Starting phenix.real_space_refine on Thu Feb 15 08:49:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5e_12027/02_2024/7b5e_12027.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5e_12027/02_2024/7b5e_12027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5e_12027/02_2024/7b5e_12027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5e_12027/02_2024/7b5e_12027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5e_12027/02_2024/7b5e_12027.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5e_12027/02_2024/7b5e_12027.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 Ca 4 9.91 5 S 74 5.16 5 C 7678 2.51 5 N 1936 2.21 5 O 2072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 298": "NH1" <-> "NH2" Residue "A TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 425": "OE1" <-> "OE2" Residue "A ARG 429": "NH1" <-> "NH2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 686": "NH1" <-> "NH2" Residue "A PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 756": "OD1" <-> "OD2" Residue "A PHE 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 788": "NH1" <-> "NH2" Residue "A TYR 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 883": "OD1" <-> "OD2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 298": "NH1" <-> "NH2" Residue "B TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 318": "OD1" <-> "OD2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 405": "OD1" <-> "OD2" Residue "B PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 425": "OE1" <-> "OE2" Residue "B ARG 429": "NH1" <-> "NH2" Residue "B PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 535": "NH1" <-> "NH2" Residue "B TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 686": "NH1" <-> "NH2" Residue "B PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 756": "OD1" <-> "OD2" Residue "B PHE 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 788": "NH1" <-> "NH2" Residue "B TYR 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 883": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11764 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5880 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 31, 'TRANS': 686} Chain breaks: 4 Chain: "B" Number of atoms: 5880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5880 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 31, 'TRANS': 686} Chain breaks: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.50, per 1000 atoms: 0.55 Number of scatterers: 11764 At special positions: 0 Unit cell: (122.452, 98.164, 121.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 74 16.00 O 2072 8.00 N 1936 7.00 C 7678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 395 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 836 " distance=2.04 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 386 " distance=2.03 Simple disulfide: pdb=" SG CYS A 625 " - pdb=" SG CYS A 630 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 395 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 836 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 625 " - pdb=" SG CYS B 630 " distance=2.03 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: 4.98 Conformation dependent library (CDL) restraints added in 2.4 seconds 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 6 sheets defined 63.0% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 166 through 181 Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 204 through 211 removed outlier: 3.664A pdb=" N GLU A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 257 removed outlier: 3.651A pdb=" N THR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 275 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 316 through 325 Processing helix chain 'A' and resid 325 through 359 removed outlier: 3.752A pdb=" N GLY A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.899A pdb=" N MET A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 393 Processing helix chain 'A' and resid 394 through 403 removed outlier: 3.760A pdb=" N LEU A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 438 Processing helix chain 'A' and resid 452 through 466 Processing helix chain 'A' and resid 489 through 518 removed outlier: 4.285A pdb=" N ASN A 493 " --> pdb=" O ALA A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 568 Processing helix chain 'A' and resid 572 through 592 Processing helix chain 'A' and resid 593 through 602 Processing helix chain 'A' and resid 630 through 648 removed outlier: 4.194A pdb=" N LEU A 634 " --> pdb=" O CYS A 630 