Starting phenix.real_space_refine on Sat Apr 6 15:03:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t57_41044/04_2024/8t57_41044_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t57_41044/04_2024/8t57_41044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t57_41044/04_2024/8t57_41044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t57_41044/04_2024/8t57_41044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t57_41044/04_2024/8t57_41044_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t57_41044/04_2024/8t57_41044_updated.pdb" } resolution = 2.7 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= 0.004 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 26 5.16 5 C 5752 2.51 5 N 1270 2.21 5 O 1418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8466 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4033 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 29, 'TRANS': 474} Chain breaks: 5 Chain: "B" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4033 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 29, 'TRANS': 474} Chain breaks: 5 Chain: "A" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 200 Unusual residues: {'CLR': 2, 'PLM': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 200 Unusual residues: {'CLR': 2, 'PLM': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 4.99, per 1000 atoms: 0.59 Number of scatterers: 8466 At special positions: 0 Unit cell: (85.49, 120.51, 85.49, 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 26 16.00 O 1418 8.00 N 1270 7.00 C 5752 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: 3.23 Conformation dependent library (CDL) restraints added in 1.4 seconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1936 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 2 sheets defined 73.6% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 3 through 25 Processing helix chain 'A' and resid 67 through 70 No H-bonds generated for 'chain 'A' and resid 67 through 70' Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 83 through 108 Processing helix chain 'A' and resid 111 through 114 No H-bonds generated for 'chain 'A' and resid 111 through 114' Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 144 through 181 removed outlier: 3.533A pdb=" N PHE A 150 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A 156 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 171 " --> pdb=" O HIS A 168 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 177 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 204 through 215 Processing helix chain 'A' and resid 311 through 319 Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 349 through 367 Processing helix chain 'A' and resid 411 through 432 Proline residue: A 423 - end of helix removed outlier: 3.509A pdb=" N LEU A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 456 Processing helix chain 'A' and resid 458 through 462 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 477 through 511 Proline residue: A 481 - end of helix Proline residue: A 489 - end of helix removed outlier: 3.938A pdb=" N ALA A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N SER A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N PHE A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 561 Proline residue: A 546 - end of helix removed outlier: 3.908A pdb=" N PHE A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 586 Proline residue: A 567 - end of helix removed outlier: 3.524A pdb=" N LEU A 570 " --> pdb=" O PRO A 567 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 580 " --> pdb=" O TYR A 577 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 584 " --> pdb=" O ARG A 581 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN A 586 " --> pdb=" O GLN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 623 Processing helix chain 'A' and resid 627 through 632 Processing helix chain 'A' and resid 634 through 650 removed outlier: 3.565A pdb=" N VAL A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 655 Processing helix chain 'A' and resid 660 through 673 removed outlier: 3.671A pdb=" N ARG A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 685 removed outlier: 4.083A pdb=" N SER A 681 " --> pdb=" O SER A 677 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 685 " --> pdb=" O SER A 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 67 through 70 No H-bonds generated for 'chain 'B' and