Starting phenix.real_space_refine on Tue Feb 13 20:49:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xot_22279/02_2024/6xot_22279.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xot_22279/02_2024/6xot_22279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xot_22279/02_2024/6xot_22279.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xot_22279/02_2024/6xot_22279.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xot_22279/02_2024/6xot_22279.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xot_22279/02_2024/6xot_22279.pdb" } resolution = 3.9 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 4901 2.51 5 N 1305 2.21 5 O 1459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 44": "OD1" <-> "OD2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A ASP 83": "OD1" <-> "OD2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A ASP 191": "OD1" <-> "OD2" Residue "A ASP 212": "OD1" <-> "OD2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 339": "OD1" <-> "OD2" Residue "A ASP 377": "OD1" <-> "OD2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A ASP 409": "OD1" <-> "OD2" Residue "A ASP 413": "OD1" <-> "OD2" Residue "A ASP 507": "OD1" <-> "OD2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A ASP 564": "OD1" <-> "OD2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A GLU 609": "OE1" <-> "OE2" Residue "A ASP 656": "OD1" <-> "OD2" Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A ASP 679": "OD1" <-> "OD2" Residue "A GLU 754": "OE1" <-> "OE2" Residue "A ASP 757": "OD1" <-> "OD2" Residue "A ASP 798": "OD1" <-> "OD2" Residue "A PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A GLU 901": "OE1" <-> "OE2" Residue "A ASP 925": "OD1" <-> "OD2" Residue "A GLU 930": "OE1" <-> "OE2" Residue "A ASP 940": "OD1" <-> "OD2" Residue "A GLU 954": "OE1" <-> "OE2" Residue "A ASP 971": "OD1" <-> "OD2" Residue "A GLU 984": "OE1" <-> "OE2" Residue "A ASP 1006": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7704 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7704 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 966, 7698 Classifications: {'peptide': 966} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 903} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 966, 7698 Classifications: {'peptide': 966} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 903} Chain breaks: 1 bond proxies already assigned to first conformer: 7882 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER A 723 " occ=0.42 ... (10 atoms not shown) pdb=" OG BSER A 723 " occ=0.58 Time building chain proxies: 8.46, per 1000 atoms: 1.10 Number of scatterers: 7704 At special positions: 0 Unit cell: (83.032, 86.456, 101.864, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1459 8.00 N 1305 7.00 C 4901 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 3.1 seconds 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1826 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 7 sheets defined 54.1% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 32 through 39 removed outlier: 3.796A pdb=" N ARG A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 111 removed outlier: 3.774A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 128 removed outlier: 3.827A pdb=" N ASN A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 169 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 200 through 212 Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 229 through 233 removed outlier: 3.610A pdb=" N VAL A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 245 removed outlier: 3.515A pdb=" N GLU A 244 " --> pdb=" O CYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 272 through 284 removed outlier: 4.022A pdb=" N HIS A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 288 removed outlier: 3.559A pdb=" N PHE A 288 " --> pdb=" O LEU A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 285 through 288' Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 400 through 419 Processing helix chain 'A' and resid 421 through 438 