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN A 646 " --> pdb=" O MET A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 668 Proline residue: A 658 - end of helix Processing helix chain 'A' and resid 685 through 693 removed outlier: 4.320A pdb=" N ASN A 692 " --> pdb=" O GLU A 688 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 716 Processing helix chain 'A' and resid 722 through 745 removed outlier: 4.211A pdb=" N PHE A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG A 736 " --> pdb=" O ILE A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 782 removed outlier: 4.110A pdb=" N VAL A 772 " --> pdb=" O GLY A 768 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE A 777 " --> pdb=" O ILE A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 794 Processing helix chain 'A' and resid 803 through 809 Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 854 through 885 removed outlier: 3.899A pdb=" N TRP A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 908 Processing helix chain 'B' and resid 166 through 181 Proline residue: B 177 - end of helix Processing helix chain 'B' and resid 204 through 211 removed outlier: 3.664A pdb=" N GLU B 211 " --> pdb=" O PRO B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 257 removed outlier: 3.651A pdb=" N THR B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 275 Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 307 through 311 Processing helix chain 'B' and resid 316 through 325 Processing helix chain 'B' and resid 325 through 359 removed outlier: 3.752A pdb=" N GLY B 329 " --> pdb=" O GLY B 325 " (cutoff:3.500A) Proline residue: B 344 - end of helix Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.899A pdb=" N MET B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 393 Processing helix chain 'B' and resid 394 through 403 removed outlier: 3.760A pdb=" N LEU B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 438 Processing helix chain 'B' and resid 452 through 466 Processing helix chain 'B' and resid 489 through 518 removed outlier: 4.285A pdb=" N ASN B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 568 Processing helix chain 'B' and resid 572 through 592 Processing helix chain 'B' and resid 593 through 602 Processing helix chain 'B' and resid 630 through 648 removed outlier: 4.194A pdb=" N LEU B 634 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN B 646 " --> pdb=" O MET B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 668 Proline residue: B 658 - end of helix Processing helix chain 'B' and resid 685 through 693 removed outlier: 4.320A pdb=" N ASN B 692 " --> pdb=" O GLU B 688 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 716 Processing helix chain 'B' and resid 722 through 745 removed outlier: 4.211A pdb=" N PHE B 726 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG B 736 " --> pdb=" O ILE B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 782 removed outlier: 4.111A pdb=" N VAL B 772 " --> pdb=" O GLY B 768 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE B 773 " --> pdb=" O LYS B 769 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE B 777 " --> pdb=" O ILE B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 794 Processing helix chain 'B' and resid 803 through 809 Processing helix chain 'B' and resid 815 through 817 No H-bonds generated for 'chain 'B' and resid 815 through 817' Processing helix chain 'B' and resid 854 through 885 removed outlier: 3.898A pdb=" N TRP B 858 " --> pdb=" O SER B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 908 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 188 Processing sheet with id=AA2, first strand: chain 'A' and resid 217 through 218 Processing sheet with id=AA3, first strand: chain 'A' and resid 810 through 813 Processing sheet with id=AA4, first strand: chain 'B' and resid 186 through 188 Processing sheet with id=AA5, first strand: chain 'B' and resid 217 through 218 Processing sheet with id=AA6, first strand: chain 'B' and resid 810 through 813 652 hydrogen bonds defined for protein. 