Starting phenix.real_space_refine on Sat Apr 6 18:13:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfw_13950/04_2024/7qfw_13950.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfw_13950/04_2024/7qfw_13950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfw_13950/04_2024/7qfw_13950.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfw_13950/04_2024/7qfw_13950.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfw_13950/04_2024/7qfw_13950.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfw_13950/04_2024/7qfw_13950.pdb" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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 64 5.49 5 S 32 5.16 5 C 5395 2.51 5 N 1492 2.21 5 O 1782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 32": "NH1" <-> "NH2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ASP 152": "OD1" <-> "OD2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A ASP 187": "OD1" <-> "OD2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A ASP 277": "OD1" <-> "OD2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A ASP 302": "OD1" <-> "OD2" Residue "A ASP 308": "OD1" <-> "OD2" Residue "A ASP 310": "OD1" <-> "OD2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ASP 353": "OD1" <-> "OD2" Residue "A TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 414": "OD1" <-> "OD2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A ASP 433": "OD1" <-> "OD2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A GLU 458": "OE1" <-> "OE2" Residue "A ASP 488": "OD1" <-> "OD2" Residue "A ARG 490": "NH1" <-> "NH2" Residue "A ASP 491": "OD1" <-> "OD2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A ASP 604": "OD1" <-> "OD2" Residue "A ARG 619": "NH1" <-> "NH2" Residue "A GLU 620": "OE1" <-> "OE2" Residue "A ASP 633": "OD1" <-> "OD2" Residue "A ASP 639": "OD1" <-> "OD2" Residue "A TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 678": "OE1" <-> "OE2" Residue "A ASP 682": "OD1" <-> "OD2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "A ASP 717": "OD1" <-> "OD2" Residue "A ASP 721": "OD1" <-> "OD2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "A PHE 749": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 792": "OD1" <-> "OD2" Residue "A GLU 794": "OE1" <-> "OE2" Residue "A ASP 825": "OD1" <-> "OD2" Residue "A TYR 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 843": "OE1" <-> "OE2" Residue "A TYR 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 871": "OE1" <-> "OE2" Residue "A GLU 881": "OE1" <-> "OE2" Residue "A ASP 883": "OD1" <-> "OD2" Residue "A ARG 897": "NH1" <-> "NH2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B ASP 395": "OD1" <-> "OD2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ASP 468": "OD1" <-> "OD2" Residue "B ARG 490": "NH1" <-> "NH2" Residue "B ASP 500": "OD1" <-> "OD2" Residue "B ASP 501": "OD1" <-> "OD2" Residue "B PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 508": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8765 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 823, 6643 Classifications: {'peptide': 823} Link IDs: {'PTRANS': 20, 'TRANS': 802} Chain breaks: 3 Chain: "B" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 810 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain breaks: 1 Chain: "C" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 672 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "D" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 640 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Time building chain proxies: 4.86, per 1000 atoms: 0.55 Number of scatterers: 8765 At special positions: 0 Unit cell: (79.04, 111.28, 132.08, 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 32 16.00 P 64 15.00 O 1782 8.00 N 1492 7.00 C 5395 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: 3.71 Conformation dependent library (CDL) restraints added in 1.5 seconds 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1786 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 0 sheets defined 73.9% alpha, 0.0% beta 30 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 8 through 24 removed outlier: 4.032A pdb=" N PHE A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 49 removed outlier: 3.811A pdb=" N ALA A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 64 Processing helix chain 'A' and resid 72 through 98 removed outlier: 3.737A pdb=" N ASP A 76 " --> pdb=" O GLU A 72 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU A 81 " --> pdb=" O ARG A 77 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 123 removed