Starting phenix.real_space_refine on Mon Mar 11 04:45:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxa_10337/03_2024/6sxa_10337.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxa_10337/03_2024/6sxa_10337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxa_10337/03_2024/6sxa_10337.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxa_10337/03_2024/6sxa_10337.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxa_10337/03_2024/6sxa_10337.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxa_10337/03_2024/6sxa_10337.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.050 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: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 4499 2.51 5 N 1219 2.21 5 O 1271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F GLU 179": "OE1" <-> "OE2" Residue "F ARG 195": "NH1" <-> "NH2" Residue "F GLU 239": "OE1" <-> "OE2" Residue "F TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 314": "NH1" <-> "NH2" Residue "F ARG 415": "NH1" <-> "NH2" Residue "F TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 799": "NH1" <-> "NH2" Residue "F PHE 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7014 Number of models: 1 Model: "" Number of chains: 2 Chain: "F" Number of atoms: 5620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5620 Classifications: {'peptide': 747} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 104} Link IDs: {'PTRANS': 34, 'TRANS': 712} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 389 Unresolved non-hydrogen angles: 468 Unresolved non-hydrogen dihedrals: 321 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 27, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 225 Chain: "G" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1394 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 11, 'TRANS': 184} Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 98 Time building chain proxies: 4.33, per 1000 atoms: 0.62 Number of scatterers: 7014 At special positions: 0 Unit cell: (84.18, 111.78, 128.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 1271 8.00 N 1219 7.00 C 4499 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: 2.74 Conformation dependent library (CDL) restraints added in 1.3 seconds 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1808 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 7 sheets defined 52.6% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'F' and resid 16 through 29 removed outlier: 4.034A pdb=" N LEU F 22 " --> pdb=" O TYR F 18 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU F 24 " --> pdb=" O ARG F 20 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP F 28 " --> pdb=" O LEU F 24 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 53 removed outlier: 3.544A pdb=" N LEU F 44 " --> pdb=" O GLY F 40 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU F 45 " --> pdb=" O ALA F 41 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR F 46 " --> pdb=" O ASP F 42 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS F 47 " --> pdb=" O ARG F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 80 removed outlier: 3.875A pdb=" N GLU F 69 " --> pdb=" O GLN F 65 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU F 79 " --> pdb=" O GLN F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 98 removed outlier: 4.214A pdb=" N ARG F 97 " --> pdb=" O THR F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 104 Processing helix chain 'F' and resid 110 through 121 removed outlier: 3.797A pdb=" N LEU F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL F 115 " --> pdb=" O SER F 111 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL F 116 " --> pdb=" O ARG F 112 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP F 117 " --> pdb=" O ILE F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 141 removed outlier: 3.544A pdb=" N GLU F 141 " --> pdb=" O ARG F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 153 removed outlier: 4.022A pdb=" N PHE F 147 " --> pdb=" O CYS F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 185 Processing helix chain 'F' and resid 197 through 202 removed outlier: 4.015A pdb=" N SER F 202 " --> pdb=" O VAL F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 207 removed outlier: 4.057A pdb=" N GLN F 206 " --> pdb=" O SER F 202 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS F 207 " --> pdb=" O PHE F 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 202 through 207' Processing helix chain 'F' and resid 222 through 243 removed outlier: 4.281A pdb=" N ALA F 228 " --> pdb=" O ALA F 224 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP F 231 " --> pdb=" O THR F 227 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS F 238 " --> pdb=" O ASN F 234 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS F 243 " --> pdb=" O GLU F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 