1926 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: 3.69 Time building geometry restraints manager: 5.32 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: 3639 1.34 - 1.46: 2725 1.46 - 1.58: 5572 1.58 - 1.70: 0 1.70 - 1.81: 122 Bond restraints: 12058 Sorted by residual: bond pdb=" C ALA B 723 " pdb=" N PRO B 724 " ideal model delta sigma weight residual 1.335 1.370 -0.036 1.19e-02 7.06e+03 8.91e+00 bond pdb=" C ALA A 723 " pdb=" N PRO A 724 " ideal model delta sigma weight residual 1.335 1.370 -0.035 1.19e-02 7.06e+03 8.82e+00 bond pdb=" C ASP A 203 " pdb=" N PRO A 204 " ideal model delta sigma weight residual 1.337 1.362 -0.025 1.11e-02 8.12e+03 5.27e+00 bond pdb=" C ASP B 203 " pdb=" N PRO B 204 " ideal model delta sigma weight residual 1.337 1.362 -0.025 1.11e-02 8.12e+03 5.08e+00 bond pdb=" C SER A 527 " pdb=" N PRO A 528 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.05e+00 ... (remaining 12053 not shown) Histogram of bond angle deviations from ideal: 98.71 - 105.85: 269 105.85 - 112.98: 6241 112.98 - 120.11: 4850 120.11 - 127.24: 4830 127.24 - 134.38: 122 Bond angle restraints: 16312 Sorted by residual: angle pdb=" N VAL A 181 " pdb=" CA VAL A 181 " pdb=" C VAL A 181 " ideal model delta sigma weight residual 111.91 108.42 3.49 8.90e-01 1.26e+00 1.54e+01 angle pdb=" N VAL B 181 " pdb=" CA VAL B 181 " pdb=" C VAL B 181 " ideal model delta sigma weight residual 111.91 108.42 3.49 8.90e-01 1.26e+00 1.53e+01 angle pdb=" N ASP A 123 " pdb=" CA ASP A 123 " pdb=" C ASP A 123 " ideal model delta sigma weight residual 111.02 115.59 -4.57 1.25e+00 6.40e-01 1.34e+01 angle pdb=" N ASP B 123 " pdb=" CA ASP B 123 " pdb=" C ASP B 123 " ideal model delta sigma weight residual 111.02 115.58 -4.56 1.25e+00 6.40e-01 1.33e+01 angle pdb=" CA LEU A 381 " pdb=" CB LEU A 381 " pdb=" CG LEU A 381 " ideal model delta sigma weight residual 116.30 128.79 -12.49 3.50e+00 8.16e-02 1.27e+01 ... (remaining 16307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.00: 5973 14.00 - 28.00: 884 28.00 - 42.00: 273 42.00 - 56.01: 64 56.01 - 70.01: 20 Dihedral angle restraints: 7214 sinusoidal: 2962 harmonic: 4252 Sorted by residual: dihedral pdb=" CB CYS B 625 " pdb=" SG CYS B 625 " pdb=" SG CYS B 630 " pdb=" CB CYS B 630 " ideal model delta sinusoidal sigma weight residual -86.00 -151.87 65.87 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CB CYS A 625 " pdb=" SG CYS A 625 " pdb=" SG CYS A 630 " pdb=" CB CYS A 630 " ideal model delta sinusoidal sigma weight residual -86.00 -151.86 65.86 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CA THR A 235 " pdb=" C THR A 235 " pdb=" N ASP A 236 " pdb=" CA ASP A 236 " ideal model delta harmonic sigma weight residual 180.00 155.71 24.29 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 7211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1462 0.072 - 0.144: 305 0.144 - 0.216: 19 0.216 - 0.289: 6 0.289 - 0.361: 2 Chirality restraints: 1794 Sorted by residual: chirality pdb=" CB ILE B 786 " pdb=" CA ILE B 786 " pdb=" CG1 ILE B 786 " pdb=" CG2 ILE B 786 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CB ILE A 786 " pdb=" CA ILE A 786 " pdb=" CG1 ILE A 786 " pdb=" CG2 ILE A 786 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CB VAL A 310 " pdb=" CA VAL A 310 " pdb=" CG1 VAL A 310 " pdb=" CG2 VAL A 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1791 not shown) Planarity restraints: 2044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 206 " 0.059 5.00e-02 4.00e+02 8.94e-02 1.28e+01 pdb=" N PRO A 207 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 206 " -0.059 5.00e-02 4.00e+02 8.93e-02 1.28e+01 pdb=" N PRO B 207 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO B 207 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 207 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 406 " -0.047 5.00e-02 4.00e+02 7.07e-02 8.00e+00 pdb=" N PRO A 407 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 407 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 407 " -0.039 5.00e-02 4.00e+02 ... (remaining 2041 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3347 2.80 - 3.33: 11951 3.33 - 3.85: 19704 3.85 - 4.37: 21530 4.37 - 4.90: 35729 Nonbonded interactions: 92261 Sorted by model distance: nonbonded pdb=" O VAL A 778 " pdb=" OG1 THR A 782 " model vdw 2.275 2.440 nonbonded pdb=" O VAL B 778 " pdb=" OG1 THR B 782 " model vdw 2.275 2.440 nonbonded pdb=" O LYS B 740 " pdb=" OG1 THR B 744 " model vdw 2.278 2.440 nonbonded pdb=" O LYS A 740 " pdb=" OG1 THR A 744 " model vdw 2.279 2.440 nonbonded pdb=" OG SER B 387 " pdb=" O ASP B 825 " model vdw 2.293 2.440 ... (remaining 92256 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.930 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 34.360 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 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 0.056 12058 Z= 0.394 Angle : 0.935 12.492 16312 Z= 0.514 Chirality : 0.057 0.361 1794 Planarity : 0.008 0.089 2044 Dihedral : 15.024 70.006 4438 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.31 % Allowed : 10.56 % Favored : 89.12 % 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: -3.56 (0.18), residues: 1416 helix: -1.68 (0.15), residues: 834 sheet: None (None), residues: 0 loop : -3.37 (0.21), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 760 HIS 0.010 0.002 HIS B 402 PHE 0.017 0.002 PHE A 585 TYR 0.022 0.002 TYR A 666 ARG 0.005 0.001 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 181 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 TYR cc_start: 0.8626 (t80) cc_final: 0.8365 (t80) REVERT: A 416 MET cc_start: 0.7452 (tpp) cc_final: 0.7159 (tpp) REVERT: A 424 MET cc_start: 0.8724 (tpp) cc_final: 0.8423 (tpp) REVERT: A 436 TYR cc_start: 0.6872 (t80) cc_final: 0.5979 (t80) REVERT: A 508 VAL cc_start: 0.8668 (t) cc_final: 0.8414 (p) REVERT: A 580 LEU cc_start: 0.8626 (tp) cc_final: 0.8323 (tt) REVERT: B 197 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8857 (t) REVERT: B 436 TYR cc_start: 0.6566 (t80) cc_final: 0.6345 (t80) REVERT: B 524 MET cc_start: -0.1256 (ttm) cc_final: -0.2110 (tmm) REVERT: B 760 TRP cc_start: 0.8467 (m100) cc_final: 0.8225 (m-90) outliers start: 4 outliers final: 0 residues processed: 183 average time/residue: 0.2597 time to fit residues: 66.7128 Evaluate side-chains 127 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 ASN A 692 ASN ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 ASN B 183 HIS ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 ASN B 692 ASN ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 ASN B 898 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12058 Z= 0.164 Angle : 0.618 9.729 16312 Z= 0.319 Chirality : 0.041 0.248 1794 Planarity : 0.006 0.068 2044 Dihedral : 5.150 19.979 1584 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % 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: -1.77 (0.21), residues: 1416 helix: -0.04 (0.17), residues: 826 sheet: -3.71 (0.85), residues: 24 loop : -2.83 (0.23), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 760 HIS 0.004 0.001 HIS A 402 PHE 0.010 0.001 PHE B 620 TYR 0.019 0.001 TYR A 436 ARG 0.006 0.000 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 MET cc_start: 0.7355 (tpp) cc_final: 0.7097 (tpp) REVERT: A 500 MET cc_start: 0.7950 (mtp) cc_final: 0.7376 (mtm) REVERT: A 660 MET cc_start: 0.5238 (mmt) cc_final: 0.4942 (mmp) REVERT: A 704 MET cc_start: 0.8121 (mmm) cc_final: 0.7915 (mmt) REVERT: B 322 LYS cc_start: 0.8552 (ptmm) cc_final: 0.8320 (tttm) REVERT: B 524 MET cc_start: -0.0896 (ttm) cc_final: -0.1913 (tmm) REVERT: B 704 MET cc_start: 0.8130 (tpp) cc_final: 0.7827 (mmt) REVERT: B 760 TRP cc_start: 0.8401 (m100) cc_final: 0.8077 (m-90) REVERT: B 900 GLU cc_start: 0.8082 (pt0) cc_final: 0.7853 (tm-30) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2241 time to fit residues: 59.6379 Evaluate side-chains 124 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12058 Z= 0.174 Angle : 0.604 9.844 16312 Z= 0.311 Chirality : 0.041 0.231 1794 Planarity : 0.005 0.060 2044 Dihedral : 4.882 17.987 1584 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % 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: -0.98 (0.21), residues: 1416 helix: 0.62 (0.17), residues: 834 sheet: -3.54 (0.82), residues: 24 loop : -2.56 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 760 HIS 0.004 0.001 HIS A 402 PHE 0.018 0.001 PHE B 499 TYR 0.022 0.001 TYR A 436 ARG 0.006 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.7875 (t0) cc_final: 0.7277 (p0) REVERT: A 500 MET cc_start: 0.7973 (mtp) cc_final: 0.7355 (mtm) REVERT: B 322 LYS cc_start: 0.8636 (ptmm) cc_final: 0.8311 (tttm) REVERT: B 760 TRP cc_start: 0.8410 (m100) cc_final: 0.8115 (m-90) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2334 time to fit residues: 62.6672 Evaluate side-chains 128 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 GLN A 730 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12058 Z= 0.204 Angle : 0.622 9.661 16312 Z= 0.318 Chirality : 0.042 0.252 1794 Planarity : 0.005 0.056 2044 Dihedral : 4.785 17.619 1584 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % 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 (0.22), residues: 1416 helix: 0.88 (0.17), residues: 840 sheet: -3.26 (0.80), residues: 24 loop : -2.40 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 760 HIS 0.005 0.001 HIS A 402 PHE 0.023 0.001 PHE A 712 TYR 0.023 0.001 TYR A 182 ARG 0.003 0.000 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.7752 (t0) cc_final: 0.7298 (p0) REVERT: A 508 VAL cc_start: 0.8579 (t) cc_final: 