Starting phenix.real_space_refine on Sun Jul 21 11:30:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wh5_37529/07_2024/8wh5_37529.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wh5_37529/07_2024/8wh5_37529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wh5_37529/07_2024/8wh5_37529.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wh5_37529/07_2024/8wh5_37529.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wh5_37529/07_2024/8wh5_37529.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wh5_37529/07_2024/8wh5_37529.cif" } resolution = 3.58 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 266 5.49 5 S 29 5.16 5 C 8448 2.51 5 N 2701 2.21 5 O 3219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14663 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 766 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 617 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 662 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 3, 'TRANS': 84} Chain: "D" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 694 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "E" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 695 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "F" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 706 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 750 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "H" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "I" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2710 Classifications: {'DNA': 133} Link IDs: {'rna3p': 132} Chain: "J" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2743 Classifications: {'DNA': 133} Link IDs: {'rna3p': 132} Chain: "K" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3604 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 16, 'TRANS': 428} Chain breaks: 1 Time building chain proxies: 8.65, per 1000 atoms: 0.59 Number of scatterers: 14663 At special positions: 0 Unit cell: (135.09, 135.945, 117.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 266 15.00 O 3219 8.00 N 2701 7.00 C 8448 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: 8.09 Conformation dependent library (CDL) restraints added in 1.8 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 9 sheets defined 64.7% alpha, 4.1% beta 103 base pairs and 208 stacking pairs defined. Time for finding SS restraints: 5.94 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.524A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN A 55 " --> pdb=" O ILE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.911A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.803A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.793A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.567A pdb=" N GLY B 28 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.054A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 38 through 40 No H-bonds generated for 'chain 'C' and resid 38 through 40' Processing helix chain 'C' and resid 46 through 75 removed outlier: 4.082A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 removed outlier: 3.625A pdb=" N ILE C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 98 Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 80 through 108 removed outlier: 3.521A pdb=" N MET D 84 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 127 removed outlier: 3.604A pdb=" N ILE D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 149 removed outlier: 3.823A pdb=" N SER D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 55 Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 87 through 114 removed outlier: 3.680A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.711A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 40 Processing helix chain 'F' and resid 50 through 75 removed outlier: 4.243A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL F 57 " --> pdb=" O GLU F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.636A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 46 through 75 removed outlier: 4.423A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG G 72 " --> pdb=" O GLY G 68 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP G 73 " --> pdb=" O ASN G 69 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.512A pdb=" N ILE G 84 " --> pdb=" O VAL G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 98 Processing helix chain 'H' and resid 62 through 74 removed outlier: 3.701A