resid 67 through 70' Processing helix chain 'B' and resid 74 through 80 Processing helix chain 'B' and resid 83 through 108 Processing helix chain 'B' and resid 111 through 114 No H-bonds generated for 'chain 'B' and resid 111 through 114' Processing helix chain 'B' and resid 131 through 134 Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 144 through 181 removed outlier: 3.533A pdb=" N PHE B 150 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE B 156 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 171 " --> pdb=" O HIS B 168 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 177 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 204 through 215 Processing helix chain 'B' and resid 311 through 319 Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 342 through 346 Processing helix chain 'B' and resid 349 through 367 Processing helix chain 'B' and resid 411 through 432 Proline residue: B 423 - end of helix removed outlier: 3.510A pdb=" N LEU B 429 " --> pdb=" O MET B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 456 Processing helix chain 'B' and resid 458 through 462 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 477 through 511 Proline residue: B 481 - end of helix Proline residue: B 489 - end of helix removed outlier: 3.938A pdb=" N ALA B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N SER B 493 " --> pdb=" O PRO B 489 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N PHE B 494 " --> pdb=" O ALA B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 561 Proline residue: B 546 - end of helix removed outlier: 3.909A pdb=" N PHE B 560 " --> pdb=" O ILE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 586 Proline residue: B 567 - end of helix removed outlier: 3.524A pdb=" N LEU B 570 " --> pdb=" O PRO B 567 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR B 580 " --> pdb=" O TYR B 577 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 584 " --> pdb=" O ARG B 581 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN B 586 " --> pdb=" O GLN B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 623 Processing helix chain 'B' and resid 627 through 632 Processing helix chain 'B' and resid 634 through 650 removed outlier: 3.565A pdb=" N VAL B 638 " --> pdb=" O ILE B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 655 Processing helix chain 'B' and resid 660 through 673 removed outlier: 3.670A pdb=" N ARG B 672 " --> pdb=" O LYS B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 685 removed outlier: 4.083A pdb=" N SER B 681 " --> pdb=" O SER B 677 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL B 685 " --> pdb=" O SER B 681 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 303 through 307 Processing sheet with id= B, first strand: chain 'B' and resid 303 through 307 496 hydrogen bonds defined for protein. 1098 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: 2.33 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1283 1.30 - 1.43: 2361 1.43 - 1.55: 4707 1.55 - 1.67: 301 1.67 - 1.80: 40 Bond restraints: 8692 Sorted by residual: bond pdb=" C10 CLR B 802 " pdb=" C9 CLR B 802 " ideal model delta sigma weight residual 1.551 1.715 -0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" C10 CLR A 802 " pdb=" C9 CLR A 802 " ideal model delta sigma weight residual 1.551 1.715 -0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" C4 CLR B 802 " pdb=" C5 CLR B 802 " ideal model delta sigma weight residual 1.506 1.660 -0.154 2.00e-02 2.50e+03 5.94e+01 bond pdb=" C4 CLR A 802 " pdb=" C5 CLR A 802 " ideal model delta sigma weight residual 1.506 1.659 -0.153 2.00e-02 2.50e+03 5.87e+01 bond pdb=" C10 CLR A 801 " pdb=" C9 CLR A 801 " ideal model delta sigma weight residual 1.551 1.704 -0.153 2.00e-02 2.50e+03 5.87e+01 ... (remaining 8687 not shown) Histogram of bond angle deviations from ideal: 98.24 - 105.41: 260 105.41 - 112.58: 4273 112.58 - 119.76: 3518 119.76 - 126.93: 3639 126.93 - 134.10: 90 Bond angle restraints: 11780 Sorted by residual: angle pdb=" C SER B 562 " pdb=" N PRO B 563 " pdb=" CA PRO B 563 " ideal model delta sigma weight residual 119.56 128.55 -8.99 1.02e+00 9.61e-01 7.77e+01 angle pdb=" C SER A 562 " pdb=" N PRO A 563 " pdb=" CA PRO A 563 " ideal model delta sigma weight residual 119.56 128.53 -8.97 1.02e+00 9.61e-01 7.74e+01 angle pdb=" C TYR A 658 " pdb=" N PRO A 659 " pdb=" CA PRO A 659 " ideal model delta sigma weight residual 120.21 127.68 -7.47 9.60e-01 1.09e+00 6.06e+01 angle pdb=" C TYR B 658 " pdb=" N PRO B 659 " pdb=" CA PRO B 659 " ideal model delta sigma weight residual 120.21 127.65 -7.44 9.60e-01 1.09e+00 6.01e+01 angle pdb=" C LEU A 410 " pdb=" N PRO A 411 " pdb=" CA PRO A 411 " ideal model delta sigma weight residual 119.82 127.26 -7.44 9.80e-01 1.04e+00 5.76e+01 ... (remaining 11775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.82: 4982 15.82 - 31.64: 250 31.64 - 47.46: 46 47.46 - 63.28: 34 63.28 - 79.09: 4 Dihedral angle restraints: 5316 sinusoidal: 2338 harmonic: 2978 Sorted by residual: dihedral pdb=" N LEU A 652 " pdb=" C LEU A 652 " pdb=" CA LEU A 652 " pdb=" CB LEU A 652 " ideal model delta harmonic sigma weight residual 122.80 131.22 -8.42 0 2.50e+00 1.60e-01 1.13e+01 dihedral pdb=" N LEU B 652 " pdb=" C LEU B 652 " pdb=" CA LEU B 652 " pdb=" CB LEU B 652 " ideal model delta harmonic sigma weight residual 122.80 131.16 -8.36 0 2.50e+00 1.60e-01 1.12e+01 dihedral pdb=" C TRP B 599 " pdb=" N TRP B 599 " pdb=" CA TRP B 599 " pdb=" CB TRP B 599 " ideal model delta harmonic sigma weight residual -122.60 -130.71 8.11 0 2.50e+00 1.60e-01 1.05e+01 ... (remaining 5313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 912 0.102 - 0.203: 338 0.203 - 0.304: 80 0.304 - 0.406: 16 0.406 - 0.507: 16 Chirality restraints: 1362 Sorted by residual: chirality pdb=" CB ILE B 26 " pdb=" CA ILE B 26 " pdb=" CG1 ILE B 26 " pdb=" CG2 ILE B 26 " both_signs ideal model delta sigma weight residual False 2.64 3.15 -0.51 2.00e-01 2.50e+01 6.43e+00 chirality pdb=" CB ILE A 26 " pdb=" CA ILE A 26 " pdb=" CG1 ILE A 26 " pdb=" CG2 ILE A 26 " both_signs ideal model delta sigma weight residual False 2.64 3.15 -0.51 2.00e-01 2.50e+01 6.38e+00 chirality pdb=" CB ILE B 368 " pdb=" CA ILE B 368 " pdb=" CG1 ILE B 368 " pdb=" CG2 ILE B 368 " both_signs ideal model delta sigma weight residual False 2.64 3.13 -0.49 2.00e-01 2.50e+01 5.97e+00 ... (remaining 1359 not shown) Planarity restraints: 1398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 24 " -0.052 2.00e-02 2.50e+03 3.15e-02 1.98e+01 pdb=" CG TYR B 24 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR B 24 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 24 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 24 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR B 24 " 0.026 2.00e-02 2.50e+03 pdb=" CZ TYR B 24 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 24 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 24 " 0.052 2.00e-02 2.50e+03 3.14e-02 1.97e+01 pdb=" CG TYR A 24 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR A 24 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 24 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR A 24 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR A 24 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR A 24 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 24 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 215 " -0.059 2.00e-02 2.50e+03 2.98e-02 1.78e+01 pdb=" CG TYR B 215 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 215 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 215 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR B 215 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 215 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 215 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 215 " -0.037 2.00e-02 2.50e+03 ... (remaining 1395 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 3372 2.89 - 3.39: 8675 3.39 - 3.89: 14250 3.89 - 4.40: 18174 4.40 - 4.90: 27848 Nonbonded interactions: 72319 Sorted by model distance: nonbonded pdb=" OD1 ASP A 75 " pdb=" NZ LYS A 174 " model vdw 2.385 2.520 nonbonded pdb=" OD1 ASP B 75 " pdb=" NZ LYS B 174 " model vdw 2.385 2.520 nonbonded pdb=" CB GLU A 510 " pdb=" OE1 GLU A 510 " model vdw 2.412 2.752 nonbonded pdb=" CB GLU B 510 " pdb=" OE1 GLU B 510 " model vdw 2.412 2.752 nonbonded pdb=" N PRO A 335 " pdb=" O PRO A 335 " model vdw 2.508 2.496 ... (remaining 72314 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 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: 2.200 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.470 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 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:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 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 : 0.027 0.164 