259 removed outlier: 3.701A pdb=" N ILE F 258 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY F 259 " --> pdb=" O GLU F 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 254 through 259' Processing helix chain 'F' and resid 262 through 270 removed outlier: 3.563A pdb=" N ILE F 266 " --> pdb=" O PHE F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 301 removed outlier: 4.270A pdb=" N GLN F 286 " --> pdb=" O LYS F 282 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU F 295 " --> pdb=" O LEU F 291 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN F 296 " --> pdb=" O ARG F 292 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER F 299 " --> pdb=" O LEU F 295 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN F 300 " --> pdb=" O GLN F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 313 Processing helix chain 'F' and resid 333 through 344 removed outlier: 3.890A pdb=" N ARG F 342 " --> pdb=" O ASN F 338 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL F 343 " --> pdb=" O ALA F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 397 removed outlier: 3.911A pdb=" N THR F 385 " --> pdb=" O TRP F 381 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU F 386 " --> pdb=" O GLU F 382 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL F 387 " --> pdb=" O ALA F 383 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS F 389 " --> pdb=" O THR F 385 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU F 392 " --> pdb=" O LEU F 388 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA F 393 " --> pdb=" O LYS F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 403 removed outlier: 4.033A pdb=" N GLY F 403 " --> pdb=" O GLU F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 426 Processing helix chain 'F' and resid 427 through 440 removed outlier: 3.809A pdb=" N PHE F 431 " --> pdb=" O GLY F 427 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU F 432 " --> pdb=" O ALA F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 573 Processing helix chain 'F' and resid 584 through 595 removed outlier: 3.940A pdb=" N VAL F 588 " --> pdb=" O GLU F 584 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN F 590 " --> pdb=" O THR F 586 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU F 592 " --> pdb=" O VAL F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 613 through 638 removed outlier: 3.786A pdb=" N ALA F 622 " --> pdb=" O ARG F 618 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU F 631 " --> pdb=" O LYS F 627 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU F 633 " --> pdb=" O ALA F 629 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE F 634 " --> pdb=" O PHE F 630 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG F 635 " --> pdb=" O GLU F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 689 through 692 removed outlier: 4.015A pdb=" N ARG F 692 " --> pdb=" O ARG F 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 689 through 692' Processing helix chain 'F' and resid 694 through 700 Processing helix chain 'F' and resid 729 through 738 removed outlier: 3.688A pdb=" N ILE F 733 " --> pdb=" O ILE F 729 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN F 737 " --> pdb=" O ILE F 733 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 752 removed outlier: 3.731A pdb=" N ILE F 746 " --> pdb=" O TYR F 742 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER F 747 " --> pdb=" O SER F 743 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG F 750 " --> pdb=" O ILE F 746 " (cutoff:3.500A) Processing helix chain 'F' and resid 771 through 778 Processing helix chain 'F' and resid 783 through 795 removed outlier: 3.850A pdb=" N HIS F 794 " --> pdb=" O LEU F 790 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE F 795 " --> pdb=" O LEU F 791 " (cutoff:3.500A) Processing helix chain 'F' and resid 805 through 817 removed outlier: 4.326A pdb=" N ALA F 810 " --> pdb=" O PRO F 806 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU F 811 " --> pdb=" O HIS F 807 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU F 814 " --> pdb=" O ALA F 810 " (cutoff:3.500A) Processing helix chain 'F' and resid 827 through 832 removed outlier: 4.449A pdb=" N THR F 832 " --> pdb=" O ALA F 828 " (cutoff:3.500A) Processing helix chain 'F' and resid 847 through 855 removed outlier: 3.958A pdb=" N PHE F 851 " --> pdb=" O GLY F 847 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS F 854 " --> pdb=" O ASP F 850 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET F 855 " --> pdb=" O PHE F 851 " (cutoff:3.500A) Processing helix chain 'F' and resid 859 through 868 Processing helix chain 'F' and resid 880 through 889 Processing helix chain 'F' and resid 891 through 902 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.700A pdb=" N VAL G 116 " --> pdb=" O LEU G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 