pdb=" N LYS H 68 " --> pdb=" O ILE H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 109 removed outlier: 4.328A pdb=" N SER H 89 " --> pdb=" O GLY H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 126 Processing helix chain 'H' and resid 129 through 148 removed outlier: 3.927A pdb=" N LYS H 133 " --> pdb=" O GLY H 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 220 Processing helix chain 'K' and resid 233 through 245 removed outlier: 3.789A pdb=" N PHE K 240 " --> pdb=" O GLN K 236 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU K 241 " --> pdb=" O THR K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 249 removed outlier: 4.175A pdb=" N LEU K 249 " --> pdb=" O GLY K 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 246 through 249' Processing helix chain 'K' and resid 258 through 269 Processing helix chain 'K' and resid 285 through 294 removed outlier: 4.216A pdb=" N ARG K 292 " --> pdb=" O ARG K 288 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG K 293 " --> pdb=" O ASP K 289 " (cutoff:3.500A) Processing helix chain 'K' and resid 310 through 317 Processing helix chain 'K' and resid 317 through 323 removed outlier: 4.067A pdb=" N ILE K 321 " --> pdb=" O ASP K 317 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG K 323 " --> pdb=" O LYS K 319 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 339 Processing helix chain 'K' and resid 343 through 352 removed outlier: 3.873A pdb=" N HIS K 351 " --> pdb=" O ARG K 347 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU K 352 " --> pdb=" O GLU K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 380 Processing helix chain 'K' and resid 416 through 425 removed outlier: 3.652A pdb=" N ILE K 423 " --> pdb=" O LYS K 419 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 465 Processing helix chain 'K' and resid 467 through 474 removed outlier: 3.534A pdb=" N GLU K 474 " --> pdb=" O ALA K 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 488 through 499 Processing helix chain 'K' and resid 500 through 508 Processing helix chain 'K' and resid 519 through 522 Processing helix chain 'K' and resid 523 through 536 Processing helix chain 'K' and resid 550 through 564 removed outlier: 3.563A pdb=" N LYS K 563 " --> pdb=" O TYR K 559 " (cutoff:3.500A) Processing helix chain 'K' and resid 575 through 587 Processing helix chain 'K' and resid 604 through 608 removed outlier: 3.520A pdb=" N ILE K 607 " --> pdb=" O GLY K 604 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN K 608 " --> pdb=" O LEU K 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 604 through 608' Processing helix chain 'K' and resid 623 through 635 removed outlier: 4.322A pdb=" N ASP K 627 " --> pdb=" O ASN K 623 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS K 634 " --> pdb=" O ALA K 630 " (cutoff:3.500A) Processing helix chain 'K' and resid 653 through 674 removed outlier: 3.654A pdb=" N VAL K 672 " --> pdb=" O LEU K 668 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.379A pdb=" N ARG A 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.401A pdb=" N ARG C 43 " --> pdb=" O ILE D 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA5, first strand: chain 'F' and resid 97 through 98 removed outlier: 3.696A pdb=" N TYR F 98 " --> pdb=" O THR G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.507A pdb=" N ARG G 43 " --> pdb=" O ILE H 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'K' and resid 278 through 280 removed outlier: 6.673A pdb=" N TYR K 253 " --> pdb=" O VAL K 307 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N THR K 309 " --> pdb=" O TYR K 253 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL K 255 " --> pdb=" O THR K 309 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU K 254 " --> pdb=" O VAL K 331 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 444 through 450 removed outlier: 3.587A pdb=" N MET K 448 " --> pdb=" O ARG K 647 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER K 649 " --> pdb=" O MET K 448 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N CYS K 615 " --> pdb=" O TYR K 646 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU K 648 " --> pdb=" O CYS K 615 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU K 617 " --> pdb=" O LEU K 648 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N THR K 650 " --> pdb=" O LEU K 617 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU K 544 " --> pdb=" O ILE K 616 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 568 through 570 removed outlier: 6.350A pdb=" N CYS K 568 " --> pdb=" O LEU K 597 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 500 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 269 hydrogen bonds 530 hydrogen bond angles 0 basepair planarities 103 basepair parallelities 208 stacking parallelities Total time for adding SS restraints: 6.54 Time building geometry restraints manager: 8.