outlier: 3.629A pdb=" N ARG A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 removed outlier: 3.780A pdb=" N ARG A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 removed outlier: 4.112A pdb=" N GLY A 149 " --> pdb=" O MET A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 Processing helix chain 'A' and resid 171 through 184 removed outlier: 3.658A pdb=" N ARG A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.949A pdb=" N THR A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 228 removed outlier: 3.540A pdb=" N ALA A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 242 Processing helix chain 'A' and resid 243 through 246 Processing helix chain 'A' and resid 248 through 258 removed outlier: 3.571A pdb=" N ARG A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 265 through 268 removed outlier: 3.699A pdb=" N PHE A 268 " --> pdb=" O ARG A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 268' Processing helix chain 'A' and resid 272 through 285 removed outlier: 3.734A pdb=" N GLN A 278 " --> pdb=" O HIS A 274 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLU A 281 " --> pdb=" O ASP A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 301 removed outlier: 3.508A pdb=" N ARG A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 347 through 351 removed outlier: 3.791A pdb=" N ILE A 350 " --> pdb=" O PRO A 347 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TRP A 351 " --> pdb=" O GLU A 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 347 through 351' Processing helix chain 'A' and resid 355 through 372 Processing helix chain 'A' and resid 374 through 380 Processing helix chain 'A' and resid 384 through 401 Processing helix chain 'A' and resid 414 through 430 Processing helix chain 'A' and resid 436 through 451 Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 474 through 500 removed outlier: 3.681A pdb=" N PHE A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 493 " --> pdb=" O ILE A 489 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 587 removed outlier: 3.502A pdb=" N ILE A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 607 through 612 removed outlier: 3.655A pdb=" N ARG A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 631 Processing helix chain 'A' and resid 633 through 650 removed outlier: 3.837A pdb=" N ALA A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N TYR A 642 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE A 643 " --> pdb=" O ASP A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 671 Processing helix chain 'A' and resid 682 through 695 Processing helix chain 'A' and resid 699 through 716 Processing helix chain 'A' and resid 722 through 734 Processing helix chain 'A' and resid 740 through 751 removed outlier: 3.659A pdb=" N ILE A 751 " --> pdb=" O PHE A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 758 removed outlier: 3.760A pdb=" N SER A 757 " --> pdb=" O VAL A 753 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS A 758 " --> pdb=" O TYR A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 785 removed outlier: 4.404A pdb=" N ALA A 770 " --> pdb=" O SER A 766 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASP A 771 " --> pdb=" O ARG A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 810 Processing helix chain 'A' and resid 820 through 825 removed outlier: 3.711A pdb=" N LYS A 823 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP A 825 " --> pdb=" O THR A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 839 Processing helix chain 'A' and resid 840 through 842 No H-bonds generated for 'chain 'A' and resid 840 through 842' Processing helix chain 'A' and resid 846 through 853 Processing helix chain 'A' and resid 854 through 858 removed outlier: 3.886A pdb=" N ALA A 857 " --> pdb=" O ASN A 854 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 858 " --> pdb=" O ILE A 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 854 through 858' Processing helix chain 'A' and resid 866 through 883 removed outlier: 4.207A pdb=" N LEU A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A 883 " --> pdb=" O ILE A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 908 removed outlier: 4.311A pdb=" N ALA A 892 " --> pdb=" O VAL A 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 398 Processing helix chain 'B' and resid 399 through 401 No H-bonds generated for 'chain 'B' and resid 399 through 401' Processing helix chain 'B' and resid 470 through 474 Processing helix chain 'B' and resid 486 through 490 removed outlier: 3.519A pdb=" N ASN B 