8692 Z= 1.698 Angle : 1.654 11.819 11780 Z= 1.110 Chirality : 0.120 0.507 1362 Planarity : 0.008 0.031 1398 Dihedral : 11.192 79.094 3380 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 984 helix: 0.45 (0.18), residues: 706 sheet: 2.58 (0.99), residues: 24 loop : 0.92 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.007 TRP A 599 HIS 0.007 0.003 HIS A 614 PHE 0.039 0.006 PHE A 99 TYR 0.059 0.009 TYR B 215 ARG 0.005 0.001 ARG B 470 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.059 Fit side-chains REVERT: A 426 MET cc_start: 0.8327 (mmt) cc_final: 0.7787 (mmt) REVERT: B 426 MET cc_start: 0.8314 (mmt) cc_final: 0.7575 (mmt) outliers start: 0 outliers final: 2 residues processed: 151 average time/residue: 0.9777 time to fit residues: 160.0979 Evaluate side-chains 68 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain B residue 109 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 543 GLN B 223 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8692 Z= 0.256 Angle : 0.620 9.144 11780 Z= 0.328 Chirality : 0.046 0.148 1362 Planarity : 0.006 0.036 1398 Dihedral : 9.808 58.090 1566 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Rotamer: Outliers : 3.10 % Allowed : 7.63 % Favored : 89.27 % 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: 1.43 (0.26), residues: 984 helix: 1.05 (0.19), residues: 710 sheet: 1.34 (1.05), residues: 24 loop : 0.97 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 504 HIS 0.008 0.001 HIS B 223 PHE 0.021 0.002 PHE A 415 TYR 0.022 0.002 TYR B 580 ARG 0.002 0.000 ARG B 650 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 88 time to evaluate : 0.913 Fit side-chains REVERT: A 174 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.7995 (mtpp) REVERT: A 508 SER cc_start: 0.8067 (p) cc_final: 0.7718 (p) REVERT: B 174 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.7957 (mtpp) REVERT: B 426 MET cc_start: 0.7979 (mmt) cc_final: 0.7692 (mmt) outliers start: 28 outliers final: 10 residues processed: 105 average time/residue: 0.8766 time to fit residues: 101.0370 Evaluate side-chains 78 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 444 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8692 Z= 0.200 Angle : 0.542 6.099 11780 Z= 0.282 Chirality : 0.043 0.131 1362 Planarity : 0.005 0.039 1398 Dihedral : 9.154 57.516 1566 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.21 % Allowed : 10.29 % Favored : 87.50 % 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: 1.31 (0.27), residues: 984 helix: 1.02 (0.19), residues: 696 sheet: 0.95 (1.03), residues: 24 loop : 0.79 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 504 HIS 0.002 0.000 HIS B 223 PHE 0.015 0.001 PHE A 99 TYR 0.018 0.001 TYR A 580 ARG 0.001 0.000 ARG B 470 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 0.929 Fit side-chains REVERT: A 174 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.7993 (mtpp) REVERT: B 174 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.7844 (mtpp) REVERT: B 426 MET cc_start: 0.8028 (mmt) cc_final: 0.7686 (mmt) outliers start: 20 outliers final: 16 residues processed: 105 average time/residue: 0.8665 time to fit residues: 100.9842 Evaluate side-chains 91 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 688 ARG Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 478 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8692 Z= 0.200 Angle : 0.542 10.751 11780 Z= 0.275 Chirality : 0.043 0.164 1362 Planarity : 0.005 0.039 1398 Dihedral : 8.931 58.790 1566 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.54 % Allowed : 11.06 % Favored : 86.39 % 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: 1.29 (0.27), residues: 984 helix: 1.02 (0.19), residues: 698 sheet: 0.52 (1.00), residues: 24 loop : 0.81 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 504 HIS 0.002 0.000 HIS A 438 PHE 0.029 0.001 PHE B 415 TYR 0.018 0.001 TYR A 580 ARG 0.001 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 0.978 Fit side-chains REVERT: A 174 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.7891 (mtpp) REVERT: A 426 MET cc_start: 0.7910 (mmt) cc_final: 0.7450 (mmt) REVERT: B 174 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.7815 (mtpp) REVERT: B 426 MET cc_start: 0.7967 (mmt) cc_final: 0.7571 (mmt) outliers start: 23 outliers final: 10 residues processed: 99 average time/residue: 0.8093 time to fit residues: 88.6742 Evaluate side-chains 89 