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1730 1.28 - 1.42: 4899 1.42 - 1.55: 8153 1.55 - 1.69: 643 1.69 - 1.82: 48 Bond restraints: 15473 Sorted by residual: bond pdb=" C SER K 653 " pdb=" O SER K 653 " ideal model delta sigma weight residual 1.235 1.315 -0.080 1.02e-02 9.61e+03 6.15e+01 bond pdb=" C VAL H 136 " pdb=" O VAL H 136 " ideal model delta sigma weight residual 1.237 1.148 0.089 1.14e-02 7.69e+03 6.11e+01 bond pdb=" C PRO K 258 " pdb=" O PRO K 258 " ideal model delta sigma weight residual 1.235 1.150 0.085 1.30e-02 5.92e+03 4.30e+01 bond pdb=" C ILE K 491 " pdb=" O ILE K 491 " ideal model delta sigma weight residual 1.237 1.185 0.051 9.80e-03 1.04e+04 2.76e+01 bond pdb=" CA SER K 653 " pdb=" C SER K 653 " ideal model delta sigma weight residual 1.524 1.588 -0.064 1.25e-02 6.40e+03 2.59e+01 ... (remaining 15468 not shown) Histogram of bond angle deviations from ideal: 97.55 - 104.90: 1156 104.90 - 112.26: 8087 112.26 - 119.61: 5771 119.61 - 126.97: 6352 126.97 - 134.32: 654 Bond angle restraints: 22020 Sorted by residual: angle pdb=" O3' DC I 107 " pdb=" C3' DC I 107 " pdb=" C2' DC I 107 " ideal model delta sigma weight residual 111.50 126.76 -15.26 1.50e+00 4.44e-01 1.04e+02 angle pdb=" O3' DG J 112 " pdb=" C3' DG J 112 " pdb=" C2' DG J 112 " ideal model delta sigma weight residual 111.50 126.00 -14.50 1.50e+00 4.44e-01 9.35e+01 angle pdb=" N LYS H 104 " pdb=" CA LYS H 104 " pdb=" C LYS H 104 " ideal model delta sigma weight residual 111.28 103.00 8.28 1.09e+00 8.42e-01 5.77e+01 angle pdb=" N GLU K 518 " pdb=" CA GLU K 518 " pdb=" C GLU K 518 " ideal model delta sigma weight residual 114.56 104.94 9.62 1.27e+00 6.20e-01 5.74e+01 angle pdb=" N ARG D 107 " pdb=" CA ARG D 107 " pdb=" C ARG D 107 " ideal model delta sigma weight residual 110.97 103.50 7.47 1.09e+00 8.42e-01 4.69e+01 ... (remaining 22015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.56: 7380 35.56 - 71.12: 1198 71.12 - 106.68: 26 106.68 - 142.25: 5 142.25 - 177.81: 5 Dihedral angle restraints: 8614 sinusoidal: 5274 harmonic: 3340 Sorted by residual: dihedral pdb=" CA VAL B 81 " pdb=" C VAL B 81 " pdb=" N THR B 82 " pdb=" CA THR B 82 " ideal model delta harmonic sigma weight residual -180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" C4' DC I 110 " pdb=" C3' DC I 110 " pdb=" O3' DC I 110 " pdb=" P DC I 111 " ideal model delta sinusoidal sigma weight residual -140.00 37.81 -177.81 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC I 3 " pdb=" C3' DC I 3 " pdb=" O3' DC I 3 " pdb=" P DG I 4 " ideal model delta sinusoidal sigma weight residual -140.00 29.39 -169.39 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 8611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 2433 0.163 - 0.327: 63 0.327 - 0.490: 1 0.490 - 0.654: 0 0.654 - 0.817: 2 Chirality restraints: 2499 Sorted by residual: chirality pdb=" C3' DG J 112 " pdb=" C4' DG J 112 " pdb=" O3' DG J 112 " pdb=" C2' DG J 112 " both_signs ideal model delta sigma weight residual False -2.66 -1.84 -0.82 2.00e-01 2.50e+01 1.67e+01 chirality pdb=" C3' DC I 107 " pdb=" C4' DC I 107 " pdb=" O3' DC I 107 " pdb=" C2' DC I 107 " both_signs ideal model delta sigma weight residual False -2.66 -1.96 -0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CA LEU K 372 " pdb=" N LEU K 372 " pdb=" C LEU K 372 " pdb=" CB LEU K 372 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 2496 not shown) Planarity restraints: 1858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER H 148 " 0.024 2.00e-02 2.50e+03 4.70e-02 2.21e+01 pdb=" C SER H 148 " -0.081 2.00e-02 2.50e+03 pdb=" O SER H 148 " 0.030 2.00e-02 2.50e+03 pdb=" N SER H 149 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU K 376 " 0.021 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C LEU K 376 " -0.076 2.00e-02 2.50e+03 pdb=" O LEU K 376 " 0.028 2.00e-02 2.50e+03 pdb=" N ASN K 377 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 85 " 0.021 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C