Starting phenix.real_space_refine on Mon Mar 11 02:30:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nus_0521/03_2024/6nus_0521.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nus_0521/03_2024/6nus_0521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nus_0521/03_2024/6nus_0521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nus_0521/03_2024/6nus_0521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nus_0521/03_2024/6nus_0521.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nus_0521/03_2024/6nus_0521.pdb" } resolution = 3.5 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= 0.005 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 Zn 2 6.06 5 S 54 5.16 5 C 4235 2.51 5 N 1115 2.21 5 O 1226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 833": "OD1" <-> "OD2" Residue "A PHE 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6632 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5767 Classifications: {'peptide': 715} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 689} Chain breaks: 6 Chain: "B" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 863 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 106} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1481 SG CYS A 301 37.503 61.634 35.610 1.00 36.78 S ATOM 1522 SG CYS A 306 37.698 60.632 32.501 1.00 62.98 S ATOM 1554 SG CYS A 310 41.314 60.514 34.574 1.00 33.81 S ATOM 2658 SG CYS A 487 19.463 58.580 43.739 1.00 37.60 S ATOM 3783 SG CYS A 645 18.191 58.310 40.576 1.00 36.07 S ATOM 3789 SG CYS A 646 21.574 60.826 41.973 1.00 36.63 S Time building chain proxies: 4.00, per 1000 atoms: 0.60 Number of scatterers: 6632 At special positions: 0 Unit cell: (86.25, 93.15, 97.75, 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) Zn 2 29.99 S 54 16.00 O 1226 8.00 N 1115 7.00 C 4235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " Number of angles added : 6 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 7 sheets defined 52.4% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 199 Processing helix chain 'A' and resid 234 through 242 Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.763A pdb=" N SER A 255 " --> pdb=" O ALA A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.517A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.505A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 512 through 517 Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 561 through 581 removed outlier: 5.213A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 removed outlier: 4.206A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 715 removed outlier: 3.804A pdb=" N ILE A 715 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 729 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 772 Processing helix chain 'A' and resid 778 through 790 Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 833 through 840 Processing helix chain 'A' and resid 855 through 867 Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 891 removed outlier: 4.068A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 915 Processing helix chain 'A' and resid 916 through 918 No H-bonds generated for 'chain 'A' and resid 916 through 918' Processing helix chain 'B' and resid 81 through 99 Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 176 through 180 Processing sheet with id=AA1, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.589A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ILE A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLY A 203 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.533A pdb=" N VAL A 335 " --> pdb=" O PRO A 339 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N VAL A 341 " --> pdb=" O ILE A 333 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE A 333 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N SER A 343 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ARG A 331 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 345 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 390 removed outlier: 6.281A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 390 removed outlier: 6.281A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 400 removed outlier: 6.189A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA7, first strand: chain 'A' and resid 816 through 821 319 hydrogen bonds defined for protein. 