149 Processing helix chain 'G' and resid 152 through 161 removed outlier: 4.143A pdb=" N GLN G 158 " --> pdb=" O HIS G 154 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER G 159 " --> pdb=" O GLY G 155 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU G 160 " --> pdb=" O ARG G 156 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY G 161 " --> pdb=" O LEU G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 191 removed outlier: 3.944A pdb=" N LYS G 187 " --> pdb=" O LYS G 183 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU G 191 " --> pdb=" O LYS G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 214 removed outlier: 3.905A pdb=" N ARG G 207 " --> pdb=" O GLU G 203 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS G 213 " --> pdb=" O LEU G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 239 Processing helix chain 'G' and resid 240 through 242 No H-bonds generated for 'chain 'G' and resid 240 through 242' Processing helix chain 'G' and resid 246 through 255 removed outlier: 3.585A pdb=" N SER G 250 " --> pdb=" O ASN G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 264 Processing helix chain 'G' and resid 269 through 273 removed outlier: 3.883A pdb=" N LEU G 273 " --> pdb=" O ASP G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 289 Processing sheet with id=AA1, first strand: chain 'F' and resid 86 through 87 removed outlier: 7.163A pdb=" N ARG F 86 " --> pdb=" O PHE F 108 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL F 59 " --> pdb=" O ILE F 107 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU F 58 " --> pdb=" O GLY F 130 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N LEU F 132 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU F 60 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE F 164 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL F 33 " --> pdb=" O THR F 165 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU F 32 " --> pdb=" O TYR F 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 214 through 216 Processing sheet with id=AA3, first strand: chain 'F' and resid 410 through 411 removed outlier: 3.770A pdb=" N ALA F 411 " --> pdb=" O HIS F 555 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 705 through 709 removed outlier: 3.865A pdb=" N GLU F 707 " --> pdb=" O ILE F 684 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL F 685 " --> pdb=" O ILE F 717 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE F 717 " --> pdb=" O VAL F 685 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 723 through 728 removed outlier: 4.001A pdb=" N GLU F 725 " --> pdb=" O VAL F 756 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU F 758 " --> pdb=" O GLU F 725 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU F 760 " --> pdb=" O LYS F 727 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LEU F 801 " --> pdb=" O PRO F 755 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU F 757 " --> pdb=" O LEU F 801 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N CYS F 803 " --> pdb=" O LEU F 757 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE F 759 " --> pdb=" O CYS F 803 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 121 through 123 removed outlier: 3.770A pdb=" N TYR G 130 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR G 136 " --> pdb=" O LEU G 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 140 through 142 removed outlier: 6.705A pdb=" N LEU G 141 " --> pdb=" O GLN G 172 " (cutoff:3.500A) 253 hydrogen bonds defined for protein. 744 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 2.97 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: 1238 1.32 - 1.44: 1766 1.44 - 1.57: 4121 1.57 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 7157 Sorted by residual: bond pdb=" C SER G 104 " pdb=" N PRO G 105 " ideal model delta sigma weight residual 1.337 1.378 -0.041 9.80e-03 1.04e+04 1.76e+01 bond pdb=" C LEU F 84 " pdb=" N PRO F 85 " ideal model delta sigma weight residual 1.331 1.379 -0.048 1.20e-02 6.94e+03 1.61e+01 bond pdb=" C ASP F 271 " pdb=" N PRO F 272 " ideal model delta sigma weight residual 1.333 1.372 -0.039 1.01e-02 9.80e+03 1.46e+01 bond pdb=" N GLN F 65 " pdb=" CA GLN F 65 " ideal model delta sigma weight residual 1.453 1.487 -0.034 9.20e-03 1.18e+04 1.37e+01 bond pdb=" N VAL F 709 " pdb=" CA VAL F 709 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.07e-02 8.73e+03 1.21e+01 ... (remaining 7152 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.50: 170 105.50 - 112.63: 3805 112.63 - 119.76: 2674 119.76 - 126.89: 3053 126.89 - 134.01: 70 Bond angle restraints: 9772 Sorted by residual: angle pdb=" N GLU F 68 " pdb=" CA GLU F 68 " pdb=" C GLU F 68 " ideal model delta sigma weight residual 111.28 103.47 7.81 1.09e+00 8.42e-01 5.14e+01 angle pdb=" N PRO F 14 " pdb=" CA PRO F 14 " pdb=" CB PRO F 14 " ideal model delta sigma