removed outlier: 3.652A pdb=" N ILE A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 457 removed outlier: 4.620A pdb=" N SER A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N CYS A 454 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N HIS A 457 " --> pdb=" O SER A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 Processing helix chain 'A' and resid 466 through 481 removed outlier: 3.630A pdb=" N ASN A 481 " --> pdb=" O CYS A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 510 through 528 removed outlier: 4.156A pdb=" N ALA A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 550 Processing helix chain 'A' and resid 561 through 565 Processing helix chain 'A' and resid 608 through 613 removed outlier: 3.567A pdb=" N ARG A 612 " --> pdb=" O GLU A 609 " (cutoff:3.500A) Proline residue: A 613 - end of helix Processing helix chain 'A' and resid 614 through 622 Processing helix chain 'A' and resid 631 through 643 Processing helix chain 'A' and resid 676 through 690 Processing helix chain 'A' and resid 695 through 713 removed outlier: 4.031A pdb=" N PHE A 699 " --> pdb=" O GLU A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 727 Processing helix chain 'A' and resid 731 through 742 Processing helix chain 'A' and resid 742 through 755 removed outlier: 3.724A pdb=" N VAL A 746 " --> pdb=" O GLY A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 763 Processing helix chain 'A' and resid 764 through 773 Processing helix chain 'A' and resid 788 through 802 Processing helix chain 'A' and resid 877 through 894 removed outlier: 4.355A pdb=" N ALA A 881 " --> pdb=" O ASP A 877 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER A 882 " --> pdb=" O PRO A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 901 Processing helix chain 'A' and resid 928 through 945 Processing helix chain 'A' and resid 948 through 964 removed outlier: 3.551A pdb=" N ASP A 964 " --> pdb=" O PHE A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 972 removed outlier: 3.762A pdb=" N LYS A 972 " --> pdb=" O PRO A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 979 Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 997 through 1008 Processing helix chain 'A' and resid 1025 through 1030 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46 removed outlier: 6.450A pdb=" N LYS A 66 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL A 54 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA A 64 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER A 56 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU A 62 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ARG A 75 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N THR A 267 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 77 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 134 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 6.450A pdb=" N LYS A 66 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL A 54 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA A 64 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER A 56 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU A 62 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ARG A 75 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N THR A 267 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 77 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.640A pdb=" N ARG A 183 " --> pdb=" O LYS A 199 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 199 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 311 removed outlier: 6.298A pdb=" N ARG A 307 " --> pdb=" O THR A 501 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N SER A 503 " --> pdb=" O ARG A 307 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE A 309 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N THR A 326 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA A 387 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP A 373 " --> pdb=" O GLN A 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 311 