Starting phenix.real_space_refine on Tue Feb 13 20:10:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by6_16321/02_2024/8by6_16321_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by6_16321/02_2024/8by6_16321.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by6_16321/02_2024/8by6_16321_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by6_16321/02_2024/8by6_16321_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by6_16321/02_2024/8by6_16321_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by6_16321/02_2024/8by6_16321.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by6_16321/02_2024/8by6_16321.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by6_16321/02_2024/8by6_16321_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by6_16321/02_2024/8by6_16321_updated.pdb" } resolution = 3.19 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= 0.000 sd= 0.012 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 3 5.49 5 S 44 5.16 5 C 4842 2.51 5 N 1307 2.21 5 O 1405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 58": "OE1" <-> "OE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A GLU 639": "OE1" <-> "OE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 700": "OE1" <-> "OE2" Residue "A GLU 745": "OE1" <-> "OE2" Residue "A GLU 766": "OE1" <-> "OE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B GLU 137": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7601 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 6120 Classifications: {'peptide': 748} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 707} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1237 Classifications: {'peptide': 152} Link IDs: {'TRANS': 151} Chain: "C" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 192 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'GTG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.48, per 1000 atoms: 0.59 Number of scatterers: 7601 At special positions: 0 Unit cell: (103.375, 91.797, 113.299, 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 44 16.00 P 3 15.00 O 1405 8.00 N 1307 7.00 C 4842 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: 3.04 Conformation dependent library (CDL) restraints added in 1.4 seconds 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1778 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 1 sheets defined 64.4% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 26 through 37 Processing helix chain 'A' and resid 46 through 59 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 65 through 78 Processing helix chain 'A' and resid 80 through 94 removed outlier: 5.428A pdb=" N THR A 84 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 117 Processing helix chain 'A' and resid 122 through 136 removed outlier: 4.077A pdb=" N ASN A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 157 removed outlier: 4.200A pdb=" N THR A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN A 157 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 205 Proline residue: A 178 - end of helix removed outlier: 6.307A pdb=" N LYS A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ALA A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 214 No H-bonds generated for 'chain 'A' and resid 211 through 214' Processing helix chain 'A' and resid 228 through 241 Processing helix chain 'A' and resid 252 through 261 removed outlier: 5.463A pdb=" N SER A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU A 260 " --> pdb=" O ASP A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 309 through 324 Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 347 through 360 Processing helix chain 'A' and resid 369 through 382 Processing helix chain 'A' and resid 387 through 404 removed outlier: 3.510A pdb=" N LEU A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP A 403 " --> pdb=" O TYR A 399 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR A 404 " --> pdb=" O MET A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 424 Processing helix chain 'A' and resid 430 through 438 removed outlier: 4.797A pdb=" N ASP A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 438 " --> pdb=" O ASP A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 458 Processing helix chain 'A' and resid 462 through 466 Processing helix chain 'A' and resid 471 through 476 removed outlier: 4.547A pdb=" N ALA A 475 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 509 Processing helix chain 'A' and resid 514 through 522 Processing helix chain 'A' and resid 541 through 554 Processing helix chain 'A' and resid 559 through 568 Processing helix chain 'A' and resid 570 through 576 Processing helix chain 'A' and resid 580 through 593 Processing