864 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1232 1.32 - 1.45: 1957 1.45 - 1.58: 3498 1.58 - 1.70: 15 1.70 - 1.83: 81 Bond restraints: 6783 Sorted by residual: bond pdb=" CB TYR A 884 " pdb=" CG TYR A 884 " ideal model delta sigma weight residual 1.512 1.424 0.088 2.20e-02 2.07e+03 1.60e+01 bond pdb=" NE ARG A 365 " pdb=" CZ ARG A 365 " ideal model delta sigma weight residual 1.326 1.370 -0.044 1.10e-02 8.26e+03 1.58e+01 bond pdb=" CB ILE B 107 " pdb=" CG1 ILE B 107 " ideal model delta sigma weight residual 1.530 1.609 -0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" CB LEU B 91 " pdb=" CG LEU B 91 " ideal model delta sigma weight residual 1.530 1.606 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" NE1 TRP A 290 " pdb=" CE2 TRP A 290 " ideal model delta sigma weight residual 1.370 1.329 0.041 1.10e-02 8.26e+03 1.38e+01 ... (remaining 6778 not shown) Histogram of bond angle deviations from ideal: 99.75 - 106.59: 236 106.59 - 113.43: 3439 113.43 - 120.27: 2865 120.27 - 127.10: 2605 127.10 - 133.94: 65 Bond angle restraints: 9210 Sorted by residual: angle pdb=" C ASP A 377 " pdb=" N PRO A 378 " pdb=" CA PRO A 378 " ideal model delta sigma weight residual 119.56 127.07 -7.51 1.02e+00 9.61e-01 5.42e+01 angle pdb=" C MET A 626 " pdb=" N PRO A 627 " pdb=" CA PRO A 627 " ideal model delta sigma weight residual 119.78 127.04 -7.26 1.03e+00 9.43e-01 4.96e+01 angle pdb=" C ASN A 168 " pdb=" N PRO A 169 " pdb=" CA PRO A 169 " ideal model delta sigma weight residual 119.82 126.63 -6.81 9.80e-01 1.04e+00 4.83e+01 angle pdb=" CA ASP A 194 " pdb=" CB ASP A 194 " pdb=" CG ASP A 194 " ideal model delta sigma weight residual 112.60 119.47 -6.87 1.00e+00 1.00e+00 4.72e+01 angle pdb=" N ILE A 757 " pdb=" CA ILE A 757 " pdb=" C ILE A 757 " ideal model delta sigma weight residual 108.11 117.41 -9.30 1.40e+00 5.10e-01 4.41e+01 ... (remaining 9205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 3896 17.22 - 34.44: 103 34.44 - 51.66: 16 51.66 - 68.88: 9 68.88 - 86.11: 5 Dihedral angle restraints: 4029 sinusoidal: 1576 harmonic: 2453 Sorted by residual: dihedral pdb=" C HIS A 295 " pdb=" N HIS A 295 " pdb=" CA HIS A 295 " pdb=" CB HIS A 295 " ideal model delta harmonic sigma weight residual -122.60 -113.98 -8.62 0 2.50e+00 1.60e-01 1.19e+01 dihedral pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CA ILE B 120 " pdb=" CB ILE B 120 " ideal model delta harmonic sigma weight residual 123.40 131.72 -8.32 0 2.50e+00 1.60e-01 1.11e+01 dihedral pdb=" CA PRO A 830 " pdb=" C PRO A 830 " pdb=" N TYR A 831 " pdb=" CA TYR A 831 " ideal model delta harmonic sigma weight residual 180.00 163.43 16.57 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 4026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 623 0.070 - 0.140: 281 0.140 - 0.210: 89 0.210 - 0.279: 29 0.279 - 0.349: 4 Chirality restraints: 1026 Sorted by residual: chirality pdb=" CA TYR A 867 " pdb=" N TYR A 867 " pdb=" C TYR A 867 " pdb=" CB TYR A 867 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA PHE B 92 " pdb=" N PHE B 92 " pdb=" C PHE B 92 " pdb=" CB PHE B 92 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA MET A 242 " pdb=" N MET A 242 " pdb=" C MET A 242 " pdb=" CB MET A 242 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 1023 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 619 " 0.072 2.00e-02 2.50e+03 3.93e-02 3.09e+01 pdb=" CG TYR A 619 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 619 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR A 619 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR A 619 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 619 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR A 619 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 619 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 509 " -0.046 2.00e-02 2.50e+03 2.25e-02 1.26e+01 pdb=" CG TRP A 509 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 509 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP A 509 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP A 509 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 509 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 509 " 0.029 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 509 " -0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 509 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 509 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 237 " 0.048 2.00e-02 2.50e+03 2.50e-02 1.25e+01 pdb=" CG TYR A 237 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 237 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 237 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR A 237 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 237 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 237 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 237 " 0.034 2.00e-02 2.50e+03 