0.8366 (p) REVERT: B 405 ASP cc_start: 0.7418 (t70) cc_final: 0.7082 (p0) REVERT: B 585 PHE cc_start: 0.8342 (t80) cc_final: 0.8113 (t80) REVERT: B 709 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8342 (tm-30) REVERT: B 760 TRP cc_start: 0.8390 (m100) cc_final: 0.8089 (m-90) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2373 time to fit residues: 59.7838 Evaluate side-chains 128 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN A 896 GLN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12058 Z= 0.282 Angle : 0.681 11.116 16312 Z= 0.351 Chirality : 0.044 0.260 1794 Planarity : 0.005 0.055 2044 Dihedral : 4.912 18.547 1584 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % 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: -0.70 (0.22), residues: 1416 helix: 0.90 (0.17), residues: 832 sheet: -3.41 (0.70), residues: 32 loop : -2.50 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 760 HIS 0.009 0.001 HIS A 230 PHE 0.021 0.002 PHE B 585 TYR 0.017 0.002 TYR A 703 ARG 0.008 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.7930 (t0) cc_final: 0.7388 (p0) REVERT: A 500 MET cc_start: 0.8141 (mtp) cc_final: 0.7476 (mtm) REVERT: B 405 ASP cc_start: 0.7622 (t70) cc_final: 0.7205 (p0) REVERT: B 580 LEU cc_start: 0.8713 (tp) cc_final: 0.8462 (tt) REVERT: B 760 TRP cc_start: 0.8498 (m100) cc_final: 0.8224 (m-90) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2224 time to fit residues: 52.1815 Evaluate side-chains 117 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 114 optimal weight: 0.2980 chunk 63 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 GLN A 898 HIS ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN B 730 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12058 Z= 0.160 Angle : 0.612 12.156 16312 Z= 0.309 Chirality : 0.042 0.261 1794 Planarity : 0.005 0.055 2044 Dihedral : 4.632 17.319 1584 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.08 % Allowed : 2.50 % Favored : 97.42 % 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: -0.32 (0.22), residues: 1416 helix: 1.14 (0.17), residues: 836 sheet: -3.01 (0.89), residues: 24 loop : -2.28 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 760 HIS 0.004 0.001 HIS A 230 PHE 0.021 0.001 PHE A 499 TYR 0.019 0.001 TYR A 436 ARG 0.005 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 500 MET cc_start: 0.7995 (mtp) cc_final: 0.7242 (mtm) REVERT: A 508 VAL cc_start: 0.8658 (t) cc_final: 0.8416 (p) REVERT: B 508 VAL cc_start: 0.8627 (t) cc_final: 0.8398 (p) REVERT: B 535 ARG cc_start: 0.5992 (mmp-170) cc_final: 0.5554 (mmm160) REVERT: B 704 MET cc_start: 0.8050 (mmm) cc_final: 0.7787 (tpp) REVERT: B 709 GLN cc_start: 0.8288 (tm-30) cc_final: 0.8055 (tm-30) REVERT: B 760 TRP cc_start: 0.8346 (m100) cc_final: 0.8077 (m-90) outliers start: 1 outliers final: 0 residues processed: 186 average time/residue: 0.2159 time to fit residues: 59.6488 Evaluate side-chains 124 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 115 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 GLN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12058 Z= 0.318 Angle : 0.712 10.157 16312 Z= 0.367 Chirality : 0.045 0.232 1794 Planarity : 0.005 0.053 2044 Dihedral : 4.925 18.610 1584 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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 (0.22), residues: 1416 helix: 0.93 (0.17), residues: 832 sheet: None (None), residues: 0 loop : -2.34 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 760 HIS 0.009 0.001 HIS A 402 PHE 0.027 0.002 PHE B 712 TYR 0.018 0.002 TYR B 331 ARG 0.006 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.465 Fit side-chains revert: symmetry clash REVERT: A 338 TYR cc_start: 0.8462 (t80) cc_final: 0.8117 (t80) REVERT: A 500 MET cc_start: 0.8219 (mtp) cc_final: 0.7479 (mtm) REVERT: B 535 ARG cc_start: 0.5964 (mmp-170) cc_final: 0.5553 (mmm160) REVERT: B 580 LEU cc_start: 0.8630 (tp) cc_final: 0.8391 (tt) REVERT: B 760 TRP cc_start: 0.8543 (m100) cc_final: 0.7788 (m-90) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2144 time to fit residues: 53.0879 Evaluate side-chains 116 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN ** A 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12058 Z= 0.189 Angle : 0.638 11.041 16312 Z= 0.324 Chirality : 0.043 0.238 1794 Planarity : 0.005 0.054 2044 Dihedral : 4.696 17.804 1584 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: -0.30 (0.22), residues: 1416 helix: 1.07 (0.18), residues: 836 sheet: -2.91 (0.86), residues: 24 loop : -2.13 