weight residual 103.36 109.47 -6.11 8.80e-01 1.29e+00 4.82e+01 angle pdb=" N GLN F 206 " pdb=" CA GLN F 206 " pdb=" C GLN F 206 " ideal model delta sigma weight residual 111.28 104.43 6.85 1.09e+00 8.42e-01 3.95e+01 angle pdb=" C PRO F 66 " pdb=" CA PRO F 66 " pdb=" CB PRO F 66 " ideal model delta sigma weight residual 113.06 103.18 9.88 1.59e+00 3.96e-01 3.86e+01 angle pdb=" N PRO F 347 " pdb=" CA PRO F 347 " pdb=" CB PRO F 347 " ideal model delta sigma weight residual 103.38 109.80 -6.42 1.05e+00 9.07e-01 3.74e+01 ... (remaining 9767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 3835 17.85 - 35.69: 352 35.69 - 53.54: 88 53.54 - 71.39: 15 71.39 - 89.23: 4 Dihedral angle restraints: 4294 sinusoidal: 1517 harmonic: 2777 Sorted by residual: dihedral pdb=" CA GLU F 394 " pdb=" C GLU F 394 " pdb=" N ASN F 395 " pdb=" CA ASN F 395 " ideal model delta harmonic sigma weight residual 180.00 154.17 25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA CYS F 143 " pdb=" C CYS F 143 " pdb=" N GLN F 144 " pdb=" CA GLN F 144 " ideal model delta harmonic sigma weight residual -180.00 -154.47 -25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA VAL F 61 " pdb=" C VAL F 61 " pdb=" N LEU F 62 " pdb=" CA LEU F 62 " ideal model delta harmonic sigma weight residual -180.00 -155.11 -24.89 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 4291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 792 0.075 - 0.149: 271 0.149 - 0.224: 90 0.224 - 0.299: 17 0.299 - 0.373: 8 Chirality restraints: 1178 Sorted by residual: chirality pdb=" CA GLU F 836 " pdb=" N GLU F 836 " pdb=" C GLU F 836 " pdb=" CB GLU F 836 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA GLU F 69 " pdb=" N GLU F 69 " pdb=" C GLU F 69 " pdb=" CB GLU F 69 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CA GLN F 206 " pdb=" N GLN F 206 " pdb=" C GLN F 206 " pdb=" CB GLN F 206 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 1175 not shown) Planarity restraints: 1249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 719 " 0.055 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO F 720 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO F 720 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 720 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 35 " 0.013 2.00e-02 2.50e+03 2.73e-02 7.47e+00 pdb=" C CYS F 35 " -0.047 2.00e-02 2.50e+03 pdb=" O CYS F 35 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA F 36 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 160 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C PHE F 160 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE F 160 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE F 161 " -0.014 2.00e-02 2.50e+03 ... (remaining 1246 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1479 2.78 - 3.31: 6795 3.31 - 3.84: 10235 3.84 - 4.37: 11496 4.37 - 4.90: 18828 Nonbonded interactions: 48833 Sorted by model distance: nonbonded pdb=" O LEU F 149 " pdb=" N PHE F 152 " model vdw 2.245 2.520 nonbonded pdb=" N ASP F 850 " pdb=" OD1 ASP F 850 " model vdw 2.257 2.520 nonbonded pdb=" N GLU F 179 " pdb=" OE1 GLU F 179 " model vdw 2.297 2.520 nonbonded pdb=" O ARG G 207 " pdb=" OG1 THR G 211 " model vdw 2.322 2.440 nonbonded pdb=" O SER F 332 " pdb=" OG SER F 332 " model vdw 2.337 2.440 ... (remaining 48828 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 group one per residue 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.100 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.290 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 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 : 0.010 0.061 7157 Z= 0.652 Angle : 1.370 9.943 9772 Z= 0.985 Chirality : 0.088 0.373 1178 Planarity : 0.007 0.083 1249 Dihedral : 15.201 89.233 2486 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.93 % Favored : 88.85 % Rotamer: Outliers : 3.18 % Allowed : 15.17 % Favored : 81.65 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.66 (0.22), residues: 933 helix: -2.92 (0.19), residues: 421 sheet: -2.74 (0.41), residues: 128 loop : -3.25 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 121 HIS 0.006 0.001 HIS G 149 PHE 0.016 0.002 PHE F 761 TYR 0.016 0.002 TYR G 130 ARG 0.006 0.000 ARG F 754 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 630 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6863 (m-80) outliers start: 22 outliers final: 7 residues processed: 149 average time/residue: 0.2026 time to fit residues: 39.4876 Evaluate side-chains 79 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 564 TYR Chi-restraints excluded: chain F residue 630 PHE Chi-restraints excluded: chain F residue 849 GLN Chi-restraints excluded: chain F residue 850 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 74 ASN ** F 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 GLN F 268 HIS F 395 ASN F 738 ASN F 782 ASN F 849 GLN F 