helix chain 'A' and resid 598 through 611 Processing helix chain 'A' and resid 616 through 623 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 635 through 675 Processing helix chain 'A' and resid 687 through 731 Processing helix chain 'A' and resid 738 through 753 Processing helix chain 'A' and resid 755 through 768 removed outlier: 4.961A pdb=" N GLN A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR A 761 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL A 763 " --> pdb=" O GLN A 759 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N THR A 764 " --> pdb=" O GLN A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 789 removed outlier: 4.057A pdb=" N VAL A 781 " --> pdb=" O HIS A 777 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 782 " --> pdb=" O ILE A 778 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN A 789 " --> pdb=" O PHE A 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 10 No H-bonds generated for 'chain 'B' and resid 7 through 10' Processing helix chain 'B' and resid 29 through 38 removed outlier: 3.728A pdb=" N LYS B 38 " --> pdb=" O LYS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 63 removed outlier: 4.176A pdb=" N SER B 63 " --> pdb=" O LEU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 100 Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 151 through 154 No H-bonds generated for 'chain 'B' and resid 151 through 154' Processing helix chain 'C' and resid 575 through 593 Processing sheet with id= A, first strand: chain 'B' and resid 112 through 115 405 hydrogen bonds defined for protein. 1146 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1330 1.32 - 1.44: 2027 1.44 - 1.57: 4352 1.57 - 1.69: 6 1.69 - 1.81: 66 Bond restraints: 7781 Sorted by residual: bond pdb=" C2E GTG B 201 " pdb=" C3E GTG B 201 " ideal model delta sigma weight residual 1.254 1.504 -0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" C3D GTG B 201 " pdb=" C4D GTG B 201 " ideal model delta sigma weight residual 1.298 1.524 -0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C5A GTG B 201 " pdb=" C6A GTG B 201 " ideal model delta sigma weight residual 1.539 1.330 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C5B GTG B 201 " pdb=" C6B GTG B 201 " ideal model delta sigma weight residual 1.538 1.331 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C4E GTG B 201 " pdb=" O4E GTG B 201 " ideal model delta sigma weight residual 1.294 1.471 -0.177 2.00e-02 2.50e+03 7.82e+01 ... (remaining 7776 not shown) Histogram of bond angle deviations from ideal: 96.25 - 103.80: 89 103.80 - 111.35: 3339 111.35 - 118.90: 2981 118.90 - 126.45: 3989 126.45 - 134.00: 136 Bond angle restraints: 10534 Sorted by residual: angle pdb=" C1D GTG B 201 " pdb=" N9A GTG B 201 " pdb=" C4A GTG B 201 " ideal model delta sigma weight residual 93.21 126.30 -33.09 3.00e+00 1.11e-01 1.22e+02 angle pdb=" C1D GTG B 201 " pdb=" N9A GTG B 201 " pdb=" C8A GTG B 201 " ideal model delta sigma weight residual 157.61 125.29 32.32 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C1E GTG B 201 " pdb=" N9B GTG B 201 " pdb=" C4B GTG B 201 " ideal model delta sigma weight residual 152.69 127.39 25.30 3.00e+00 1.11e-01 7.11e+01 angle pdb=" C1E GTG B 201 " pdb=" N9B GTG B 201 " pdb=" C8B GTG B 201 " ideal model delta sigma weight residual 99.21 124.41 -25.20 3.00e+00 1.11e-01 7.06e+01 angle pdb=" CA ASP A 29 " pdb=" CB ASP A 29 " pdb=" CG ASP A 29 " ideal model delta sigma weight residual 112.60 118.25 -5.65 1.00e+00 1.00e+00 3.19e+01 ... (remaining 10529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 3939 17.79 - 35.57: 545 35.57 - 53.36: 160 53.36 - 71.14: 32 71.14 - 88.93: 22 Dihedral angle restraints: 4698 sinusoidal: 1968 harmonic: 2730 Sorted by residual: dihedral pdb=" CA ASP B 114 " pdb=" CB ASP B 114 " pdb=" CG ASP B 114 " pdb=" OD1 ASP B 114 " ideal model delta sinusoidal sigma weight residual -30.00 -88.39 58.39 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP A 369 " pdb=" CB ASP A 369 " pdb=" CG ASP A 369 " pdb=" OD1 ASP A 369 " ideal model delta sinusoidal sigma weight residual -30.00 -88.27 58.27 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASN A 317 " pdb=" CB ASN A 317 " pdb=" CG ASN A 317 " pdb=" OD1 ASN A 317 " ideal model delta sinusoidal sigma weight residual 120.00 -166.97 -73.03 2 2.00e+01 2.50e-03 1.10e+01 ... (remaining 4695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1053 0.071 - 0.143: 84 0.143 - 0.214: 4 0.214 - 0.285: 1 0.285 - 0.356: 2 Chirality restraints: 1144 Sorted by residual: chirality pdb=" C3D GTG B 201 " pdb=" C2D GTG B 201 " pdb=" C4D GTG B 201 " pdb=" O3D GTG B 201 " both_signs ideal model delta sigma weight residual False -2.38 -2.73 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" C3E GTG B 201 " pdb=" C2E GTG B 201 " pdb=" C4E GTG B 201 " pdb=" O3E GTG B 201 " both_signs ideal model delta sigma weight residual False -2.43 -2.76 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" C2E GTG B 201 " pdb=" C1E GTG B 201 " pdb=" C3E GTG B 201 " pdb=" O2E GTG B 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1141 not shown) Planarity restraints: 1345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 61 " -0.050 5.00e-02 4.00e+02 7.36e-02 8.66e+00 pdb=" N PRO A 62 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 62 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 62 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 258 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" C SER A 258 " -0.039 2.00e-02 2.50e+03 pdb=" O SER A 258 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE A 259 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 461 " 0.021 2.00e-02 2.50e+03 1.32e-02 3.50e+00 pdb=" CG TYR A 461 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR A 461 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 461 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 461 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 461 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 461 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 461 " 0.003 2.00e-02 2.50e+03 ... (remaining 1342 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 86 2.62 - 3.19: 6912 3.19 - 3.76: 12231 3.76 - 4.33: 16415 4.33 - 4.90: 27588 Nonbonded interactions: 63232 Sorted by model distance: nonbonded pdb=" OE2 GLU A 32 " pdb=" CG LYS B 7 " model vdw 2.044 3.440 nonbonded pdb=" O SER B 63 " pdb=" OG SER B 63 " model vdw 2.221 2.440 nonbonded pdb=" OD2 ASP A 167 " pdb=" NH2 ARG A 206 " model vdw 2.229 2.520 nonbonded pdb=" OH TYR B 20 " pdb=" O2D GTG B 201 " model vdw 2.268 2.440 nonbonded pdb=" O ILE A 414 " pdb=" OG SER A 418 " model vdw 2.282 2.440 ... (remaining 63227 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: 1.020 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: 5.790 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.320 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 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 : 0.009 0.250 7781 Z= 0.610 Angle : 0.895 33.091 10534 Z= 0.432 Chirality : 0.042 0.356 1144 Planarity : 0.004 0.074 1345 Dihedral : 18.788 88.926 2920 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.88 % Allowed : 27.73 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.28), residues: 913 helix: 2.33 (0.22), residues: 594 sheet: -1.19 (1.23), residues: 11 loop : 0.25 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 416 HIS 0.013 0.001 HIS A 570 PHE 0.008 0.001 PHE A 473 TYR 0.029 0.001 TYR A 461 ARG 0.004 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7472 (p0) REVERT: A 648 MET cc_start: 0.8727 (tpp) cc_final: 0.8514 (tpt) outliers start: 24 outliers final: 11 residues processed: 147 average time/residue: 0.2185 time to fit residues: 42.6533 Evaluate side-chains 99 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 701 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 36 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.0170 chunk 53 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 111 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 HIS B 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7781 Z= 0.214 Angle : 0.540 8.101 10534 Z= 0.270 Chirality : 0.039 0.149 1144 Planarity : 0.004 0.042 1345 Dihedral : 5.834 59.965 1037 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.12 % Allowed : 26.05 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.29), residues: 913 helix: 2.63 (0.22), residues: 596 sheet: -0.67 (1.26), residues: 11 loop : 0.53 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 638 HIS 0.007 0.001 HIS A 570 PHE 0.018 0.001 PHE B 25 TYR 0.012 0.001 TYR A 86 ARG 0.005 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 78 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 ASN cc_start: 0.8858 (t0) cc_final: 0.8641 (t0) outliers start: 26 outliers final: 13 residues processed: 99 average time/residue: 0.2059 time to fit residues: 27.9228 Evaluate side-chains 86 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 585 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 89 optimal weight: 0.0060 chunk 73 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7781 Z= 0.173 Angle : 0.498 9.354 10534 Z= 0.249 Chirality : 0.037 0.126 1144 Planarity : 0.004 0.044 1345 Dihedral : 5.374 55.972 1026 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.24 % Allowed : 26.29 