GLN A 85 " -0.070 2.00e-02 2.50e+03 pdb=" O GLN A 85 " 0.025 2.00e-02 2.50e+03 pdb=" N SER A 86 " 0.024 2.00e-02 2.50e+03 ... (remaining 1855 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2326 2.76 - 3.29: 14097 3.29 - 3.83: 25940 3.83 - 4.36: 32559 4.36 - 4.90: 45781 Nonbonded interactions: 120703 Sorted by model distance: nonbonded pdb=" O SER K 620 " pdb=" OD1 ASP K 621 " model vdw 2.219 3.040 nonbonded pdb=" OD2 ASP K 621 " pdb=" OD1 ASP K 627 " model vdw 2.272 3.040 nonbonded pdb=" OD1 ASN K 368 " pdb=" N SER K 370 " model vdw 2.319 2.520 nonbonded pdb=" O LYS K 294 " pdb=" NZ LYS K 294 " model vdw 2.325 2.520 nonbonded pdb=" O GLU G 92 " pdb=" OG SER G 95 " model vdw 2.351 2.440 ... (remaining 120698 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 50 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 25 through 100) selection = (chain 'F' and resid 25 through 100) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 21 through 108) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 61 through 149) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 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: 0.610 Check model and map are aligned: 0.070 Set scattering table: 0.150 Process input model: 48.450 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 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 : 0.012 0.089 15473 Z= 0.755 Angle : 1.348 15.260 22020 Z= 0.953 Chirality : 0.070 0.817 2499 Planarity : 0.008 0.047 1858 Dihedral : 25.452 177.808 6458 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.39 % Favored : 91.81 % Rotamer: Outliers : 0.91 % Allowed : 6.30 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.21), residues: 1136 helix: -1.56 (0.17), residues: 691 sheet: -3.21 (0.55), residues: 55 loop : -3.36 (0.26), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 482 HIS 0.015 0.002 HIS H 74 PHE 0.028 0.003 PHE D 67 TYR 0.041 0.003 TYR K 329 ARG 0.006 0.001 ARG K 431 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 328 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8929 (pt) cc_final: 0.8556 (mt) REVERT: A 73 GLU cc_start: 0.8019 (tt0) cc_final: 0.7759 (tt0) REVERT: B 25 ASN cc_start: 0.5358 (m110) cc_final: 0.4649 (m-40) REVERT: D 81 SER cc_start: 0.8822 (t) cc_final: 0.8573 (p) REVERT: E 97 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7158 (mt-10) REVERT: E 123 ASP cc_start: 0.8469 (m-30) cc_final: 0.8235 (m-30) REVERT: G 74 ASN cc_start: 0.8122 (t0) cc_final: 0.7855 (t0) REVERT: K 373 TRP cc_start: 0.5573 (t60) cc_final: 0.5303 (t-100) REVERT: K 432 MET cc_start: 0.8212 (mmm) cc_final: 0.7497 (ttm) REVERT: K 615 CYS cc_start: 0.7641 (m) cc_final: 0.7156 (m) REVERT: K 631 MET cc_start: 0.9284 (mtp) cc_final: 0.9074 (mtp) outliers start: 9 outliers final: 0 residues processed: 334 average time/residue: 0.3711 time to fit residues: 163.0448 Evaluate side-chains 171 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN G 111 ASN K 629 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15473 Z= 0.287 Angle : 0.715 8.966 22020 Z= 0.411 Chirality : 0.042 0.155 2499 Planarity : 0.005 0.051 1858 Dihedral : 29.260 168.009 4149 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.02 % Favored : 94.63 % Rotamer: Outliers : 3.25 % Allowed : 14.43 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.25), residues: 1136 helix: 1.10 (0.20), residues: 698 sheet: -2.57 (0.60), residues: 51 loop : -2.81 (0.27), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 212 HIS 0.007 0.001 HIS F 75 PHE 0.020 0.002 PHE E 67 TYR 0.015 0.002 TYR D 108 ARG 0.006 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 181 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9480 (mm) cc_final: 0.9221 (mt) REVERT: C 105 ASN cc_start: 0.8067 (t0) cc_final: 0.7578 (t0) REVERT: G 74 ASN cc_start: 0.8031 (t0) cc_final: 0.7705 (t0) REVERT: G 93 GLU cc_start: 0.8461 (mp0) cc_final: 0.7768 (mt-10) REVERT: H 101 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7588 (mm-30) REVERT: K 265 TRP cc_start: 0.8413 (m100) cc_final: 0.8203 (m-10) REVERT: K 315 MET cc_start: 0.8255 (tmm) cc_final: 0.8018 (tmm) REVERT: K 333 ASP cc_start: 0.7393 (t0) cc_final: 0.7184 (t0) REVERT: K 468 LEU cc_start: 0.7955 (tp) cc_final: 0.7628 (tp) outliers start: 32 outliers final: 19 residues processed: 202 average time/residue: 0.2701 time to fit residues: 79.9865 Evaluate side-chains 167 