859 ASN F 868 HIS G 147 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7157 Z= 0.225 Angle : 0.736 11.626 9772 Z= 0.360 Chirality : 0.042 0.146 1178 Planarity : 0.005 0.064 1249 Dihedral : 6.921 63.485 1036 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.86 % Favored : 93.03 % Rotamer: Outliers : 4.48 % Allowed : 20.81 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.25), residues: 933 helix: -0.94 (0.23), residues: 447 sheet: -1.83 (0.47), residues: 123 loop : -3.05 (0.27), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 121 HIS 0.003 0.001 HIS F 54 PHE 0.019 0.002 PHE G 140 TYR 0.015 0.002 TYR G 130 ARG 0.008 0.001 ARG F 340 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 75 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 798 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7227 (mm) REVERT: G 172 GLN cc_start: 0.5746 (OUTLIER) cc_final: 0.5225 (tp-100) outliers start: 31 outliers final: 13 residues processed: 99 average time/residue: 0.1395 time to fit residues: 20.9251 Evaluate side-chains 75 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 579 VAL Chi-restraints excluded: chain F residue 581 TYR Chi-restraints excluded: chain F residue 630 PHE Chi-restraints excluded: chain F residue 634 ILE Chi-restraints excluded: chain F residue 798 LEU Chi-restraints excluded: chain F residue 850 ASP Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 172 GLN Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 230 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 84 optimal weight: 0.0970 chunk 91 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS F 286 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7157 Z= 0.161 Angle : 0.725 14.207 9772 Z= 0.333 Chirality : 0.042 0.139 1178 Planarity : 0.004 0.054 1249 Dihedral : 5.167 58.755 1022 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.54 % Favored : 93.35 % Rotamer: Outliers : 4.48 % Allowed : 23.27 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.27), residues: 933 helix: -0.23 (0.24), residues: 462 sheet: -1.61 (0.47), residues: 130 loop : -2.68 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 326 HIS 0.003 0.001 HIS F 555 PHE 0.012 0.001 PHE G 140 TYR 0.011 0.001 TYR F 564 ARG 0.005 0.000 ARG G 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 70 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 798 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7439 (mm) REVERT: F 867 MET cc_start: 0.8650 (ptm) cc_final: 0.8409 (tpt) REVERT: G 126 VAL cc_start: 0.8651 (OUTLIER) cc_final: 0.8408 (p) REVERT: G 189 CYS cc_start: 0.6685 (p) cc_final: 0.6392 (t) REVERT: G 203 GLU cc_start: 0.7592 (tp30) cc_final: 0.7377 (tp30) outliers start: 31 outliers final: 16 residues processed: 97 average time/residue: 0.1448 time to fit residues: 20.4219 Evaluate side-chains 82 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 581 TYR Chi-restraints excluded: chain F residue 630 PHE Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 745 CYS Chi-restraints excluded: chain F residue 798 LEU Chi-restraints excluded: chain F residue 805 SER Chi-restraints excluded: chain F residue 850 ASP Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 230 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.5464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7157 Z= 0.219 Angle : 0.672 11.412 9772 Z= 0.324 Chirality : 0.041 0.215 1178 Planarity : 0.004 0.049 1249 Dihedral : 5.202 57.326 1022 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.75 % Favored : 93.14 % Rotamer: Outliers : 5.35 % Allowed : 21.82 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.27), residues: 933 helix: 0.55 (0.25), residues: 451 sheet: -1.55 (0.48), residues: 118 loop : -2.43 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 326 HIS 0.003 0.001 HIS G 146 PHE 0.011 0.001 PHE F 152 TYR 0.017 0.002 TYR F 564 ARG 0.004 0.000 ARG G 106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 64 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 798 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7682 (mm) REVERT: F 867 MET cc_start: 0.8678 (ptm) cc_final: 0.8458 (tpt) REVERT: G 126 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8366 (p) outliers start: 37 outliers final: 18 residues processed: 94 average time/residue: 0.1611 time to fit residues: 22.0363 Evaluate side-chains 80 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 60 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 581 TYR Chi-restraints excluded: chain F residue 630 PHE Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 798 LEU Chi-restraints excluded: chain F residue 805 SER Chi-restraints excluded: chain F residue 850 ASP Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 230 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 66 optimal weight: 0.0870 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 80 optimal