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.28), residues: 913 helix: 2.65 (0.21), residues: 600 sheet: -0.42 (1.28), residues: 11 loop : 0.45 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 638 HIS 0.005 0.001 HIS A 570 PHE 0.011 0.001 PHE B 25 TYR 0.014 0.001 TYR A 86 ARG 0.005 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 88 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 665 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8973 (tmmt) REVERT: B 46 ASN cc_start: 0.8870 (t0) cc_final: 0.8642 (t0) outliers start: 27 outliers final: 18 residues processed: 109 average time/residue: 0.2476 time to fit residues: 35.1155 Evaluate side-chains 98 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 585 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7781 Z= 0.225 Angle : 0.513 8.285 10534 Z= 0.255 Chirality : 0.038 0.147 1144 Planarity : 0.004 0.045 1345 Dihedral : 5.192 56.445 1026 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.36 % Allowed : 26.89 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.29), residues: 913 helix: 2.59 (0.21), residues: 607 sheet: 0.11 (1.39), residues: 11 loop : 0.40 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 638 HIS 0.003 0.001 HIS A 570 PHE 0.009 0.001 PHE A 104 TYR 0.009 0.001 TYR A 202 ARG 0.013 0.000 ARG A 668 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 83 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 207 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8142 (mp10) REVERT: A 665 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8596 (tmmt) REVERT: B 46 ASN cc_start: 0.8938 (t0) cc_final: 0.8675 (t0) outliers start: 28 outliers final: 17 residues processed: 104 average time/residue: 0.2453 time to fit residues: 33.6561 Evaluate side-chains 95 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 585 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 3.9990 chunk 1 optimal weight: 0.0970 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 HIS A 753 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7781 Z= 0.214 Angle : 0.511 7.905 10534 Z= 0.255 Chirality : 0.038 0.135 1144 Planarity : 0.004 0.059 1345 Dihedral : 4.931 55.982 1024 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.24 % Allowed : 27.49 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.28), residues: 913 helix: 2.57 (0.21), residues: 608 sheet: 0.03 (1.39), residues: 11 loop : 0.41 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 416 HIS 0.003 0.001 HIS A 754 PHE 0.007 0.001 PHE A 508 TYR 0.017 0.001 TYR A 86 ARG 0.006 0.000 ARG A 668 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 81 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8132 (mp10) REVERT: B 46 ASN cc_start: 0.8940 (t0) cc_final: 0.8676 (t0) REVERT: B 48 SER cc_start: 0.8834 (p) cc_final: 0.8616 (p) outliers start: 27 outliers final: 15 residues processed: 103 average time/residue: 0.2544 time to fit residues: 34.7626 Evaluate side-chains 92 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 585 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 HIS ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7781 Z= 0.224 Angle : 0.513 7.172 10534 Z= 0.257 Chirality : 0.038 0.124 1144 Planarity : 0.004 0.044 1345 Dihedral : 4.676 56.130 1021 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.88 % Allowed : 27.37 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.28), residues: 913 helix: 2.59 (0.21), residues: 605 sheet: -0.04 (1.37), residues: 11 loop : 0.38 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 638 HIS 0.003 0.001 HIS A 319 PHE 0.007 0.001 PHE A 100 TYR 0.018 0.001 TYR A 86 ARG 0.006 0.000 ARG A 668 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 76 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8148 (mp10) REVERT: B 46 ASN cc_start: 0.8979 (t0) cc_final: 0.8695 (t0) REVERT: B 48 SER cc_start: 0.8825 (p) cc_final: 0.8594 (p) outliers start: 24 outliers final: 16 residues processed: 95 average time/residue: 0.2052 time to fit residues: 26.9093 Evaluate side-chains 97 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 585 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 317 ASN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7781 Z= 0.195 Angle : 0.504 7.051 10534 Z= 0.252 Chirality : 0.037 0.122 1144 Planarity : 0.004 0.043 1345 Dihedral : 4.592 57.999 1021 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.52 % Allowed : 28.57 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.28), residues: 913 helix: 2.63 (0.21), residues: 604 sheet: 0.02 (1.40), residues: 11 loop : 0.38 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 638 HIS 0.003 0.001 HIS A 754 PHE 0.011 0.001 PHE A 100 TYR 0.017 0.001 