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1997 2.82 - 3.34: 6272 3.34 - 3.86: 11632 3.86 - 4.38: 14206 4.38 - 4.90: 22527 Nonbonded interactions: 56634 Sorted by model distance: nonbonded pdb=" OH TYR A 175 " pdb=" OH TYR A 787 " model vdw 2.301 2.440 nonbonded pdb=" OG1 THR A 189 " pdb=" OH TYR A 237 " model vdw 2.418 2.440 nonbonded pdb=" NZ LYS A 478 " pdb=" OD1 ASP A 743 " model vdw 2.458 2.520 nonbonded pdb=" N ASP A 258 " pdb=" OD1 ASP A 258 " model vdw 2.460 2.520 nonbonded pdb=" N ASP B 112 " pdb=" OD1 ASP B 112 " model vdw 2.464 2.520 ... (remaining 56629 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 3.980 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 23.040 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 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 : 0.016 0.094 6783 Z= 1.029 Angle : 1.568 9.299 9210 Z= 1.081 Chirality : 0.090 0.349 1026 Planarity : 0.009 0.039 1176 Dihedral : 9.782 86.106 2445 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 (0.28), residues: 811 helix: -0.34 (0.24), residues: 354 sheet: 0.55 (0.60), residues: 63 loop : 0.94 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.011 TRP A 509 HIS 0.017 0.002 HIS A 613 PHE 0.032 0.006 PHE A 859 TYR 0.072 0.008 TYR A 619 ARG 0.008 0.001 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 263 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 GLN cc_start: 0.7702 (mt0) cc_final: 0.7485 (mt0) outliers start: 1 outliers final: 1 residues processed: 264 average time/residue: 0.2049 time to fit residues: 69.4956 Evaluate side-chains 168 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 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 209 ASN A 210 GLN A 572 HIS ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A 752 HIS ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6783 Z= 0.224 Angle : 0.602 7.253 9210 Z= 0.329 Chirality : 0.043 0.239 1026 Planarity : 0.004 0.043 1176 Dihedral : 4.723 35.743 909 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.47 % Allowed : 10.70 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.90 (0.29), residues: 811 helix: 0.85 (0.27), residues: 358 sheet: 0.36 (0.59), residues: 74 loop : 0.61 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 917 HIS 0.006 0.001 HIS A 872 PHE 0.026 0.002 PHE A 471 TYR 0.023 0.002 TYR A 530 ARG 0.005 0.001 ARG A 631 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 171 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 666 MET cc_start: 0.5499 (mmm) cc_final: 0.4960 (mmm) REVERT: A 914 SER cc_start: 0.8108 (p) cc_final: 0.7902 (t) outliers start: 18 outliers final: 11 residues processed: 177 average time/residue: 0.1940 time to fit residues: 45.4113 Evaluate side-chains 158 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 147 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 483 TYR Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 66 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 613 HIS ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 168 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6783 Z= 0.227 Angle : 0.567 6.370 9210 Z= 0.305 Chirality : 0.043 0.174 1026 Planarity : 0.005 0.042 1176 Dihedral : 4.671 30.361 909 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.02 % Allowed : 12.62 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 (0.29), residues: 811 helix: 0.91 (0.28), residues: 357 sheet: 0.35 (0.56), residues: 73 loop : 0.20 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 509 HIS 0.005 0.001 HIS A 599 PHE 0.025 0.002 PHE A 368 TYR 0.025 0.002 TYR A 530 ARG 0.008 0.001 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 153 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 666 MET cc_start: 0.5798 (mmm) cc_final: 0.5112 (mmm) REVERT: A 714 LYS cc_start: 0.7646 (mmtm) cc_final: 0.7169 (tptp) REVERT: B 89 THR cc_start: 0.8235 (m) cc_final: 0.7946 (p) outliers start: 22 outliers final: 15 residues processed: 163 average time/residue: 0.1562 time to fit residues: 35.2659 Evaluate side-chains 160 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 50 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6783 Z= 0.255 Angle : 0.572 6.700 9210 Z= 0.305 Chirality : 0.043 0.139 1026 Planarity : 0.004 0.045 1176 Dihedral : 4.567 24.993 907 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.43 % Allowed : 13.31 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.42 (0.29), residues: 811 helix: 0.73 (0.28), residues: 364 sheet: 0.10 (0.56), residues: 69 loop : -0.00 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 154 HIS 0.008 0.001 