : -1.92 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 46 HIS 0.003 0.001 HIS A 329 PHE 0.021 0.001 PHE A 75 TYR 0.019 0.001 TYR B 293 ARG 0.012 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 146 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 141 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 142 average time/residue: 0.2467 time to fit residues: 46.6202 Evaluate side-chains 136 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 133 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1036 time to fit residues: 1.6414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 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 ** 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 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 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 = 0.4180 r_free = 0.4180 target = 0.136230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.109138 restraints weight = 22754.768| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 5.48 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8758 Z= 0.223 Angle : 0.749 14.003 12040 Z= 0.377 Chirality : 0.044 0.176 1319 Planarity : 0.005 0.072 1372 Dihedral : 18.933 177.651 1565 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.61 % Allowed : 37.32 % Favored : 62.07 % 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: -1.39 (0.28), residues: 909 helix: 0.52 (0.30), residues: 323 sheet: -1.09 (0.46), residues: 126 loop : -1.99 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 46 HIS 0.003 0.001 HIS A 329 PHE 0.024 0.002 PHE A 75 TYR 0.022 0.001 TYR B 392 ARG 0.012 0.001 ARG B 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2019.48 seconds wall clock time: 37 minutes 28.57 seconds (2248.57 seconds total)