489 " --> pdb=" O PRO B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 511 421 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 3.43 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2296 1.34 - 1.45: 1885 1.45 - 1.57: 4689 1.57 - 1.69: 126 1.69 - 1.81: 50 Bond restraints: 9046 Sorted by residual: bond pdb=" CA ASN A 672 " pdb=" C ASN A 672 " ideal model delta sigma weight residual 1.524 1.480 0.044 1.40e-02 5.10e+03 9.69e+00 bond pdb=" N GLN A 99 " pdb=" CA GLN A 99 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.60e+00 bond pdb=" N ASP A 319 " pdb=" CA ASP A 319 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 3.91e+00 bond pdb=" C ILE A 751 " pdb=" N PRO A 752 " ideal model delta sigma weight residual 1.335 1.356 -0.022 1.28e-02 6.10e+03 2.92e+00 bond pdb=" CA GLY A 149 " pdb=" C GLY A 149 " ideal model delta sigma weight residual 1.530 1.513 0.018 1.04e-02 9.25e+03 2.87e+00 ... (remaining 9041 not shown) Histogram of bond angle deviations from ideal: 96.10 - 103.73: 239 103.73 - 111.37: 3878 111.37 - 119.00: 3705 119.00 - 126.63: 4389 126.63 - 134.27: 283 Bond angle restraints: 12494 Sorted by residual: angle pdb=" C LYS A 98 " pdb=" N GLN A 99 " pdb=" CA GLN A 99 " ideal model delta sigma weight residual 121.54 130.88 -9.34 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C3' DT D 9 " pdb=" O3' DT D 9 " pdb=" P DT D 10 " ideal model delta sigma weight residual 120.20 127.45 -7.25 1.50e+00 4.44e-01 2.34e+01 angle pdb=" CA LEU A 307 " pdb=" CB LEU A 307 " pdb=" CG LEU A 307 " ideal model delta sigma weight residual 116.30 131.77 -15.47 3.50e+00 8.16e-02 1.95e+01 angle pdb=" C LEU A 318 " pdb=" N ASP A 319 " pdb=" CA ASP A 319 " ideal model delta sigma weight residual 121.54 129.70 -8.16 1.91e+00 2.74e-01 1.82e+01 angle pdb=" CA ARG B 411 " pdb=" CB ARG B 411 " pdb=" CG ARG B 411 " ideal model delta sigma weight residual 114.10 121.76 -7.66 2.00e+00 2.50e-01 1.47e+01 ... (remaining 12489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.37: 4651 27.37 - 54.74: 670 54.74 - 82.11: 81 82.11 - 109.48: 6 109.48 - 136.84: 2 Dihedral angle restraints: 5410 sinusoidal: 2689 harmonic: 2721 Sorted by residual: dihedral pdb=" CA LYS A 98 " pdb=" C LYS A 98 " pdb=" N GLN A 99 " pdb=" CA GLN A 99 " ideal model delta harmonic sigma weight residual -180.00 -154.13 -25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA ASP B 462 " pdb=" C ASP B 462 " pdb=" N PHE B 463 " pdb=" CA PHE B 463 " ideal model delta harmonic sigma weight residual 180.00 -154.39 -25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA GLN A 818 " pdb=" C GLN A 818 " pdb=" N THR A 819 " pdb=" CA THR A 819 " ideal model delta harmonic sigma weight residual -180.00 -156.27 -23.73 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 5407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 953 0.044 - 0.088: 354 0.088 - 0.132: 95 0.132 - 0.175: 28 0.175 - 0.219: 8 Chirality restraints: 1438 Sorted by residual: chirality pdb=" P DT D 10 " pdb=" OP1 DT D 10 " pdb=" OP2 DT D 10 " pdb=" O5' DT D 10 " both_signs ideal model delta sigma weight residual True 2.35 -2.56 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ASP A 319 " pdb=" N ASP A 319 " pdb=" C ASP A 319 " pdb=" CB ASP A 319 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" C1' DA C 16 " pdb=" O4' DA C 16 " pdb=" C2' DA C 16 " pdb=" N9 DA C 16 " both_signs ideal model delta sigma weight residual False 2.42 2.23 0.19 2.00e-01 2.50e+01 9.39e-01 ... (remaining 1435 not shown) Planarity restraints: 1373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 66 " -0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO A 67 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 67 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 67 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 608 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.05e+00 pdb=" N PRO A 609 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 609 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 609 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 798 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.41e+00 pdb=" N PRO A 799 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 799 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 799 " 0.038 5.00e-02 4.00e+02 ... (remaining 1370 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2303 2.80 - 3.33: 8063 3.33 - 3.85: 15330 3.85 - 4.38: 17579 4.38 - 4.90: 27470 Nonbonded interactions: 70745 Sorted by model distance: nonbonded pdb=" O PRO A 383 " pdb=" OH TYR A 432 " model vdw 2.276 2.440 nonbonded pdb=" O THR A 826 " pdb=" OG1 THR A 830 " model vdw 2.298 2.440 nonbonded pdb=" O SER A 862 " pdb=" OG SER A 862 " model vdw 2.329 2.440 nonbonded pdb=" O GLU A 430 " pdb=" OG SER A 470 " model vdw 2.337 2.440 nonbonded pdb=" O THR A 727 " pdb=" OG SER A 731 " model vdw 2.346 2.440 ... (remaining 70740 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: 1.050 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: 0.000 Extract box with map and model: 3.810 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 29.480 Find NCS groups from input model: 0.210 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 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 : 0.006 0.065 9046 Z= 0.379 Angle : 0.984 15.467 12494 Z= 0.579 Chirality : 0.052 0.219 1438 Planarity : 0.008 0.079 1373 Dihedral : 22.546 136.844 3624 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.36 % Allowed : 6.92 % Favored : 92.72 % 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: -4.68 (0.20), residues: 905 helix: -2.90 (0.14), residues: 630 sheet: None (None), residues: 0 loop : -3.13 (0.29), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 780 HIS 0.008 0.001 HIS A 394 PHE 0.023 0.002 PHE A 354 TYR 0.018 0.002 TYR B 496 ARG 0.005 0.001 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 194 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7665 (mttm) cc_final: 0.7382 (mmtp) REVERT: A 13 ILE cc_start: 0.7989 (mm) cc_final: 0.7588 (mt) REVERT: A 39 LYS cc_start: 0.7811 (tptt) cc_final: 0.7554 (tptt) REVERT: A 47 GLU cc_start: 0.6706 (tm-30) cc_final: 0.6286 (tm-30) REVERT: A 72 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7153 (tm-30) REVERT: A 107 GLU cc_start: 0.8005 (mp0) cc_final: 0.7695 (mm-30) REVERT: A 136 ARG cc_start: 0.7191 (mmt-90) cc_final: 0.6952 (mmt-90) REVERT: A 266 LYS cc_start: 0.7948 (mmmm) cc_final: 0.7733 (mtmm) REVERT: A 285 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6817 (mm-30) REVERT: A 384 GLU cc_start: 0.6657 (tm-30) cc_final: 0.6238 (tm-30) REVERT: A 421 ILE cc_start: 0.6590 (mt) cc_final: 0.6382 (mm) REVERT: A 471 LEU cc_start: 0.7946 (tp) cc_final: 0.7728 (tp) REVERT: A 641 MET cc_start: 0.7488 (tpp) cc_final: 0.7086 (tpt) REVERT: A 644 LEU cc_start: 0.8161 (mt) cc_final: 0.7891 (mp) REVERT: A 648 VAL cc_start: 0.7331 (p) cc_final: 0.7103 (p) REVERT: A 695 LYS cc_start: 0.7067 (mttt) cc_final: 0.6836 (mttp) REVERT: A 705 ILE cc_start: 0.8051 (pt) cc_final: 0.7699 (mt) REVERT: A 808 PHE cc_start: 0.7944 (t80) cc_final: 0.7727 (t80) REVERT: A 837 LYS cc_start: 0.7459 (mttm) cc_final: 0.7235 (ttmm) REVERT: A 841 GLN cc_start: 0.7527 (mt0) cc_final: 0.7208 (tt0) REVERT: A 895 LYS cc_start: 0.7385 (tttt) cc_final: 0.7183 (ttpt) REVERT: B 408 TRP cc_start: 0.6047 (p-90) cc_final: 0.4806 (p-90) outliers start: 3 outliers final: 0 residues processed: 195 average time/residue: 0.2576 time to fit residues: 65.6978 Evaluate side-chains 176 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 HIS A 42 GLN ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 HIS A 216 ASN A 372 ASN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS A 402 HIS A 613 ASN A 697 ASN A 758 HIS A 804 GLN A 884 ASN B 401 ASN B 495 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9046 Z= 0.237 Angle : 0.632 8.304 12494 Z= 0.354 Chirality : 0.040 0.182 1438 Planarity : 0.006 0.059 1373 Dihedral : 24.818 138.214 1749 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.55 % Allowed : 13.84 % Favored : 84.61 % 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: -2.62 (0.24), residues: 905 helix: -1.14 (0.19), residues: 619 sheet: None (None), residues: 0 loop : -2.89 (0.29), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 408 HIS 0.004 0.001 HIS B 495 PHE 0.015 0.001 PHE A 749 TYR 0.016 0.002 TYR A 657 ARG 0.007 0.001 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 182 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7565 (mttm) cc_final: 0.7276 (mmtp) REVERT: A 13 ILE cc_start: 0.7997 (mm) cc_final: 0.7623 (mt) REVERT: A 19 GLU cc_start: 0.7181 (tt0) cc_final: 0.6966 (tt0) REVERT: A 31 HIS cc_start: 0.6826 (OUTLIER) cc_final: 0.6137 (m-70) REVERT: A 39 LYS cc_start: 0.7855 (tptt) cc_final: 0.7485 (tptt) REVERT: A 72 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7578 (tm-30) REVERT: A 107 GLU cc_start: 0.8039 (mp0) cc_final: 0.7697 (mm-30) REVERT: A 118 PHE cc_start: 0.7599 (t80) cc_final: 0.7397 (t80) REVERT: A 227 MET cc_start: 0.7352 (ttm) cc_final: 0.7135 (ttm) REVERT: A 288 GLU cc_start: 0.6678 (tm-30) cc_final: 0.6452 (tm-30) REVERT: A 291 VAL cc_start: 0.7517 (p) cc_final: 0.7312 (m) REVERT: A 333 LEU cc_start: 0.8131 (mt) cc_final: 0.7781 (tp) REVERT: A 391 HIS cc_start: 0.6591 (m-70) cc_final: 0.6372 (m170) REVERT: A 421 ILE cc_start: 0.6555 (mt) cc_final: 0.6346 (mm) REVERT: A 644 LEU cc_start: 0.8159 (mt) cc_final: 0.7912 (mp) REVERT: A 689 ILE cc_start: 0.7710 (mt) cc_final: 0.7503 (mt) REVERT: A 692 LYS cc_start: 0.7841 (mmmt) cc_final: 0.7544 (mmmt) REVERT: A 695 LYS cc_start: 0.7095 (mttt) cc_final: 0.6869 (mttp) REVERT: A 705 ILE cc_start: 0.7894 (pt) cc_final: 0.7692 (tp) REVERT: A 753 VAL cc_start: 0.7967 (p) cc_final: 0.7690 (t) REVERT: A 841 GLN cc_start: 0.7558 (mt0) cc_final: 0.7319 (tt0) REVERT: A 895 LYS cc_start: 0.7447 (tttt) cc_final: 0.7186 (ttpt) REVERT: B 391 MET cc_start: 0.6484 (OUTLIER) cc_final: 0.5972 (mmt) REVERT: B 492 ASN cc_start: 0.8234 (t0) cc_final: 0.7801 (m-40) outliers start: 13 outliers final: 5 residues processed: 189 average time/residue: 0.2455 time to fit residues: 60.9353 Evaluate side-chains 178 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 171 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.0670 chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 0.0570 chunk 95 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 70 optimal weight: 0.4980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN A 401 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9046 Z= 0.188 Angle : 0.594 7.025 12494 Z= 0.331 Chirality : 0.039 0.193 1438 Planarity : 0.005 0.054 1373 Dihedral : 24.530 139.935 1749 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.51 % Allowed : 15.04 % Favored : 82.46 % 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: -1.72 (0.26), residues: 905 helix: -0.38 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.85 (0.30), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 780 HIS 0.007 0.001 HIS A 121 PHE 0.012 0.001 PHE A 354 TYR 0.013 0.001 TYR A 657 ARG 0.009 0.001 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 172 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7560 (mttm) cc_final: 0.7319 (mmtp) REVERT: A 13 ILE cc_start: 0.8024 (mm) cc_final: 0.7667 (mt) REVERT: A 39 LYS cc_start: 0.7843 (tptt) cc_final: 0.7529 (tptt) REVERT: A 107 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7684 (mm-30) REVERT: A 333 LEU cc_start: 0.8097 (mt) cc_final: 0.7759 (tt) REVERT: A 431 ARG cc_start: 0.5163 (mtp180) cc_final: 0.4538 (mtp180) REVERT: A 641 MET cc_start: 0.7231 (tpt) cc_final: 0.6764 (tpt) REVERT: A 692 LYS cc_start: 0.7830 (mmmt) cc_final: 0.7552 (mmmt) REVERT: A 695 LYS cc_start: 0.7031 (mttt) cc_final: 0.6826 (mttp) REVERT: A 808 PHE cc_start: 0.7949 (t80) cc_final: 0.7574 (t80) REVERT: B 391 MET cc_start: 0.6523 (OUTLIER) cc_final: 0.6051 (mmt) REVERT: B 408 TRP cc_start: 0.5568 (p-90) cc_final: 0.4496 (p-90) REVERT: B 475 PHE cc_start: 0.8125 (m-10) cc_final: 0.7925 (m-10) REVERT: B 492 ASN cc_start: 0.8174 (t0) cc_final: 0.7690 (m-40) outliers start: 21 outliers final: 9 residues processed: 182 average time/residue: 0.2344 time to fit residues: 56.8855 Evaluate side-chains 179 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 168 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.0030 chunk 66 optimal weight: 0.2980 chunk 45 optimal weight: 0.6980 chunk 9 optimal weight: 0.0970 chunk 42 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 0.0770 chunk 93 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS A 424 GLN ** A 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9046 Z= 0.168 Angle : 0.574 6.623 12494 Z= 0.320 Chirality : 0.038 0.194 1438 Planarity : 0.004 0.048 1373 Dihedral : 24.238 141.950 1749 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.15 % Allowed : 17.18 % Favored : 80.67 % 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: -1.17 (0.27), residues: 905 helix: 0.08 (0.21), residues: 643 sheet: None (None), residues: 0 loop : -2.88 (0.30), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 780 HIS 0.017 0.001 HIS A 391 PHE 0.023 0.001 PHE A 118 TYR 0.010 0.001 TYR A 657 ARG 0.010 0.001 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 171 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.7994 (mm) cc_final: 0.7660 (mt) REVERT: A 39 LYS cc_start: 0.7829 (tptt) cc_final: 0.7504 (tptt) REVERT: A 107 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7687 (mm-30) REVERT: A 147 ASN cc_start: 0.7695 (t0) cc_final: 0.7491 (t0) REVERT: A 185 PHE cc_start: 0.7103 (m-80) cc_final: 0.6706 (m-10) REVERT: A 227 