weight: 0.0980 chunk 22 optimal weight: 0.8980 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 571 HIS F 737 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7157 Z= 0.149 Angle : 0.684 13.851 9772 Z= 0.307 Chirality : 0.042 0.229 1178 Planarity : 0.004 0.047 1249 Dihedral : 4.973 57.550 1022 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.32 % Favored : 93.57 % Rotamer: Outliers : 4.05 % Allowed : 23.70 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.28), residues: 933 helix: 0.73 (0.25), residues: 458 sheet: -1.41 (0.49), residues: 118 loop : -2.25 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 326 HIS 0.002 0.000 HIS F 555 PHE 0.008 0.001 PHE F 152 TYR 0.019 0.001 TYR F 564 ARG 0.003 0.000 ARG G 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 66 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 867 MET cc_start: 0.8633 (ptm) cc_final: 0.8391 (tpt) REVERT: G 126 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8402 (p) outliers start: 28 outliers final: 14 residues processed: 89 average time/residue: 0.1384 time to fit residues: 18.7831 Evaluate side-chains 75 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 581 TYR Chi-restraints excluded: chain F residue 630 PHE Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 805 SER Chi-restraints excluded: chain F residue 850 ASP Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 230 ASP Chi-restraints excluded: chain G residue 239 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 89 optimal weight: 0.0570 chunk 74 optimal weight: 0.0870 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 47 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7157 Z= 0.138 Angle : 0.675 13.865 9772 Z= 0.297 Chirality : 0.042 0.365 1178 Planarity : 0.004 0.049 1249 Dihedral : 4.777 57.755 1022 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.11 % Favored : 93.78 % Rotamer: Outliers : 3.90 % Allowed : 23.84 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.28), residues: 933 helix: 0.82 (0.25), residues: 466 sheet: -1.25 (0.49), residues: 118 loop : -2.10 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 326 HIS 0.002 0.000 HIS F 555 PHE 0.008 0.001 PHE F 431 TYR 0.008 0.001 TYR F 134 ARG 0.002 0.000 ARG F 624 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 67 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 408 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6776 (pp) outliers start: 27 outliers final: 18 residues processed: 88 average time/residue: 0.1341 time to fit residues: 17.6443 Evaluate side-chains 81 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 62 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 581 TYR Chi-restraints excluded: chain F residue 630 PHE Chi-restraints excluded: chain F residue 717 ILE Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 805 SER Chi-restraints excluded: chain F residue 850 ASP Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 230 ASP Chi-restraints excluded: chain G residue 239 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.0870 chunk 10 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.6525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7157 Z= 0.169 Angle : 0.649 9.673 9772 Z= 0.298 Chirality : 0.042 0.306 1178 Planarity : 0.004 0.047 1249 Dihedral : 4.693 56.646 1022 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.22 % Favored : 93.68 % Rotamer: Outliers : 3.61 % Allowed : 24.71 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.28), residues: 933 helix: 1.01 (0.25), residues: 468 sheet: -1.16 (0.49), residues: 118 loop : -1.95 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 802 HIS 0.003 0.001 HIS F 555 PHE 0.014 0.001 PHE F 431 TYR 0.009 0.001 TYR F 301 ARG 0.002 0.000 ARG F 576 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 60 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 19 residues processed: 79 average time/residue: 0.1427 time to fit residues: 16.9115 Evaluate side-chains 77 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 58 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 581 TYR Chi-restraints excluded: chain F residue 630 PHE Chi-restraints excluded: chain F residue 717 ILE Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 805 SER Chi-restraints excluded: chain F residue 850 ASP Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 230 ASP Chi-restraints excluded: chain G residue 239 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.6717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7157 Z= 0.142 Angle : 0.640 9.579 9772 Z= 0.286 Chirality : 0.041 0.257 1178 Planarity : 0.003 0.047 1249 Dihedral : 4.473 56.624 1022 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.11 % Favored : 93.78 % Rotamer: Outliers : 3.61 % Allowed : 24.57 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.29), residues: 933 helix: 1.10 (0.25), residues: 