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 688 ARG Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 0 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8692 Z= 0.195 Angle : 0.549 9.964 11780 Z= 0.274 Chirality : 0.043 0.132 1362 Planarity : 0.005 0.039 1398 Dihedral : 8.812 55.778 1562 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.88 % Allowed : 9.85 % Favored : 87.28 % 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: 1.36 (0.27), residues: 984 helix: 1.11 (0.20), residues: 694 sheet: 0.08 (0.99), residues: 24 loop : 0.76 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 504 HIS 0.002 0.000 HIS B 223 PHE 0.016 0.001 PHE B 99 TYR 0.015 0.001 TYR A 580 ARG 0.001 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 83 time to evaluate : 0.883 Fit side-chains REVERT: A 174 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.7852 (mtpp) REVERT: B 174 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.7848 (mtpp) outliers start: 26 outliers final: 14 residues processed: 103 average time/residue: 0.7818 time to fit residues: 89.3135 Evaluate side-chains 94 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 688 ARG Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 688 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.0770 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 GLN B 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8692 Z= 0.209 Angle : 0.556 8.434 11780 Z= 0.277 Chirality : 0.043 0.134 1362 Planarity : 0.005 0.038 1398 Dihedral : 8.714 57.815 1562 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.32 % Allowed : 10.84 % Favored : 86.84 % 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: 1.36 (0.27), residues: 984 helix: 1.13 (0.20), residues: 694 sheet: -0.20 (0.99), residues: 24 loop : 0.70 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 504 HIS 0.002 0.000 HIS B 223 PHE 0.015 0.001 PHE B 99 TYR 0.014 0.001 TYR A 580 ARG 0.001 0.000 ARG B 672 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 0.873 Fit side-chains REVERT: A 174 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.7832 (mtpp) REVERT: B 174 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.7784 (mtpp) outliers start: 21 outliers final: 13 residues processed: 97 average time/residue: 0.7781 time to fit residues: 83.8891 Evaluate side-chains 92 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 688 ARG Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 457 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 0.0570 chunk 54 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 60 optimal weight: 0.0970 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 GLN B 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 8692 Z= 0.161 Angle : 0.514 7.433 11780 Z= 0.261 Chirality : 0.042 0.135 1362 Planarity : 0.005 0.040 1398 Dihedral : 8.450 59.507 1562 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.54 % Allowed : 11.06 % Favored : 86.39 % 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: 1.49 (0.27), residues: 984 helix: 1.26 (0.20), residues: 692 sheet: -0.23 (1.00), residues: 24 loop : 0.67 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 504 HIS 0.001 0.000 HIS B 223 PHE 0.011 0.001 PHE A 99 TYR 0.013 0.001 TYR A 580 ARG 0.001 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 0.935 Fit side-chains REVERT: A 174 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.7764 (mtpp) REVERT: A 426 MET cc_start: 0.7830 (mmt) cc_final: 0.7459 (mmt) REVERT: B 174 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.7790 (mtpp) outliers start: 23 outliers final: 11 residues processed: 101 average time/residue: 0.8310 time to fit residues: 93.3951 Evaluate side-chains 93 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 504 TRP Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 504 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 0.0270 chunk 92 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN A 543 GLN B 433 GLN B 543 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8692 Z= 0.174 Angle : 0.526 8.560 11780 Z= 0.263 Chirality : 0.042 0.134 1362 Planarity : 0.005 0.039 1398 Dihedral : 8.416 59.900 1562 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.77 % Allowed : 12.50 % Favored : 85.73 % 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: 1.51 (0.27), residues: 984 helix: 1.26 (0.20), residues: 692 sheet: -0.93 (0.88), residues: 30 loop : 0.86 