MET cc_start: 0.7566 (ttp) cc_final: 0.7310 (ttp) REVERT: A 291 VAL cc_start: 0.7443 (m) cc_final: 0.7109 (m) REVERT: A 399 ARG cc_start: 0.6731 (tpt90) cc_final: 0.6227 (tmt-80) REVERT: A 431 ARG cc_start: 0.4998 (mtp180) cc_final: 0.4491 (mtp180) REVERT: A 443 MET cc_start: 0.7629 (tpp) cc_final: 0.7321 (tpt) REVERT: A 692 LYS cc_start: 0.7874 (mmmt) cc_final: 0.7572 (mmmt) REVERT: A 808 PHE cc_start: 0.7877 (t80) cc_final: 0.7642 (t80) REVERT: A 824 LYS cc_start: 0.7334 (mttm) cc_final: 0.7070 (mmtt) REVERT: B 408 TRP cc_start: 0.5403 (p-90) cc_final: 0.4510 (p-90) REVERT: B 475 PHE cc_start: 0.8035 (m-10) cc_final: 0.7796 (m-10) REVERT: B 492 ASN cc_start: 0.7997 (t0) cc_final: 0.7546 (m-40) outliers start: 18 outliers final: 9 residues processed: 182 average time/residue: 0.2311 time to fit residues: 55.9279 Evaluate side-chains 175 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 165 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 69 optimal weight: 0.0970 chunk 38 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 84 optimal weight: 0.0050 chunk 23 optimal weight: 0.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN A 670 HIS B 495 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9046 Z= 0.189 Angle : 0.581 7.117 12494 Z= 0.323 Chirality : 0.039 0.181 1438 Planarity : 0.004 0.045 1373 Dihedral : 24.080 147.586 1749 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.15 % Allowed : 19.21 % Favored : 78.64 % 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: -0.82 (0.27), residues: 905 helix: 0.36 (0.21), residues: 637 sheet: None (None), residues: 0 loop : -2.74 (0.30), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 408 HIS 0.005 0.001 HIS A 121 PHE 0.014 0.001 PHE A 118 TYR 0.013 0.001 TYR A 657 ARG 0.009 0.000 ARG A 910 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.7826 (tptt) cc_final: 0.7496 (tptt) REVERT: A 107 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7666 (mm-30) REVERT: A 147 ASN cc_start: 0.7703 (t0) cc_final: 0.7489 (t0) REVERT: A 185 PHE cc_start: 0.7077 (m-80) cc_final: 0.6700 (m-10) REVERT: A 291 VAL cc_start: 0.7534 (m) cc_final: 0.7098 (p) REVERT: A 399 ARG cc_start: 0.6813 (tpt90) cc_final: 0.6324 (tmt-80) REVERT: A 431 ARG cc_start: 0.5004 (mtp180) cc_final: 0.4492 (mtp180) REVERT: A 641 MET cc_start: 0.6981 (tpt) cc_final: 0.6644 (tpt) REVERT: A 692 LYS cc_start: 0.7893 (mmmt) cc_final: 0.7580 (mmmt) REVERT: A 808 PHE cc_start: 0.7942 (t80) cc_final: 0.7686 (t80) REVERT: A 824 LYS cc_start: 0.7331 (mttm) cc_final: 0.7106 (mmtp) REVERT: B 408 TRP cc_start: 0.5406 (p-90) cc_final: 0.4423 (p-90) REVERT: B 490 ARG cc_start: 0.7617 (mtt-85) cc_final: 0.7347 (mtt90) REVERT: B 492 ASN cc_start: 0.7986 (t0) cc_final: 0.7674 (m-40) outliers start: 18 outliers final: 12 residues processed: 180 average time/residue: 0.2536 time to fit residues: 60.3506 Evaluate side-chains 178 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 165 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 43 optimal weight: 0.0070 chunk 7 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 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 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN A 670 HIS A 882 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9046 Z= 0.216 Angle : 0.595 8.969 12494 Z= 0.328 Chirality : 0.039 0.153 1438 Planarity : 0.004 0.045 1373 Dihedral : 24.041 151.578 1749 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.03 % Allowed : 21.36 % Favored : 76.61 % 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: -0.77 (0.27), residues: 905 helix: 0.35 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -2.63 (0.31), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 408 HIS 0.004 0.001 HIS A 121 PHE 0.010 0.001 PHE A 118 TYR 0.017 0.001 TYR A 657 ARG 0.011 0.001 ARG A 910 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8037 (mm) cc_final: 0.7767 (mt) REVERT: A 19 GLU cc_start: 0.7204 (tt0) cc_final: 0.6996 (tt0) REVERT: A 39 LYS cc_start: 0.7888 (tptt) cc_final: 0.7612 (tptt) REVERT: A 107 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7662 (mm-30) REVERT: A 291 VAL cc_start: 0.7529 (m) cc_final: 0.7096 (p) REVERT: A 431 ARG cc_start: 0.5010 (mtp180) cc_final: 0.4403 (mtp180) REVERT: A 641 MET cc_start: 0.6971 (tpt) cc_final: 0.6717 (tpt) REVERT: A 689 ILE cc_start: 0.7666 (mt) cc_final: 0.7413 (mt) REVERT: A 692 LYS cc_start: 0.7890 (mmmt) cc_final: 0.7591 (mmmt) REVERT: A 808 PHE cc_start: 0.7896 (t80) cc_final: 0.7662 (t80) REVERT: A 852 ILE cc_start: 0.7800 (mm) cc_final: 0.7487 (mm) REVERT: B 408 TRP cc_start: 0.5632 (p-90) cc_final: 0.4530 (p-90) REVERT: B 492 ASN cc_start: 0.8037 (t0) cc_final: 0.7731 (m-40) outliers start: 17 outliers final: 13 residues processed: 175 average time/residue: 0.2640 time to fit residues: 61.8018 Evaluate side-chains 178 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 0.0000 chunk 53 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 56 optimal weight: 0.0570 chunk 43 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 overall best weight: 0.