HIS A 309 PHE 0.052 0.002 PHE B 92 TYR 0.026 0.002 TYR A 530 ARG 0.007 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 151 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 343 SER cc_start: 0.7387 (m) cc_final: 0.6969 (m) REVERT: A 509 TRP cc_start: 0.7261 (m-90) cc_final: 0.6980 (m-90) REVERT: A 540 THR cc_start: 0.7388 (t) cc_final: 0.7085 (t) REVERT: A 588 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8763 (p) REVERT: A 666 MET cc_start: 0.5726 (mmm) cc_final: 0.5099 (mmm) REVERT: A 714 LYS cc_start: 0.7635 (mmtm) cc_final: 0.7071 (tptp) REVERT: A 794 MET cc_start: 0.5937 (ttp) cc_final: 0.5451 (ptm) outliers start: 25 outliers final: 20 residues processed: 161 average time/residue: 0.1582 time to fit residues: 35.4583 Evaluate side-chains 157 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 788 TYR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 0.0060 chunk 71 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6783 Z= 0.178 Angle : 0.532 6.329 9210 Z= 0.278 Chirality : 0.042 0.168 1026 Planarity : 0.004 0.044 1176 Dihedral : 4.431 24.593 907 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.43 % Allowed : 13.85 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 (0.30), residues: 811 helix: 0.83 (0.28), residues: 365 sheet: 0.16 (0.57), residues: 69 loop : 0.06 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 917 HIS 0.005 0.001 HIS A 309 PHE 0.034 0.002 PHE B 92 TYR 0.011 0.001 TYR A 788 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 145 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 343 SER cc_start: 0.7317 (m) cc_final: 0.6908 (m) REVERT: A 509 TRP cc_start: 0.7171 (m-90) cc_final: 0.6818 (m-90) REVERT: A 540 THR cc_start: 0.7456 (t) cc_final: 0.7194 (t) REVERT: A 666 MET cc_start: 0.5602 (mmm) cc_final: 0.4955 (mmm) REVERT: A 714 LYS cc_start: 0.7639 (mmtm) cc_final: 0.7101 (tptp) REVERT: A 794 MET cc_start: 0.5869 (ttp) cc_final: 0.5286 (ptm) outliers start: 25 outliers final: 20 residues processed: 156 average time/residue: 0.1518 time to fit residues: 33.5118 Evaluate side-chains 156 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 HIS A 572 HIS ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6783 Z= 0.252 Angle : 0.578 7.692 9210 Z= 0.302 Chirality : 0.043 0.135 1026 Planarity : 0.004 0.043 1176 Dihedral : 4.523 24.614 907 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.39 % Allowed : 13.85 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 (0.30), residues: 811 helix: 0.72 (0.28), residues: 365 sheet: 0.19 (0.59), residues: 69 loop : -0.17 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 154 HIS 0.004 0.001 HIS A 309 PHE 0.029 0.002 PHE A 753 TYR 0.026 0.002 TYR A 530 ARG 0.007 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 0.693 Fit side-chains REVERT: A 343 SER cc_start: 0.7547 (m) cc_final: 0.7186 (m) REVERT: A 509 TRP cc_start: 0.7201 (m-90) cc_final: 0.6881 (m-90) REVERT: A 540 THR cc_start: 0.7412 (t) cc_final: 0.7195 (t) REVERT: A 666 MET cc_start: 0.5625 (mmm) cc_final: 0.5013 (mmm) REVERT: A 714 LYS cc_start: 0.7648 (mmtm) cc_final: 0.7172 (tptp) REVERT: A 794 MET cc_start: 0.5956 (ttp) cc_final: 0.5316 (ptm) outliers start: 32 outliers final: 23 residues processed: 156 average time/residue: 0.1377 time to fit residues: 30.8952 Evaluate side-chains 162 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 139 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6783 Z= 0.204 Angle : 0.558 7.909 9210 Z= 0.291 Chirality : 0.043 0.346 1026 Planarity : 0.004 0.049 1176 Dihedral : 4.484 24.124 907 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.70 % Allowed : 14.68 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.34 (0.30), residues: 811 helix: 0.72 (0.28), residues: 370 sheet: 0.11 (0.59), residues: 69 loop : -0.13 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 154 HIS 0.004 0.001 HIS A 309 PHE 0.022 0.002 PHE A 753 TYR 0.029 0.001 TYR A 530 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 0.806 Fit side-chains REVERT: A 343 SER cc_start: 0.7536 (m) cc_final: 0.7198 (m) REVERT: A 509 TRP cc_start: 0.7178 (m-90) cc_final: 0.6842 (m-90) REVERT: A 666 MET cc_start: 0.5618 (mmm) cc_final: 0.4997 (mmm) REVERT: A 714 LYS cc_start: 0.7745 (mmtm) cc_final: 0.7254 (tptp) outliers start: 27 outliers final: 21 residues processed: 150 average time/residue: 0.1431 time to fit residues: 30.8885 Evaluate side-chains 155 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 0.3980 chunk 75 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.6004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6783 