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 760 HIS 0.005 0.001 HIS A 402 PHE 0.024 0.001 PHE A 499 TYR 0.018 0.001 TYR A 436 ARG 0.007 0.000 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 MET cc_start: 0.8003 (ppp) cc_final: 0.7786 (tmm) REVERT: A 405 ASP cc_start: 0.7334 (t70) cc_final: 0.7037 (p0) REVERT: A 500 MET cc_start: 0.8073 (mtp) cc_final: 0.7301 (mtm) REVERT: A 508 VAL cc_start: 0.8567 (t) cc_final: 0.8312 (p) REVERT: A 580 LEU cc_start: 0.8617 (tp) cc_final: 0.8374 (tt) REVERT: A 606 PHE cc_start: 0.6823 (m-80) cc_final: 0.6260 (t80) REVERT: B 535 ARG cc_start: 0.5908 (mmp-170) cc_final: 0.5443 (mmm160) REVERT: B 580 LEU cc_start: 0.8599 (tp) cc_final: 0.8330 (tt) REVERT: B 760 TRP cc_start: 0.8480 (m100) cc_final: 0.7750 (m-90) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2208 time to fit residues: 54.5518 Evaluate side-chains 117 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 0.0370 chunk 100 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 115 optimal weight: 0.0010 chunk 120 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 134 optimal weight: 10.0000 overall best weight: 0.5666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12058 Z= 0.155 Angle : 0.624 10.849 16312 Z= 0.314 Chirality : 0.042 0.231 1794 Planarity : 0.005 0.054 2044 Dihedral : 4.543 18.052 1584 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -0.09 (0.23), residues: 1416 helix: 1.25 (0.18), residues: 836 sheet: -2.75 (0.87), residues: 24 loop : -2.06 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 760 HIS 0.006 0.001 HIS B 230 PHE 0.024 0.001 PHE A 499 TYR 0.017 0.001 TYR A 436 ARG 0.005 0.000 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 MET cc_start: 0.7968 (ppp) cc_final: 0.7681 (tmm) REVERT: A 500 MET cc_start: 0.7895 (mtp) cc_final: 0.7154 (mtm) REVERT: A 508 VAL cc_start: 0.8507 (t) cc_final: 0.8269 (p) REVERT: A 606 PHE cc_start: 0.6799 (m-80) cc_final: 0.6241 (t80) REVERT: B 535 ARG cc_start: 0.5743 (mmp-170) cc_final: 0.5270 (mmm160) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2206 time to fit residues: 58.5878 Evaluate side-chains 127 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 11 optimal weight: 0.3980 chunk 87 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN ** A 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 GLN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12058 Z= 0.271 Angle : 0.695 11.901 16312 Z= 0.354 Chirality : 0.045 0.264 1794 Planarity : 0.005 0.052 2044 Dihedral : 4.787 19.533 1584 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -0.29 (0.23), residues: 1416 helix: 1.06 (0.18), residues: 830 sheet: -2.89 (0.88), residues: 24 loop : -2.04 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 760 HIS 0.008 0.001 HIS A 402 PHE 0.027 0.002 PHE B 712 TYR 0.016 0.002 TYR B 388 ARG 0.005 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.517 Fit side-chains revert: symmetry clash REVERT: A 500 MET cc_start: 0.8020 (mtp) cc_final: 0.7245 (mtm) REVERT: A 513 ILE cc_start: 0.8839 (tp) cc_final: 0.8585 (tp) REVERT: A 580 LEU cc_start: 0.8662 (tp) cc_final: 0.8403 (tt) REVERT: A 606 PHE cc_start: 0.6908 (m-80) cc_final: 0.6286 (t80) REVERT: A 632 MET cc_start: 0.8495 (mmt) cc_final: 0.8211 (tpt) REVERT: B 535 ARG cc_start: 0.5907 (mmp-170) cc_final: 0.5551 (mmm160) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2164 time to fit residues: 51.5696 Evaluate side-chains 115 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 0.0000 chunk 103 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 99 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.106228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.089711 restraints weight = 32659.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.091322 restraints weight = 21155.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.092444 restraints weight = 15735.784| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12058 Z= 0.159 Angle : 0.628 12.009 16312 Z= 0.314 Chirality : 0.042 0.234 1794 Planarity : 0.005 0.053 2044 Dihedral : 4.496 17.499 1584 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -0.03 (0.23), residues: 1416 helix: 1.27 (0.18), residues: 830 sheet: -2.54 (0.94), residues: 24 loop : -1.95 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 760 HIS 0.005 0.001 HIS B 230 PHE 0.021 0.001 PHE B 712 TYR 0.020 0.001 TYR A 436 ARG 0.005 0.000 ARG B 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2124.22 seconds wall clock time: 39 minutes 49.32 seconds (2389.32 seconds total)