removed outlier: 6.298A pdb=" N ARG A 307 " --> pdb=" O THR A 501 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N SER A 503 " --> pdb=" O ARG A 307 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE A 309 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N THR A 326 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA A 387 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 575 through 579 removed outlier: 3.742A pdb=" N ASP A 575 " --> pdb=" O TYR A 587 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL A 782 " --> pdb=" O PRO A 584 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLN A 586 " --> pdb=" O VAL A 782 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ALA A 784 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N CYS A 588 " --> pdb=" O ALA A 784 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 671 " --> pdb=" O GLY A 645 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY A 645 " --> pdb=" O LEU A 671 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 912 removed outlier: 3.551A pdb=" N GLY A 909 " --> pdb=" O TYR A 921 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL A 866 " --> pdb=" O SER A 922 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LYS A 854 " --> pdb=" O ILE A1035 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ARG A1037 " --> pdb=" O LYS A 854 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N HIS A 856 " --> pdb=" O ARG A1037 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1342 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: 2.95 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2042 1.33 - 1.46: 1640 1.46 - 1.58: 4152 1.58 - 1.70: 0 1.70 - 1.82: 62 Bond restraints: 7896 Sorted by residual: bond pdb=" C VAL A 615 " pdb=" N PRO A 616 " ideal model delta sigma weight residual 1.335 1.369 -0.034 1.36e-02 5.41e+03 6.23e+00 bond pdb=" C ASP A 238 " pdb=" N PRO A 239 " ideal model delta sigma weight residual 1.333 1.367 -0.033 1.44e-02 4.82e+03 5.39e+00 bond pdb=" C ILE A 714 " pdb=" N PRO A 715 " ideal model delta sigma weight residual 1.335 1.361 -0.025 1.36e-02 5.41e+03 3.45e+00 bond pdb=" C ASP A 321 " pdb=" N PRO A 322 " ideal model delta sigma weight residual 1.335 1.361 -0.025 1.36e-02 5.41e+03 3.43e+00 bond pdb=" C VAL A 102 " pdb=" N PRO A 103 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.25e-02 6.40e+03 3.37e+00 ... (remaining 7891 not shown) Histogram of bond angle deviations from ideal: 95.95 - 103.82: 144 103.82 - 111.68: 3352 111.68 - 119.55: 3295 119.55 - 127.41: 3827 127.41 - 135.28: 90 Bond angle restraints: 10708 Sorted by residual: angle pdb=" N LEU A 529 " pdb=" CA LEU A 529 " pdb=" C LEU A 529 " ideal model delta sigma weight residual 109.76 116.03 -6.27 1.59e+00 3.96e-01 1.55e+01 angle pdb=" N LEU A 772 " pdb=" CA LEU A 772 " pdb=" C LEU A 772 " ideal model delta sigma weight residual 113.88 118.47 -4.59 1.23e+00 6.61e-01 1.39e+01 angle pdb=" CA ILE A 242 " pdb=" C ILE A 242 " pdb=" N PRO A 243 " ideal model delta sigma weight residual 118.88 124.38 -5.50 1.54e+00 4.22e-01 1.27e+01 angle pdb=" C ALA A 580 " pdb=" N GLY A 581 " pdb=" CA GLY A 581 " ideal model delta sigma weight residual 121.70 127.85 -6.15 1.80e+00 3.09e-01 1.17e+01 angle pdb=" N THR A 340 " pdb=" CA THR A 340 " pdb=" C THR A 340 " ideal model delta sigma weight residual 111.11 115.07 -3.96 1.20e+00 6.94e-01 1.09e+01 ... (remaining 10703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 4372 17.75 - 35.50: 304 35.50 - 53.25: 68 53.25 - 71.00: 20 71.00 - 88.75: 11 Dihedral angle restraints: 4775 sinusoidal: 1953 harmonic: 2822 Sorted by residual: dihedral pdb=" CA PRO A 170 " pdb=" C PRO A 170 " pdb=" N CYS A 171 " pdb=" CA CYS A 171 " ideal model delta harmonic sigma weight residual 180.00 157.86 22.14 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" C VAL A 102 " pdb=" N VAL A 102 " pdb=" CA VAL A 102 " pdb=" CB VAL A 102 " ideal model delta harmonic sigma weight residual -122.00 -131.41 9.41 0 2.50e+00 1.60e-01 1.42e+01 dihedral