TYR A 86 ARG 0.005 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8135 (mp10) REVERT: B 46 ASN cc_start: 0.8959 (t0) cc_final: 0.8662 (t0) REVERT: B 48 SER cc_start: 0.8801 (p) cc_final: 0.8577 (p) outliers start: 21 outliers final: 17 residues processed: 93 average time/residue: 0.2024 time to fit residues: 25.9959 Evaluate side-chains 96 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 585 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 59 optimal weight: 0.0980 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7781 Z= 0.173 Angle : 0.497 7.407 10534 Z= 0.249 Chirality : 0.037 0.120 1144 Planarity : 0.004 0.042 1345 Dihedral : 4.526 59.797 1021 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.28 % Allowed : 28.33 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.29), residues: 913 helix: 2.59 (0.21), residues: 612 sheet: 0.14 (1.43), residues: 11 loop : 0.52 (0.39), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 638 HIS 0.003 0.001 HIS A 420 PHE 0.009 0.001 PHE A 100 TYR 0.015 0.001 TYR A 86 ARG 0.005 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 73 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8121 (mp10) REVERT: A 399 TYR cc_start: 0.8525 (t80) cc_final: 0.8295 (t80) REVERT: B 46 ASN cc_start: 0.8961 (t0) cc_final: 0.8667 (t0) REVERT: B 48 SER cc_start: 0.8770 (p) cc_final: 0.8530 (p) outliers start: 19 outliers final: 14 residues processed: 87 average time/residue: 0.2181 time to fit residues: 25.6492 Evaluate side-chains 93 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 585 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 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 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7781 Z= 0.196 Angle : 0.515 9.813 10534 Z= 0.256 Chirality : 0.037 0.124 1144 Planarity : 0.004 0.042 1345 Dihedral : 4.484 60.760 1021 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.28 % Allowed : 28.33 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.29), residues: 913 helix: 2.63 (0.21), residues: 607 sheet: 0.26 (1.48), residues: 11 loop : 0.76 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 638 HIS 0.003 0.001 HIS A 319 PHE 0.011 0.001 PHE A 104 TYR 0.009 0.001 TYR A 461 ARG 0.005 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8122 (mp10) REVERT: B 46 ASN cc_start: 0.8963 (t0) cc_final: 0.8669 (t0) REVERT: B 48 SER cc_start: 0.8752 (p) cc_final: 0.8530 (p) outliers start: 19 outliers final: 17 residues processed: 93 average time/residue: 0.2469 time to fit residues: 30.1948 Evaluate side-chains 94 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 76 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 585 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 0.0980 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7781 Z= 0.178 Angle : 0.532 9.365 10534 Z= 0.262 Chirality : 0.037 0.134 1144 Planarity : 0.004 0.041 1345 Dihedral : 4.449 61.046 1021 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.40 % Allowed : 28.81 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.29), residues: 913 helix: 2.63 (0.21), residues: 607 sheet: 0.32 (1.52), residues: 11 loop : 0.77 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 638 HIS 0.003 0.001 HIS A 420 PHE 0.010 0.001 PHE A 104 TYR 0.015 0.001 TYR A 86 ARG 0.006 0.000 ARG B 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8074 (mp10) REVERT: B 46 ASN cc_start: 0.8947 (t0) cc_final: 0.8668 (t0) REVERT: B 48 SER cc_start: 0.8752 (p) cc_final: 0.8522 (p) outliers start: 20 outliers final: 18 residues processed: 94 average time/residue: 0.2341 time to fit residues: 29.2344 Evaluate side-chains 91 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 72 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 585 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.076539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.056805 restraints weight = 19672.142| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.34 r_work: 0.2648 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7781 Z= 0.212 Angle : 0.533 9.579 10534 Z= 0.266 Chirality : 0.037 0.141 1144 Planarity : 0.004 0.041 1345 Dihedral : 4.457 61.325 1021 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.28 % Allowed : 28.81 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.29), residues: 913 helix: 2.58 (0.21), residues: 607 sheet: 0.23 (1.49), residues: 11 loop : 0.83 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 638 HIS 0.003 0.001 HIS A 319 PHE 0.014 0.001 PHE A 104 TYR 0.008 0.001 TYR A 461 ARG 0.005 0.000 ARG B 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1876.68 seconds wall clock time: 34 minutes 48.88 seconds (2088.88 seconds total)