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 111 ASN Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 512 LEU Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 609 LEU Chi-restraints excluded: chain K residue 668 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 102 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 34 optimal weight: 0.4980 chunk 123 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN C 90 ASN D 72 GLN E 85 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 341 HIS ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15473 Z= 0.292 Angle : 0.659 9.777 22020 Z= 0.381 Chirality : 0.039 0.276 2499 Planarity : 0.005 0.055 1858 Dihedral : 29.219 178.594 4149 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.28 % Favored : 94.45 % Rotamer: Outliers : 4.37 % Allowed : 16.16 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1136 helix: 1.80 (0.20), residues: 699 sheet: -1.95 (0.64), residues: 65 loop : -2.53 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 265 HIS 0.011 0.002 HIS G 113 PHE 0.017 0.002 PHE E 67 TYR 0.018 0.002 TYR K 618 ARG 0.005 0.001 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 158 time to evaluate : 1.388 Fit side-chains revert: symmetry clash REVERT: C 90 ASN cc_start: 0.7712 (m-40) cc_final: 0.7437 (m-40) REVERT: D 101 GLU cc_start: 0.8261 (tp30) cc_final: 0.7792 (tp30) REVERT: G 74 ASN cc_start: 0.8167 (t0) cc_final: 0.7780 (t0) REVERT: G 94 LEU cc_start: 0.9106 (mt) cc_final: 0.8823 (mt) REVERT: H 63 LYS cc_start: 0.8893 (mmtt) cc_final: 0.8682 (mmtp) REVERT: H 101 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7248 (mm-30) REVERT: H 111 LYS cc_start: 0.8181 (mtmt) cc_final: 0.7861 (mmtm) REVERT: K 333 ASP cc_start: 0.7575 (t0) cc_final: 0.7251 (t0) outliers start: 43 outliers final: 18 residues processed: 184 average time/residue: 0.2633 time to fit residues: 70.9631 Evaluate side-chains 156 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 609 LEU Chi-restraints excluded: chain K residue 615 CYS Chi-restraints excluded: chain K residue 666 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN F 18 HIS F 75 HIS ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 295 HIS ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15473 Z= 0.259 Angle : 0.611 5.977 22020 Z= 0.355 Chirality : 0.037 0.153 2499 Planarity : 0.004 0.042 1858 Dihedral : 29.036 179.094 4149 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.37 % Favored : 94.37 % Rotamer: Outliers : 3.56 % Allowed : 19.21 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.26), residues: 1136 helix: 2.11 (0.20), residues: 706 sheet: -1.34 (0.68), residues: 64 loop : -2.43 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 217 HIS 0.005 0.001 HIS K 282 PHE 0.011 0.001 PHE B 100 TYR 0.027 0.002 TYR D 108 ARG 0.005 0.000 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 148 time to evaluate : 1.291 Fit side-chains revert: symmetry clash REVERT: D 101 GLU cc_start: 0.8248 (tp30) cc_final: 0.7801 (tp30) REVERT: E 52 ARG cc_start: 0.5509 (OUTLIER) cc_final: 0.4456 (mpp-170) REVERT: H 101 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7133 (mm-30) REVERT: K 307 VAL cc_start: 0.8401 (t) cc_final: 0.8159 (p) REVERT: K 333 ASP cc_start: 0.7611 (t0) cc_final: 0.7293 (t0) REVERT: K 432 MET cc_start: 0.7497 (mmp) cc_final: 0.6668 (tpt) REVERT: K 626 MET cc_start: 0.8839 (mmt) cc_final: 0.8598 (mmm) outliers start: 35 outliers final: 27 residues processed: 172 average time/residue: 0.2634 time to fit residues: 67.8169 Evaluate side-chains 165 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 242 SER Chi-restraints excluded: chain K residue 317 ASP Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 512 LEU Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 609 LEU Chi-restraints excluded: chain K residue 615 CYS Chi-restraints excluded: chain K residue 666 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 117 optimal weight: 0.0170 chunk 33 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 overall best weight: 2.3024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN B 93 GLN ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 HIS H 88 ASN ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.6034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15473 Z= 0.223 Angle : 0.590 9.711 22020 Z= 0.342 Chirality : 0.036 0.155 2499 Planarity : 0.004 0.041 1858 Dihedral : 28.964 179.685 4149 