pdb=" CA GLU A 187 " pdb=" C GLU A 187 " pdb=" N ASN A 188 " pdb=" CA ASN A 188 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 4772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 905 0.069 - 0.138: 234 0.138 - 0.207: 28 0.207 - 0.276: 6 0.276 - 0.345: 1 Chirality restraints: 1174 Sorted by residual: chirality pdb=" CB ILE A 242 " pdb=" CA ILE A 242 " pdb=" CG1 ILE A 242 " pdb=" CG2 ILE A 242 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CA VAL A 102 " pdb=" N VAL A 102 " pdb=" C VAL A 102 " pdb=" CB VAL A 102 " both_signs ideal model delta sigma weight residual False 2.44 2.19 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB VAL A1004 " pdb=" CA VAL A1004 " pdb=" CG1 VAL A1004 " pdb=" CG2 VAL A1004 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1171 not shown) Planarity restraints: 1398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 86 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" CG ASN A 86 " 0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN A 86 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 86 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 897 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.03e+00 pdb=" C THR A 897 " 0.049 2.00e-02 2.50e+03 pdb=" O THR A 897 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU A 898 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 178 " -0.017 2.00e-02 2.50e+03 1.51e-02 5.66e+00 pdb=" CG TRP A 178 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 178 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 178 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 178 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 178 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 178 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 178 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 178 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 178 " -0.001 2.00e-02 2.50e+03 ... (remaining 1395 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1951 2.80 - 3.32: 7043 3.32 - 3.85: 13060 3.85 - 4.37: 14686 4.37 - 4.90: 25359 Nonbonded interactions: 62099 Sorted by model distance: nonbonded pdb=" OG1 THR A 729 " pdb=" O TRP A 851 " model vdw 2.272 2.440 nonbonded pdb=" OG1 THR A 326 " pdb=" O ILE A 396 " model vdw 2.279 2.440 nonbonded pdb=" OG1 THR A 384 " pdb=" O GLU A 386 " model vdw 2.286 2.440 nonbonded pdb=" O LEU A 957 " pdb=" OG SER A 961 " model vdw 2.298 2.440 nonbonded pdb=" O SER A 351 " pdb=" OG SER A 355 " model vdw 2.308 2.440 ... (remaining 62094 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=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.970 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 32.380 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 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 0.071 7896 Z= 0.375 Angle : 1.071 10.580 10708 Z= 0.577 Chirality : 0.061 0.345 1174 Planarity : 0.007 0.058 1398 Dihedral : 14.015 88.752 2949 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.23 % Allowed : 1.75 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -1.51 (0.24), residues: 965 helix: -1.00 (0.20), residues: 449 sheet: 0.31 (0.37), residues: 170 loop : -1.48 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 178 HIS 0.016 0.002 HIS A 186 PHE 0.026 0.003 PHE A 123 TYR 0.023 0.003 TYR A 388 ARG 0.009 0.001 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.8864 (tt) cc_final: 0.8626 (mt) REVERT: A 145 LEU cc_start: 0.9033 (tp) cc_final: 0.8802 (tp) REVERT: A 219 GLN cc_start: 0.8554 (tp-100) cc_final: 0.8006 (tp-100) REVERT: A 332 PHE cc_start: 0.7613 (m-80) cc_final: 0.7078 (m-80) REVERT: A 333 LEU cc_start: 0.8832 (tp) cc_final: 0.8626 (tt) REVERT: A 400 ASP cc_start: 0.8427 (m-30) cc_final: 0.8166 (t0) REVERT: A 567 PRO cc_start: 0.7225 (Cg_endo) cc_final: 0.6783 (Cg_exo) REVERT: A 587 TYR cc_start: 0.7579 (m-80) cc_final: 0.6789 (m-10) REVERT: A 680 MET cc_start: 0.7767 (ttp) cc_final: 0.7452 (ttm) REVERT: A 915 ASN cc_start: 0.8941 (p0) cc_final: 0.8401 (p0) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2288 time to fit residues: 59.6687 Evaluate side-chains 119 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 7.9990 chunk 72 optimal weight: 0.0010 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 87 optimal weight: 0.0980 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 104 HIS A 151 GLN A 204 ASN A 219 GLN ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN A 470 GLN ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 GLN A 552 GLN ** A 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN A 856 HIS A 864 ASN ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7896 Z= 0.226 Angle : 0.770 10.163 10708 Z= 0.383 Chirality : 0.046 0.242 1174 Planarity : 0.005 0.048 1398 Dihedral : 4.512 20.790 1037 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.52 % Allowed : 16.08 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.16 (0.26), residues: 965 helix: 0.72 (0.24), residues: 460 sheet: 0.60 (0.37), residues: 170 loop : -0.93 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 178 HIS 0.019 0.002 HIS A 229 PHE 0.033 0.002 PHE A 389 TYR 0.030 0.002 TYR A 721 ARG 0.011 0.001 ARG A 505 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7492 (t80) REVERT: A 219 GLN cc_start: 0.8383 (tp40) cc_final: 0.7727 (tp-100) REVERT: A 400 ASP cc_start: 0.8512 (m-30) cc_final: 0.8200 (t0) REVERT: A 414 GLU cc_start: 0.8490 (pp20) cc_final: 0.8271 (pp20) REVERT: A 721 TYR cc_start: 0.8675 (m-80) cc_final: 0.8414 (m-80) REVERT: A 888 ARG cc_start: 0.8294 (tpp-160) cc_final: 0.7741 (tpm170) REVERT: A 1024 GLU cc_start: 0.7256 (tp30) cc_final: 0.6970 (tp30) outliers start: 11 outliers final: 5 residues processed: 129 average time/residue: 0.1868 time to fit residues: 34.0654 Evaluate side-chains 102 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 53 GLN A 104 HIS ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 GLN A 325 GLN A 430 HIS ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 GLN A 698 HIS A 771 HIS A1016 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7896 Z= 0.311 Angle : 0.784 11.176 10708 Z= 0.395 Chirality : 0.046 0.186 1174 Planarity : 0.006 0.047 1398 Dihedral : 4.759 20.762 1037 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.91 % Allowed : 16.32 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.31 (0.27), residues: 965 helix: 0.97 (0.24), residues: 466 sheet: 0.55 (0.38), residues: 166 loop : -0.98 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 455 HIS 0.025 0.003 HIS A 229 PHE 0.019 0.002 PHE A 699 TYR 0.017 0.002 TYR A 721 ARG 0.007 0.001 ARG A 505 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7727 (t80) REVERT: A 219 GLN cc_start: 0.8487 (tp40) cc_final: 0.7791 (tp-100) REVERT: A 414 GLU cc_start: 0.8645 (pp20) cc_final: 0.8364 (pp20) REVERT: A 436 MET cc_start: 0.8012 (mtt) cc_final: 0.7770 (mtt) REVERT: A 721 TYR cc_start: 0.8853 (m-80) cc_final: 0.8607 (m-80) REVERT: A 750 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8524 (pttm) REVERT: A 888 ARG cc_start: 0.8366 (tpp-160) cc_final: 0.7794 (tpm170) REVERT: A 1024 GLU cc_start: 0.7295 (tp30) cc_final: 0.7087 (tp30) outliers start: 23 outliers final: 12 residues processed: 112 average time/residue: 0.1834 time to fit residues: 29.0686 Evaluate side-chains 104 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 750 LYS Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 951 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS A 108 HIS ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7896 Z= 0.244 Angle : 0.744 11.835 10708 Z= 0.363 Chirality : 0.047 0.358 1174 Planarity : 0.005 0.044 1398 Dihedral : 4.606 19.244 1037 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.21 % Allowed : 18.18 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.59 (0.27), residues: 965 helix: 1.25 (0.24), residues: 458 sheet: 0.41 (0.39), residues: 167 loop : -0.73 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 455 HIS 0.020 0.002 HIS A 229 PHE 0.025 0.002 PHE A 389 