Z= 0.243 Angle : 0.576 7.749 9210 Z= 0.301 Chirality : 0.044 0.305 1026 Planarity : 0.004 0.048 1176 Dihedral : 4.532 23.776 907 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.25 % Allowed : 14.27 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.21 (0.30), residues: 811 helix: 0.65 (0.28), residues: 371 sheet: 0.10 (0.60), residues: 69 loop : -0.26 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 154 HIS 0.004 0.001 HIS A 613 PHE 0.021 0.002 PHE A 753 TYR 0.031 0.002 TYR A 530 ARG 0.011 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 0.687 Fit side-chains REVERT: A 343 SER cc_start: 0.7753 (m) cc_final: 0.7501 (m) REVERT: A 372 LEU cc_start: 0.8454 (mt) cc_final: 0.8147 (tt) REVERT: A 509 TRP cc_start: 0.7169 (m-90) cc_final: 0.6907 (m-90) REVERT: A 666 MET cc_start: 0.5479 (mmm) cc_final: 0.4901 (mmm) REVERT: A 714 LYS cc_start: 0.7725 (mmtm) cc_final: 0.7292 (tptp) outliers start: 31 outliers final: 25 residues processed: 155 average time/residue: 0.1438 time to fit residues: 32.0597 Evaluate side-chains 157 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.6213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6783 Z= 0.287 Angle : 0.610 7.556 9210 Z= 0.320 Chirality : 0.045 0.293 1026 Planarity : 0.004 0.051 1176 Dihedral : 4.717 24.645 907 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.98 % Allowed : 14.81 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 (0.30), residues: 811 helix: 0.55 (0.28), residues: 371 sheet: -0.02 (0.61), residues: 69 loop : -0.40 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 154 HIS 0.005 0.001 HIS A 599 PHE 0.024 0.002 PHE A 753 TYR 0.029 0.002 TYR A 530 ARG 0.004 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 0.793 Fit side-chains REVERT: A 343 SER cc_start: 0.7821 (m) cc_final: 0.7516 (m) REVERT: A 509 TRP cc_start: 0.7210 (m-90) cc_final: 0.6956 (m-90) REVERT: A 519 MET cc_start: 0.7701 (mtt) cc_final: 0.7272 (mtt) REVERT: A 666 MET cc_start: 0.5579 (mmm) cc_final: 0.5008 (mmm) REVERT: A 714 LYS cc_start: 0.7795 (mmtm) cc_final: 0.7400 (tptp) outliers start: 29 outliers final: 26 residues processed: 151 average time/residue: 0.1518 time to fit residues: 32.5437 Evaluate side-chains 156 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 65 optimal weight: 0.1980 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6783 Z= 0.227 Angle : 0.586 8.985 9210 Z= 0.302 Chirality : 0.043 0.276 1026 Planarity : 0.004 0.046 1176 Dihedral : 4.574 23.864 907 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.84 % Allowed : 15.50 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.13 (0.30), residues: 811 helix: 0.56 (0.28), residues: 378 sheet: 0.01 (0.62), residues: 69 loop : -0.27 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 154 HIS 0.004 0.001 HIS A 309 PHE 0.037 0.002 PHE A 368 TYR 0.028 0.001 TYR A 530 ARG 0.014 0.001 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 0.802 Fit side-chains REVERT: A 343 SER cc_start: 0.7771 (m) cc_final: 0.7499 (m) REVERT: A 368 PHE cc_start: 0.7687 (t80) cc_final: 0.7470 (t80) REVERT: A 509 TRP cc_start: 0.7145 (m-90) cc_final: 0.6914 (m-90) REVERT: A 666 MET cc_start: 0.5472 (mmm) cc_final: 0.4894 (mmm) REVERT: A 714 LYS cc_start: 0.7750 (mmtm) cc_final: 0.7425 (tptp) outliers start: 28 outliers final: 25 residues processed: 149 average time/residue: 0.1429 time to fit residues: 30.5582 Evaluate side-chains 155 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 3.9990 chunk 9 optimal weight: 0.0570 chunk 18 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.180725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.158351 restraints weight = 8843.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.162446 restraints weight = 4356.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.164942 restraints weight = 2627.154| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.6432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6783 Z= 0.180 Angle : 0.562 8.083 9210 Z= 0.289 Chirality : 0.042 0.270 1026 Planarity : 0.004 0.042 1176 Dihedral : 4.449 23.605 907 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.43 % Allowed : 16.60 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.30), residues: 811 helix: 0.74 (0.28), residues: 373 sheet: -0.07 (0.61), residues: 69 loop : -0.09 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 154 HIS 0.005 0.001 HIS A 381 PHE 0.037 0.002 PHE A 368 TYR 0.027 0.001 TYR A 530 ARG 0.006 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1669.62 seconds wall clock time: 31 minutes 8.58 seconds (1868.58 seconds total)