469 sheet: -1.11 (0.48), residues: 118 loop : -1.78 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 326 HIS 0.002 0.000 HIS F 555 PHE 0.020 0.001 PHE G 115 TYR 0.008 0.001 TYR F 301 ARG 0.002 0.000 ARG F 624 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 63 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 408 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6614 (pp) outliers start: 25 outliers final: 20 residues processed: 82 average time/residue: 0.1455 time to fit residues: 17.9340 Evaluate side-chains 80 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 59 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 581 TYR Chi-restraints excluded: chain F residue 630 PHE Chi-restraints excluded: chain F residue 717 ILE Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 805 SER Chi-restraints excluded: chain F residue 850 ASP Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 230 ASP Chi-restraints excluded: chain G residue 239 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 79 optimal weight: 0.0980 chunk 54 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.6962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7157 Z= 0.137 Angle : 0.634 11.448 9772 Z= 0.283 Chirality : 0.041 0.253 1178 Planarity : 0.003 0.048 1249 Dihedral : 4.276 56.295 1022 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.57 % Favored : 94.32 % Rotamer: Outliers : 2.89 % Allowed : 25.43 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.29), residues: 933 helix: 1.14 (0.25), residues: 469 sheet: -1.08 (0.48), residues: 118 loop : -1.65 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 326 HIS 0.003 0.000 HIS G 290 PHE 0.023 0.001 PHE G 115 TYR 0.008 0.001 TYR F 98 ARG 0.002 0.000 ARG F 624 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 62 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 15 residues processed: 76 average time/residue: 0.1400 time to fit residues: 16.3217 Evaluate side-chains 78 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 581 TYR Chi-restraints excluded: chain F residue 717 ILE Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 805 SER Chi-restraints excluded: chain F residue 850 ASP Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 230 ASP Chi-restraints excluded: chain G residue 239 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 73 optimal weight: 0.2980 chunk 7 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 45 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.7134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7157 Z= 0.140 Angle : 0.643 11.047 9772 Z= 0.285 Chirality : 0.042 0.250 1178 Planarity : 0.003 0.046 1249 Dihedral : 3.760 18.223 1019 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.25 % Favored : 94.64 % Rotamer: Outliers : 2.31 % Allowed : 26.01 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.29), residues: 933 helix: 1.13 (0.25), residues: 474 sheet: -1.00 (0.48), residues: 118 loop : -1.60 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 326 HIS 0.002 0.000 HIS F 555 PHE 0.014 0.001 PHE F 630 TYR 0.008 0.001 TYR F 301 ARG 0.004 0.000 ARG F 750 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 15 residues processed: 74 average time/residue: 0.1337 time to fit residues: 15.1276 Evaluate side-chains 75 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 581 TYR Chi-restraints excluded: chain F residue 717 ILE Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 805 SER Chi-restraints excluded: chain F residue 850 ASP Chi-restraints excluded: chain F residue 858 VAL Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 230 ASP Chi-restraints excluded: chain G residue 239 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.0000 chunk 64 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.036654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.027512 restraints weight = 55828.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.028360 restraints weight = 35919.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.028974 restraints weight = 26327.203| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.7250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7157 Z= 0.145 Angle : 0.683 17.332 9772 Z= 0.301 Chirality : 0.041 0.244 1178 Planarity : 0.003 0.039 1249 Dihedral : 3.750 18.238 1019 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.14 % Favored : 94.75 % Rotamer: Outliers : 2.46 % Allowed : 26.30 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.29), residues: 933 helix: 1.13 (0.25), residues: 474 sheet: -0.89 (0.48), residues: 119 loop : -1.54 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 326 HIS 0.002 0.000 HIS F 555 PHE 0.011 0.001 PHE F 630 TYR 0.008 0.001 TYR F 301 ARG 0.002 0.000 ARG F 750 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1470.56 seconds wall clock time: 27 minutes 35.97 seconds (1655.97 seconds total)