TYR 0.015 0.001 TYR A 721 ARG 0.005 0.001 ARG A 505 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7745 (t80) REVERT: A 97 MET cc_start: 0.8525 (mpp) cc_final: 0.8103 (mpp) REVERT: A 104 HIS cc_start: 0.7259 (OUTLIER) cc_final: 0.6384 (t-90) REVERT: A 219 GLN cc_start: 0.8363 (tp40) cc_final: 0.7657 (tp-100) REVERT: A 414 GLU cc_start: 0.8691 (pp20) cc_final: 0.8371 (pp20) REVERT: A 436 MET cc_start: 0.7984 (mtt) cc_final: 0.7732 (mtt) REVERT: A 721 TYR cc_start: 0.8873 (m-80) cc_final: 0.8605 (m-80) REVERT: A 755 MET cc_start: 0.8126 (mtp) cc_final: 0.7900 (ttt) REVERT: A 888 ARG cc_start: 0.8355 (tpp-160) cc_final: 0.7833 (tpm170) REVERT: A 971 ASP cc_start: 0.8539 (m-30) cc_final: 0.8102 (m-30) REVERT: A 1024 GLU cc_start: 0.7561 (tp30) cc_final: 0.7297 (tp30) outliers start: 17 outliers final: 10 residues processed: 109 average time/residue: 0.1763 time to fit residues: 27.4538 Evaluate side-chains 108 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 951 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 104 HIS A 108 HIS A 219 GLN A 223 ASN ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7896 Z= 0.346 Angle : 0.786 11.688 10708 Z= 0.393 Chirality : 0.048 0.388 1174 Planarity : 0.005 0.045 1398 Dihedral : 4.805 20.551 1037 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 23.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.50 % Allowed : 17.83 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.33 (0.27), residues: 965 helix: 0.96 (0.24), residues: 467 sheet: 0.31 (0.39), residues: 164 loop : -0.77 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 455 HIS 0.018 0.003 HIS A 229 PHE 0.032 0.002 PHE A 693 TYR 0.017 0.002 TYR A 450 ARG 0.004 0.001 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7858 (t80) REVERT: A 97 MET cc_start: 0.8525 (mpp) cc_final: 0.8166 (mpp) REVERT: A 229 HIS cc_start: 0.7911 (t-170) cc_final: 0.7674 (t-170) REVERT: A 245 LEU cc_start: 0.8821 (tp) cc_final: 0.8601 (tp) REVERT: A 414 GLU cc_start: 0.8798 (pp20) cc_final: 0.8471 (pp20) REVERT: A 436 MET cc_start: 0.8092 (mtt) cc_final: 0.7835 (mtt) REVERT: A 659 MET cc_start: 0.7346 (mmt) cc_final: 0.6591 (mmt) REVERT: A 721 TYR cc_start: 0.8955 (m-80) cc_final: 0.8739 (m-80) REVERT: A 755 MET cc_start: 0.8204 (mtp) cc_final: 0.7962 (ttt) outliers start: 28 outliers final: 19 residues processed: 110 average time/residue: 0.1801 time to fit residues: 28.3450 Evaluate side-chains 105 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 1030 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 20.0000 chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 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 204 ASN ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 GLN ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7896 Z= 0.199 Angle : 0.737 13.895 10708 Z= 0.352 Chirality : 0.046 0.404 1174 Planarity : 0.005 0.045 1398 Dihedral : 4.569 18.792 1037 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.86 % Allowed : 21.33 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.66 (0.28), residues: 965 helix: 1.23 (0.25), residues: 465 sheet: 0.33 (0.39), residues: 165 loop : -0.51 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 455 HIS 0.013 0.001 HIS A 229 PHE 0.025 0.002 PHE A 693 TYR 0.020 0.001 TYR A 450 ARG 0.004 0.000 ARG A 801 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7693 (t80) REVERT: A 229 HIS cc_start: 0.7699 (t-170) cc_final: 0.7394 (t-170) REVERT: A 245 LEU cc_start: 0.8733 (tp) cc_final: 0.8532 (tp) REVERT: A 388 TYR cc_start: 0.7894 (p90) cc_final: 0.7654 (p90) REVERT: A 414 GLU cc_start: 0.8734 (pp20) cc_final: 0.8388 (pp20) REVERT: A 436 MET cc_start: 0.8003 (mtt) cc_final: 0.7717 (mtt) REVERT: A 646 MET cc_start: 0.8119 (mmm) cc_final: 0.7684 (mmm) REVERT: A 659 MET cc_start: 0.7241 (mmt) cc_final: 0.6549 (mmt) REVERT: A 721 TYR cc_start: 0.8848 (m-80) cc_final: 0.8502 (m-80) REVERT: A 743 MET cc_start: 0.8597 (mmt) cc_final: 0.8390 (mmt) REVERT: A 755 MET cc_start: 0.8223 (mtp) cc_final: 