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.84 % Favored : 94.89 % Rotamer: Outliers : 3.96 % Allowed : 20.12 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1136 helix: 2.26 (0.20), residues: 708 sheet: -1.02 (0.69), residues: 64 loop : -2.21 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 217 HIS 0.011 0.001 HIS F 18 PHE 0.007 0.001 PHE K 560 TYR 0.031 0.002 TYR D 108 ARG 0.005 0.000 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 142 time to evaluate : 1.436 Fit side-chains revert: symmetry clash REVERT: D 101 GLU cc_start: 0.8232 (tp30) cc_final: 0.7792 (tp30) REVERT: E 52 ARG cc_start: 0.5497 (OUTLIER) cc_final: 0.4462 (mpp-170) REVERT: F 20 LYS cc_start: 0.8916 (mmmt) cc_final: 0.8678 (mmtt) REVERT: H 101 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7070 (mm-30) REVERT: K 256 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8241 (tt) REVERT: K 329 TYR cc_start: 0.7487 (OUTLIER) cc_final: 0.5839 (t80) REVERT: K 333 ASP cc_start: 0.7689 (t0) cc_final: 0.7339 (t0) REVERT: K 626 MET cc_start: 0.8860 (mmt) cc_final: 0.8625 (mmm) outliers start: 39 outliers final: 24 residues processed: 166 average time/residue: 0.2512 time to fit residues: 61.9989 Evaluate side-chains 164 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 137 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain K residue 242 SER Chi-restraints excluded: chain K residue 256 ILE Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 512 LEU Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 609 LEU Chi-restraints excluded: chain K residue 615 CYS Chi-restraints excluded: chain K residue 666 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.9980 chunk 25 optimal weight: 0.0170 chunk 77 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 126 optimal weight: 0.1980 overall best weight: 1.2220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS F 18 HIS H 88 ASN ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.6271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15473 Z= 0.179 Angle : 0.566 9.236 22020 Z= 0.329 Chirality : 0.035 0.158 2499 Planarity : 0.004 0.041 1858 Dihedral : 28.851 178.801 4149 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.58 % Favored : 95.16 % Rotamer: Outliers : 3.05 % Allowed : 21.44 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.27), residues: 1136 helix: 2.44 (0.20), residues: 708 sheet: -0.76 (0.70), residues: 62 loop : -2.09 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 217 HIS 0.009 0.001 HIS F 18 PHE 0.006 0.001 PHE B 61 TYR 0.029 0.001 TYR D 108 ARG 0.003 0.000 ARG K 580 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 149 time to evaluate : 1.300 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8280 (tp40) cc_final: 0.8008 (tp40) REVERT: D 101 GLU cc_start: 0.8228 (tp30) cc_final: 0.7818 (tp30) REVERT: E 52 ARG cc_start: 0.5463 (OUTLIER) cc_final: 0.4461 (mpp-170) REVERT: G 85 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8280 (tm-30) REVERT: H 101 GLU cc_start: 0.7516 (mm-30) cc_final: 0.6982 (mm-30) REVERT: K 329 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.5784 (t80) REVERT: K 333 ASP cc_start: 0.7618 (t0) cc_final: 0.7324 (t0) REVERT: K 626 MET cc_start: 0.8857 (mmt) cc_final: 0.8621 (mmm) outliers start: 30 outliers final: 18 residues processed: 164 average time/residue: 0.2510 time to fit residues: 61.1243 Evaluate side-chains 157 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain K residue 242 SER Chi-restraints excluded: chain K residue 317 ASP Chi-restraints excluded: chain K residue 325 TYR Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 512 LEU Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 609 LEU Chi-restraints excluded: chain K residue 615 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN G 111 ASN H 88 ASN ** K 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.6537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 15473 Z= 0.317 Angle : 0.630 8.388 22020 Z= 0.362 Chirality : 0.038 0.146 2499 Planarity : 0.004 0.041 1858 Dihedral : 29.033 179.751 4149 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.28 % Favored : 94.45 % Rotamer: Outliers : 3.66 % Allowed : 21.85 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.26), residues: 1136 helix: 2.23 (0.20), residues: 704 sheet: -0.68 (0.70), residues: 63 loop : -2.16 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 217 HIS 0.007 0.001 HIS F 18 PHE 