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 HIS A 401 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN A 670 HIS A 882 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9046 Z= 0.194 Angle : 0.583 8.454 12494 Z= 0.321 Chirality : 0.038 0.140 1438 Planarity : 0.004 0.049 1373 Dihedral : 23.984 154.329 1749 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.51 % Allowed : 21.48 % Favored : 76.01 % 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: -0.63 (0.28), residues: 905 helix: 0.47 (0.21), residues: 643 sheet: None (None), residues: 0 loop : -2.63 (0.30), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 408 HIS 0.004 0.001 HIS A 121 PHE 0.009 0.001 PHE A 362 TYR 0.015 0.001 TYR A 657 ARG 0.012 0.001 ARG A 910 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 165 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8004 (mm) cc_final: 0.7698 (mt) REVERT: A 19 GLU cc_start: 0.7232 (tt0) cc_final: 0.7023 (tt0) REVERT: A 185 PHE cc_start: 0.7065 (m-80) cc_final: 0.6666 (m-10) REVERT: A 291 VAL cc_start: 0.7519 (m) cc_final: 0.7099 (p) REVERT: A 333 LEU cc_start: 0.7850 (tp) cc_final: 0.7642 (tt) REVERT: A 399 ARG cc_start: 0.6693 (tpt90) cc_final: 0.6473 (tpt170) REVERT: A 431 ARG cc_start: 0.5002 (mtp180) cc_final: 0.4487 (mtp180) REVERT: A 443 MET cc_start: 0.7687 (tpp) cc_final: 0.7301 (tpt) REVERT: A 667 PHE cc_start: 0.6335 (OUTLIER) cc_final: 0.5832 (m-80) REVERT: A 689 ILE cc_start: 0.7675 (mt) cc_final: 0.7455 (mt) REVERT: A 692 LYS cc_start: 0.7876 (mmmt) cc_final: 0.7579 (mmmt) REVERT: A 808 PHE cc_start: 0.7847 (t80) cc_final: 0.7584 (t80) REVERT: A 852 ILE cc_start: 0.7845 (mm) cc_final: 0.7599 (mm) REVERT: B 408 TRP cc_start: 0.5626 (p-90) cc_final: 0.4475 (p-90) REVERT: B 492 ASN cc_start: 0.7916 (t0) cc_final: 0.7622 (m-40) outliers start: 21 outliers final: 13 residues processed: 175 average time/residue: 0.2604 time to fit residues: 59.8987 Evaluate side-chains 176 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 667 PHE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN A 670 HIS A 882 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6459 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9046 Z= 0.258 Angle : 0.636 10.300 12494 Z= 0.347 Chirality : 0.040 0.154 1438 Planarity : 0.005 0.051 1373 Dihedral : 24.029 155.320 1749 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.79 % Allowed : 22.20 % Favored : 76.01 % 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: -0.77 (0.27), residues: 905 helix: 0.32 (0.21), residues: 645 sheet: None (None), residues: 0 loop : -2.56 (0.31), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 351 HIS 0.020 0.002 HIS A 391 PHE 0.011 0.001 PHE A 803 TYR 0.014 0.001 TYR A 657 ARG 0.013 0.001 ARG A 910 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 160 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7576 (mttm) cc_final: 0.7233 (mttm) REVERT: A 13 ILE cc_start: 0.8032 (mm) cc_final: 0.7726 (mt) REVERT: A 291 VAL cc_start: 0.7640 (m) cc_final: 0.7196 (p) REVERT: A 443 MET cc_start: 0.7636 (tpp) cc_final: 0.7276 (tpt) REVERT: A 584 TYR cc_start: 0.6922 (m-80) cc_final: 0.6662 (m-80) REVERT: A 689 ILE cc_start: 0.7734 (mt) cc_final: 0.7525 (mt) REVERT: A 692 LYS cc_start: 0.7915 (mmmt) cc_final: 0.7611 (mmmt) REVERT: A 808 PHE cc_start: 0.7978 (t80) cc_final: 0.7741 (t80) REVERT: B 408 TRP cc_start: 0.5828 (p-90) cc_final: 0.4521 (p-90) outliers start: 15 outliers final: 11 residues processed: 167 average time/residue: 0.2386 time to fit residues: 52.6098 Evaluate side-chains 167 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 156 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 52 optimal weight: 0.0670 chunk 37 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 57 optimal weight: 0.0970 chunk 92 optimal weight: 2.