0.7971 (ttt) REVERT: A 888 ARG cc_start: 0.8374 (tpp-160) cc_final: 0.7714 (tpm170) REVERT: A 912 LEU cc_start: 0.8066 (tp) cc_final: 0.7818 (tp) REVERT: A 1024 GLU cc_start: 0.7390 (tp30) cc_final: 0.7075 (tp30) outliers start: 14 outliers final: 9 residues processed: 112 average time/residue: 0.1999 time to fit residues: 31.2379 Evaluate side-chains 103 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 974 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 57 optimal weight: 0.0040 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 0.2980 chunk 36 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7896 Z= 0.202 Angle : 0.738 14.034 10708 Z= 0.354 Chirality : 0.046 0.414 1174 Planarity : 0.005 0.048 1398 Dihedral : 4.456 17.345 1037 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.45 % Allowed : 21.21 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.79 (0.28), residues: 965 helix: 1.36 (0.25), residues: 460 sheet: 0.33 (0.40), residues: 165 loop : -0.44 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 455 HIS 0.011 0.001 HIS A 229 PHE 0.019 0.002 PHE A 618 TYR 0.010 0.001 TYR A 721 ARG 0.013 0.001 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7736 (t80) REVERT: A 229 HIS cc_start: 0.7761 (t-170) cc_final: 0.7436 (t-170) REVERT: A 414 GLU cc_start: 0.8759 (pp20) cc_final: 0.8383 (pp20) REVERT: A 436 MET cc_start: 0.7959 (mtt) cc_final: 0.7681 (mtt) REVERT: A 646 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7707 (mmm) REVERT: A 659 MET cc_start: 0.7295 (mmt) cc_final: 0.6669 (mmt) REVERT: A 721 TYR cc_start: 0.8884 (m-80) cc_final: 0.8618 (m-80) REVERT: A 755 MET cc_start: 0.8151 (mtp) cc_final: 0.7919 (ttt) REVERT: A 888 ARG cc_start: 0.8364 (tpp-160) cc_final: 0.7731 (tpm170) REVERT: A 912 LEU cc_start: 0.8019 (tp) cc_final: 0.7745 (tp) REVERT: A 1024 GLU cc_start: 0.7478 (tp30) cc_final: 0.7051 (tp30) outliers start: 19 outliers final: 13 residues processed: 108 average time/residue: 0.1907 time to fit residues: 29.1560 Evaluate side-chains 108 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 974 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 0.4980 chunk 63 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 7896 Z= 0.307 Angle : 0.776 13.007 10708 Z= 0.383 Chirality : 0.046 0.408 1174 Planarity : 0.005 0.045 1398 Dihedral : 4.694 18.568 1037 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 22.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.68 % Allowed : 21.33 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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 (0.28), residues: 965 helix: 1.26 (0.24), residues: 465 sheet: 0.25 (0.40), residues: 164 loop : -0.45 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 455 HIS 0.010 0.002 HIS A 229 PHE 0.021 0.002 PHE A 618 TYR 0.039 0.002 TYR A 450 ARG 0.008 0.001 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7838 (t80) REVERT: A 229 HIS cc_start: 0.7992 (t-170) cc_final: 0.7589 (t-170) REVERT: A 436 MET cc_start: 0.8051 (mtt) cc_final: 0.7820 (mtt) REVERT: A 516 GLN cc_start: 0.9206 (mt0) cc_final: 0.8846 (mt0) REVERT: A 646 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7778 (mmm) REVERT: A 659 MET cc_start: 0.7490 (mmt) cc_final: 0.6897 (mmt) REVERT: A 721 TYR cc_start: 0.8944 (m-80) cc_final: 0.8733 (m-80) REVERT: A 755 MET cc_start: 0.8254 (mtp) cc_final: 0.8023 (ttt) REVERT: A 888 ARG cc_start: 0.8394 (tpp-160) cc_final: 0.7800 (tpm170) REVERT: A 912 LEU cc_start: 0.8127 (tp) cc_final: 0.7912 (tp) REVERT: A 1024 GLU cc_start: 0.7582 (tp30) cc_final: 0.7151 (tp30) REVERT: A 1037 ARG cc_start: 0.7894 (mtp85) cc_final: 0.7521 (mtm180) outliers start: 21 outliers final: 16 residues processed: 104 average time/residue: 0.2018 time to fit residues: 29.7502 Evaluate side-chains 111 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 1030 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 91 optimal weight: 0.0570 overall best weight: 0.