0.009 0.001 PHE B 61 TYR 0.033 0.002 TYR D 108 ARG 0.005 0.001 ARG K 288 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 136 time to evaluate : 1.325 Fit side-chains revert: symmetry clash REVERT: D 101 GLU cc_start: 0.8286 (tp30) cc_final: 0.7900 (tp30) REVERT: E 52 ARG cc_start: 0.5534 (OUTLIER) cc_final: 0.4387 (mpp-170) REVERT: G 85 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8345 (tm-30) REVERT: H 84 MET cc_start: 0.8744 (mmt) cc_final: 0.8499 (mmt) REVERT: H 101 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7107 (mm-30) REVERT: H 130 GLU cc_start: 0.6853 (tp30) cc_final: 0.6535 (tm-30) REVERT: H 134 HIS cc_start: 0.7818 (OUTLIER) cc_final: 0.7328 (m90) REVERT: K 329 TYR cc_start: 0.7420 (OUTLIER) cc_final: 0.5855 (t80) REVERT: K 333 ASP cc_start: 0.7722 (t0) cc_final: 0.7384 (t0) outliers start: 36 outliers final: 21 residues processed: 161 average time/residue: 0.2647 time to fit residues: 63.7930 Evaluate side-chains 153 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 111 ASN Chi-restraints excluded: chain H residue 134 HIS Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 242 SER Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 512 LEU Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 609 LEU Chi-restraints excluded: chain K residue 615 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 10.0000 chunk 39 optimal weight: 0.4980 chunk 25 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 HIS G 111 ASN ** K 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.6726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15473 Z= 0.250 Angle : 0.603 8.365 22020 Z= 0.347 Chirality : 0.036 0.155 2499 Planarity : 0.004 0.039 1858 Dihedral : 28.893 179.436 4149 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.11 % Favored : 94.63 % Rotamer: Outliers : 2.85 % Allowed : 22.46 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.26), residues: 1136 helix: 2.23 (0.20), residues: 707 sheet: -0.40 (0.71), residues: 62 loop : -2.13 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 217 HIS 0.003 0.001 HIS K 282 PHE 0.008 0.001 PHE B 61 TYR 0.023 0.001 TYR D 108 ARG 0.003 0.000 ARG K 320 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 1.280 Fit side-chains revert: symmetry clash REVERT: D 101 GLU cc_start: 0.8298 (tp30) cc_final: 0.7921 (tp30) REVERT: E 52 ARG cc_start: 0.5412 (OUTLIER) cc_final: 0.4606 (mpp-170) REVERT: G 85 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8317 (tm-30) REVERT: H 84 MET cc_start: 0.8697 (mmt) cc_final: 0.8456 (mmt) REVERT: H 101 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7056 (mm-30) REVERT: H 130 GLU cc_start: 0.6726 (tp30) cc_final: 0.6483 (tm-30) REVERT: H 134 HIS cc_start: 0.7893 (OUTLIER) cc_final: 0.7261 (m90) REVERT: K 329 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.5903 (t80) REVERT: K 333 ASP cc_start: 0.7673 (t0) cc_final: 0.7462 (t0) REVERT: K 595 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8756 (mp) outliers start: 28 outliers final: 19 residues processed: 153 average time/residue: 0.2462 time to fit residues: 56.7399 Evaluate side-chains 155 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 111 ASN Chi-restraints excluded: chain H residue 134 HIS Chi-restraints excluded: chain K residue 242 SER Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 512 LEU Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain K residue 609 LEU Chi-restraints excluded: chain K residue 615 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN ** K 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.6892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15473 Z= 0.233 Angle : 0.602 10.290 22020 Z= 0.346 Chirality : 0.036 0.181 2499 Planarity : 0.004 0.040 1858 Dihedral : 28.826 179.435 4149 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.19 % Favored : 94.54 % Rotamer: Outliers : 2.74 % Allowed : 22.66 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.26), residues: 1136 helix: 2.22 (0.20), residues: 708 sheet: -0.30 (0.73), residues: 63 loop : -2.04 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 217 HIS 0.003 0.001 HIS G 113 PHE 0.007 0.001 PHE B 61 TYR 0.011 0.001 TYR D 108 ARG 0.012 0.000 ARG K 601 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 1.533 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8346 (mp0) cc_final: 0.8132 (mp0) REVERT: D 101 GLU cc_start: 0.8279 (tp30) cc_final: 0.7918 (tp30) REVERT: E 52 ARG cc_start: 0.5464 (OUTLIER) cc_final: 0.4503 (mpp-170) REVERT: G 85 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8312 (tm-30) REVERT: H 84 MET cc_start: 0.8696 (mmt) cc_final: 0.8451 (mmt) REVERT: H 101 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7043 (mm-30) REVERT: H 130 GLU cc_start: 0.6683 (tp30) cc_final: 0.6429 (tm-30) REVERT: H 134 HIS cc_start: 0.7891 (OUTLIER) cc_final: 0.7233 (m90) REVERT: K 329 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.5886 (t80) REVERT: K 595 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8757 (mp) outliers start: 27 outliers final: 20 residues processed: 152 average time/residue: 0.2571 time to fit residues: 59.1925 Evaluate side-chains 156 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 134 HIS Chi-restraints excluded: chain K residue 242 SER Chi-restraints excluded: chain K residue 309 THR Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 512 LEU Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain K residue 609 LEU Chi-restraints excluded: chain K residue 615 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN ** K 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.7043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15473 Z= 0.331 Angle : 0.655 7.977 22020 Z= 0.372 Chirality : 0.038 0.162 2499 Planarity : 0.004 0.039 1858 Dihedral : 28.899 179.592 4149 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.72 % Favored : 94.01 % Rotamer: Outliers : 2.74 % Allowed : 23.07 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1136 helix: 2.04 (0.20), residues: 703 sheet: -0.39 (0.73), residues: 64 loop : -2.05 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 217 HIS 0.004 0.001 HIS K 282 PHE 0.016 0.001 PHE B 100 TYR 0.027 0.002 TYR F 88 ARG 0.005 0.001 ARG K 288 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 1.283 Fit side-chains revert: symmetry clash REVERT: D 101 GLU cc_start: 0.8298 (tp30) cc_final: 0.7947 (tp30) REVERT: E 52 ARG cc_start: 0.5528 (OUTLIER) cc_final: 0.4567 (mpp-170) REVERT: G 85 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8337 (tm-30) REVERT: H 84 MET cc_start: 0.8710 (mmt) cc_final: 0.8499 (mmt) REVERT: H 101 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7119 (mm-30) REVERT: H 130 GLU cc_start: 0.6865 (tp30) cc_final: 0.6606 (tm-30) REVERT: H 134 HIS cc_start: 0.7887 (OUTLIER) cc_final: 0.7305 (m90) REVERT: K 265 TRP cc_start: 0.8779 (OUTLIER) cc_final: 0.8508 (m-10) REVERT: K 329 TYR cc_start: 0.7379 (OUTLIER) cc_final: 0.5907 (t80) REVERT: K 333 ASP cc_start: 0.7497 (t0) cc_final: 0.7288 (t0) outliers start: 27 outliers final: 20 residues processed: 153 average time/residue: 0.2498 time to fit residues: 57.6500 Evaluate side-chains 156 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 134 HIS Chi-restraints excluded: chain K residue 242 SER Chi-restraints excluded: chain K residue 265 TRP Chi-restraints excluded: chain K residue 309 THR Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 512 LEU Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain K residue 609 LEU Chi-restraints excluded: chain K residue 615 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.0870 chunk 108 optimal weight: 0.0970 chunk 45 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 94 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.091182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.063900 restraints weight = 49347.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.065655 restraints weight = 26514.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.066228 restraints weight = 16245.208| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.7284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15473 Z= 0.179 Angle : 0.586 9.297 22020 Z= 0.336 Chirality : 0.034 0.165 2499 Planarity : 0.004 0.043 1858 Dihedral : 28.594 178.512 4149 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.23 % Favored : 95.60 % Rotamer: Outliers : 2.13 % Allowed : 24.09 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.26), residues: 1136 helix: 2.34 (0.20), residues: 707 sheet: -0.10 (0.74), residues: 63 loop : -1.83 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP K 217 HIS 0.004 0.001 HIS E 113 PHE 0.009 0.001 PHE F 100 TYR 0.009 0.001 TYR K 511 ARG 0.003 0.000 ARG K 601 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2510.28 seconds wall clock time: 46 minutes 22.16 seconds (2782.16 seconds total)