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 504 HIS 0.001 0.000 HIS A 223 PHE 0.013 0.001 PHE B 99 TYR 0.013 0.001 TYR A 580 ARG 0.001 0.000 ARG A 352 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 1.010 Fit side-chains REVERT: A 174 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.7824 (mtpp) REVERT: A 426 MET cc_start: 0.7867 (mmt) cc_final: 0.7503 (mmt) REVERT: B 174 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.7782 (mtpp) outliers start: 16 outliers final: 12 residues processed: 94 average time/residue: 0.7982 time to fit residues: 82.9976 Evaluate side-chains 94 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 504 TRP Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 504 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 GLN B 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8692 Z= 0.216 Angle : 0.543 6.742 11780 Z= 0.274 Chirality : 0.043 0.171 1362 Planarity : 0.005 0.038 1398 Dihedral : 8.569 57.761 1562 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.88 % Allowed : 12.94 % Favored : 85.18 % 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: 1.40 (0.27), residues: 984 helix: 1.18 (0.20), residues: 696 sheet: -1.09 (0.88), residues: 30 loop : 0.82 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 504 HIS 0.003 0.001 HIS B 223 PHE 0.018 0.001 PHE B 99 TYR 0.013 0.001 TYR B 580 ARG 0.001 0.000 ARG A 513 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 0.986 Fit side-chains REVERT: A 174 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7811 (mtpp) REVERT: B 174 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.7753 (mtpp) outliers start: 17 outliers final: 12 residues processed: 92 average time/residue: 0.8306 time to fit residues: 84.3795 Evaluate side-chains 90 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 504 TRP Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 504 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 0.3980 chunk 91 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 0.0470 chunk 24 optimal weight: 2.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 GLN B 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8692 Z= 0.173 Angle : 0.559 9.777 11780 Z= 0.276 Chirality : 0.042 0.138 1362 Planarity : 0.005 0.039 1398 Dihedral : 8.370 57.737 1562 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.66 % Allowed : 13.50 % Favored : 84.85 % 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: 1.50 (0.27), residues: 984 helix: 1.25 (0.20), residues: 694 sheet: -1.19 (0.88), residues: 30 loop : 0.90 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 504 HIS 0.002 0.000 HIS A 149 PHE 0.013 0.001 PHE A 99 TYR 0.013 0.001 TYR A 469 ARG 0.001 0.000 ARG A 352 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.917 Fit side-chains REVERT: A 174 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.7774 (mtpp) REVERT: A 426 MET cc_start: 0.7847 (mmt) cc_final: 0.7492 (mmt) REVERT: B 174 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.7710 (mtpp) outliers start: 15 outliers final: 11 residues processed: 97 average time/residue: 0.8562 time to fit residues: 91.3659 Evaluate side-chains 93 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 504 TRP Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 504 TRP Chi-restraints excluded: chain B residue 644 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.0970 chunk 69 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 GLN B 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.129439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.105905 restraints weight = 12687.166| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.89 r_work: 0.3382 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8692 Z= 0.183 Angle : 0.542 6.777 11780 Z= 0.271 Chirality : 0.042 0.141 1362 Planarity : 0.005 0.039 1398 Dihedral : 8.352 56.702 1562 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.77 % Allowed : 13.72 % Favored : 84.51 % 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: 1.49 (0.27), residues: 984 helix: 1.25 (0.20), residues: 694 sheet: -1.21 (0.89), residues: 30 loop : 0.87 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 504 HIS 0.002 0.000 HIS B 223 PHE 0.029 0.001 PHE A 415 TYR 0.013 0.001 TYR A 580 ARG 0.001 0.000 ARG B 672 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2570.08 seconds wall clock time: 47 minutes 22.66 seconds (2842.66 seconds total)