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7896 Z= 0.195 Angle : 0.745 14.480 10708 Z= 0.354 Chirality : 0.046 0.394 1174 Planarity : 0.004 0.043 1398 Dihedral : 4.448 17.994 1037 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.63 % Allowed : 22.14 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.92 (0.28), residues: 965 helix: 1.48 (0.25), residues: 460 sheet: 0.30 (0.40), residues: 164 loop : -0.34 (0.37), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 455 HIS 0.009 0.001 HIS A 229 PHE 0.019 0.002 PHE A 618 TYR 0.010 0.001 TYR A 40 ARG 0.007 0.000 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7792 (t80) REVERT: A 229 HIS cc_start: 0.7839 (t-170) cc_final: 0.7484 (t-170) REVERT: A 646 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7744 (mmm) REVERT: A 659 MET cc_start: 0.7398 (mmt) cc_final: 0.6858 (mmt) REVERT: A 721 TYR cc_start: 0.8817 (m-80) cc_final: 0.8518 (m-80) REVERT: A 888 ARG cc_start: 0.8375 (tpp-160) cc_final: 0.7754 (tpm170) REVERT: A 912 LEU cc_start: 0.7965 (tp) cc_final: 0.7734 (tp) REVERT: A 1024 GLU cc_start: 0.7553 (tp30) cc_final: 0.7050 (tp30) outliers start: 12 outliers final: 10 residues processed: 107 average time/residue: 0.1805 time to fit residues: 27.5694 Evaluate side-chains 110 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 1030 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.0020 chunk 43 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 46 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7896 Z= 0.187 Angle : 0.751 14.784 10708 Z= 0.355 Chirality : 0.046 0.416 1174 Planarity : 0.005 0.043 1398 Dihedral : 4.427 17.842 1037 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.17 % Allowed : 21.91 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.28), residues: 965 helix: 1.54 (0.25), residues: 459 sheet: 0.27 (0.41), residues: 150 loop : -0.43 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 455 HIS 0.008 0.001 HIS A 229 PHE 0.022 0.002 PHE A 389 TYR 0.030 0.001 TYR A 450 ARG 0.007 0.000 ARG A 534 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7758 (t80) REVERT: A 229 HIS cc_start: 0.7823 (t-170) cc_final: 0.7577 (t-170) REVERT: A 436 MET cc_start: 0.7961 (mtt) cc_final: 0.7723 (mtt) REVERT: A 646 MET cc_start: 0.8009 (mmm) cc_final: 0.7562 (mmm) REVERT: A 721 TYR cc_start: 0.8788 (m-80) cc_final: 0.8504 (m-80) REVERT: A 755 MET cc_start: 0.8013 (ttt) cc_final: 0.7785 (tmm) REVERT: A 888 ARG cc_start: 0.8396 (tpp-160) cc_final: 0.7753 (tpm170) REVERT: A 912 LEU cc_start: 0.7932 (tp) cc_final: 0.7700 (tp) REVERT: A 1024 GLU cc_start: 0.7546 (tp30) cc_final: 0.7012 (tp30) outliers start: 8 outliers final: 5 residues processed: 107 average time/residue: 0.1908 time to fit residues: 28.9544 Evaluate side-chains 105 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 889 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.0040 chunk 66 optimal weight: 0.0770 chunk 4 optimal weight: 5.9990 overall best weight: 1.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.070834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.056197 restraints weight = 36015.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.058158 restraints weight = 22502.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.059553 restraints weight = 16018.347| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7896 Z= 0.213 Angle : 0.759 14.193 10708 Z= 0.359 Chirality : 0.046 0.405 1174 Planarity : 0.005 0.045 1398 Dihedral : 4.391 17.914 1037 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.28 % Allowed : 22.73 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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 (0.28), residues: 965 helix: 1.56 (0.25), residues: 461 sheet: 0.16 (0.41), residues: 152 loop : -0.41 (0.36), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 455 HIS 0.009 0.001 HIS A 229 PHE 0.022 0.002 PHE A 389 TYR 0.010 0.001 TYR A 632 ARG 0.007 0.000 ARG A 534 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1833.87 seconds wall clock time: 34 minutes 12.14 seconds (2052.14 seconds total)