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN A 670 HIS A 882 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9046 Z= 0.213 Angle : 0.620 10.465 12494 Z= 0.338 Chirality : 0.039 0.159 1438 Planarity : 0.004 0.054 1373 Dihedral : 24.005 156.168 1749 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.67 % Allowed : 22.55 % Favored : 75.78 % 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: -0.69 (0.27), residues: 905 helix: 0.39 (0.21), residues: 641 sheet: None (None), residues: 0 loop : -2.54 (0.31), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 351 HIS 0.016 0.001 HIS A 391 PHE 0.010 0.001 PHE A 354 TYR 0.014 0.001 TYR A 657 ARG 0.013 0.001 ARG A 910 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 161 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7557 (mttm) cc_final: 0.7175 (mttm) REVERT: A 13 ILE cc_start: 0.7997 (mm) cc_final: 0.7679 (mt) REVERT: A 185 PHE cc_start: 0.6912 (m-80) cc_final: 0.6488 (m-10) REVERT: A 291 VAL cc_start: 0.7632 (m) cc_final: 0.7178 (p) REVERT: A 401 HIS cc_start: 0.7119 (OUTLIER) cc_final: 0.6835 (m-70) REVERT: A 431 ARG cc_start: 0.5062 (mtp180) cc_final: 0.4354 (mtp180) REVERT: A 443 MET cc_start: 0.7620 (tpp) cc_final: 0.7223 (tpt) REVERT: A 450 MET cc_start: 0.6399 (tpp) cc_final: 0.6154 (mmm) REVERT: A 584 TYR cc_start: 0.6903 (m-80) cc_final: 0.6658 (m-80) REVERT: A 689 ILE cc_start: 0.7747 (mt) cc_final: 0.7518 (mt) REVERT: A 692 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7604 (mmmt) REVERT: A 852 ILE cc_start: 0.7842 (mm) cc_final: 0.7571 (mm) REVERT: B 408 TRP cc_start: 0.5789 (p-90) cc_final: 0.5488 (p-90) outliers start: 14 outliers final: 12 residues processed: 168 average time/residue: 0.2592 time to fit residues: 57.2869 Evaluate side-chains 174 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 161 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 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 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN A 670 HIS A 882 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9046 Z= 0.234 Angle : 0.635 10.482 12494 Z= 0.345 Chirality : 0.040 0.169 1438 Planarity : 0.005 0.056 1373 Dihedral : 24.018 158.033 1749 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.79 % Allowed : 22.20 % Favored : 76.01 % 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: -0.75 (0.27), residues: 905 helix: 0.37 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -2.60 (0.31), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 351 HIS 0.015 0.001 HIS A 391 PHE 0.029 0.001 PHE A 808 TYR 0.015 0.001 TYR A 657 ARG 0.013 0.001 ARG A 910 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 160 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7569 (mttm) cc_final: 0.7188 (mttm) REVERT: A 13 ILE cc_start: 0.8019 (mm) cc_final: 0.7698 (mt) REVERT: A 19 GLU cc_start: 0.7291 (tt0) cc_final: 0.7087 (tt0) REVERT: A 145 MET cc_start: 0.5491 (tpt) cc_final: 0.5039 (tpt) REVERT: A 185 PHE cc_start: 0.6963 (m-80) cc_final: 0.6621 (m-10) REVERT: A 291 VAL cc_start: 0.7632 (m) cc_final: 0.7177 (p) REVERT: A 387 LYS cc_start: 0.7103 (tptp) cc_final: 0.6492 (tptt) REVERT: A 443 MET cc_start: 0.7593 (tpp) cc_final: 0.7229 (tpt) REVERT: A 689 ILE cc_start: 0.7748 (mt) cc_final: 0.7525 (mt) REVERT: A 692 LYS cc_start: 0.7902 (mmmt) cc_final: 0.7605 (mmmt) REVERT: A 852 ILE cc_start: 0.7864 (mm) cc_final: 0.7596 (mm) REVERT: B 408 TRP cc_start: 0.5769 (p-90) cc_final: 0.5503 (p-90) outliers start: 15 outliers final: 13 residues processed: 167 average time/residue: 0.2507 time to fit residues: 55.0861 Evaluate side-chains 173 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN A 670 HIS A 882 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.162505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.139005 restraints weight = 12658.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.142646 restraints weight = 6954.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.145174 restraints weight = 4441.912| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9046 Z= 0.268 Angle : 0.663 10.253 12494 Z= 0.360 Chirality : 0.041 0.167 1438 Planarity : 0.005 0.057 1373 Dihedral : 24.135 166.788 1749 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.43 % Allowed : 22.55 % Favored : 76.01 % 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: -0.89 (0.27), residues: 905 helix: 0.25 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -2.63 (0.31), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 351 HIS 0.015 0.002 HIS A 391 PHE 0.016 0.001 PHE A 808 TYR 0.016 0.002 TYR A 657 ARG 0.013 0.001 ARG A 910 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2022.07 seconds wall clock time: 37 minutes 31.77 seconds (2251.77 seconds total)