Starting phenix.real_space_refine on Sat Mar 16 04:14:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ho8_34922/03_2024/8ho8_34922_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ho8_34922/03_2024/8ho8_34922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ho8_34922/03_2024/8ho8_34922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ho8_34922/03_2024/8ho8_34922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ho8_34922/03_2024/8ho8_34922_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ho8_34922/03_2024/8ho8_34922_neut.pdb" } resolution = 2.24 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= 1.000 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 52 5.16 5 C 8418 2.51 5 N 2184 2.21 5 O 2800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 247": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A GLU 595": "OE1" <-> "OE2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A GLU 807": "OE1" <-> "OE2" Residue "B GLU 274": "OE1" <-> "OE2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "B GLU 510": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13454 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6550 Classifications: {'peptide': 809} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 779} Chain: "B" Number of atoms: 6549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6549 Classifications: {'peptide': 809} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 779} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 158 Classifications: {'water': 158} Link IDs: {None: 157} Chain: "B" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 151 Classifications: {'water': 151} Link IDs: {None: 150} Time building chain proxies: 7.14, per 1000 atoms: 0.53 Number of scatterers: 13454 At special positions: 0 Unit cell: (145.25, 92.13, 97.11, 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 52 16.00 O 2800 8.00 N 2184 7.00 C 8418 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 Links applied BETA1-4 " BGC C 1 " - " BGC C 2 " " BGC D 1 " - " BGC D 2 " Time building additional restraints: 5.32 Conformation dependent library (CDL) restraints added in 2.1 seconds 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 26 sheets defined 33.7% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 222 through 228 Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.867A pdb=" N PHE A 291 " --> pdb=" O MET A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 313 Processing helix chain 'A' and resid 321 through 330 Processing helix chain 'A' and resid 330 through 343 Processing helix chain 'A' and resid 359 through 370 removed outlier: 3.685A pdb=" N LEU A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 387 removed outlier: 3.721A pdb=" N THR A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 432 removed outlier: 3.914A pdb=" N TRP A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 421 " --> pdb=" O PRO A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 removed outlier: 4.012A pdb=" N ILE A 436 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 467 removed outlier: 3.707A pdb=" N VAL A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 532 removed outlier: 3.954A pdb=" N LYS A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASP A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 556 Processing helix chain 'A' and resid 585 through 594 Processing helix chain 'A' and resid 601 through 614 Processing helix chain 'A' and resid 636 through 640 removed outlier: 3.823A pdb=" N TYR A 640 " --> pdb=" O ILE A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 665 removed outlier: 3.837A pdb=" N ALA A 656 " --> pdb=" O CYS A 652 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TRP A 657 " --> pdb=" O HIS A 653 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 679 removed outlier: 4.082A pdb=" N ILE A 678 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 684 Processing helix chain 'A' and resid 686 through 691 Processing helix chain 'A' and resid 719 through 730 Processing helix chain 'B' and resid 156 through 163 Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 209 through 213 Processing helix chain 'B' and resid 222 through 228 Processing helix chain 'B' and resid 268 through 271 Processing helix chain 'B' and resid 281 through 291 removed outlier: 3.853A pdb=" N PHE B 291 " --> pdb=" O MET B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 312 Processing helix chain 'B' and resid 321 through 330 Processing helix chain 'B' and resid 330 through 343 Processing helix chain 'B' and resid 359 through 370 removed outlier: 3.760A pdb=" N LEU B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 387 removed outlier: 3.730A pdb=" N THR B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 removed outlier: 3.922A pdb=" N TRP B 419 " --> pdb=" O ASP B 415 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 421 " --> pdb=" O PRO B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 removed outlier: 3.998A pdb=" N ILE B 436 " --> pdb=" O ASP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 465 removed outlier: 4.033A pdb=" N VAL B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 465 " --> pdb=" O PHE B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 468 No H-bonds generated for 'chain 'B' and resid 466 through 468' Processing helix chain 'B' and resid 512 through 532 removed outlier: 3.921A pdb=" N LYS B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASP B 524 " --> pdb=" O PHE B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 556 Processing helix chain 'B' and resid 585 through 594 Processing helix chain 'B' and resid 601 through 614 Processing helix chain 'B' and resid 636 through 640 removed outlier: 3.828A pdb=" N TYR B 640 " --> pdb=" O ILE B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 665 removed outlier: 3.733A pdb=" N ALA B 656 " --> pdb=" O CYS B 652 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TRP B 657 " --> pdb=" O HIS B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 677 Processing helix chain 'B' and resid 679 through 684 Processing helix chain 'B' and resid 686 through 691 Processing helix chain 'B' and resid 719 through 730 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.677A pdb=" N SER A 94 " --> pdb=" O LYS A 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 28 Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 56 removed outlier: 5.628A pdb=" N ILE A 55 " --> pdb=" O CYS A 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 56 removed outlier: 5.628A pdb=" N ILE A 55 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS A 244 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER A 207 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N SER A 243 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE A 205 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 273 through 275 removed outlier: 6.856A pdb=" N VAL A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 315 through 318 Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 440 through 443 removed outlier: 5.753A pdb=" N LYS A 449 " --> pdb=" O PHE A 443 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 510 through 511 Processing sheet with id=AB1, first strand: chain 'A' and resid 583 through 584 Processing sheet with id=AB2, first strand: chain 'A' and resid 615 through 616 Processing sheet with id=AB3, first strand: chain 'A' and resid 650 through 651 removed outlier: 6.442A pdb=" N ALA A 698 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SER A 715 " --> pdb=" O ALA A 698 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 735 through 738 removed outlier: 3.889A pdb=" N LEU A 742 " --> pdb=" O LEU A 795 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.636A pdb=" N SER B 94 " --> pdb=" O LYS B 109 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 25 through 28 Processing sheet with id=AB7, first strand: chain 'B' and resid 54 through 56 removed outlier: 5.622A pdb=" N ILE B 55 " --> pdb=" O CYS B 153 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 54 through 56 removed outlier: 5.622A pdb=" N ILE B 55 " --> pdb=" O CYS B 153 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS B 244 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER B 207 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER B 243 " --> pdb=" O PHE B 205 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE B 205 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 273 through 275 removed outlier: 6.850A pdb=" N VAL B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 315 through 318 removed outlier: 4.811A pdb=" N ILE B 783 " --> pdb=" O ILE B 790 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AC3, first strand: chain 'B' and resid 440 through 443 removed outlier: 5.728A pdb=" N LYS B 449 " --> pdb=" O PHE B 443 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 510 through 511 Processing sheet with id=AC5, first strand: chain 'B' and resid 583 through 584 Processing sheet with id=AC6, first strand: chain 'B' and resid 615 through 616 Processing sheet with id=AC7, first strand: chain 'B' and resid 650 through 651 removed outlier: 6.446A pdb=" N ALA B 698 " --> pdb=" O SER B 715 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER B 715 " --> pdb=" O ALA B 698 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 735 through 738 removed outlier: 3.949A pdb=" N LEU B 742 " --> pdb=" O LEU B 795 " (cutoff:3.500A) 591 hydrogen bonds defined for protein. 1650 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: 5.38 Time building geometry restraints manager: 5.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4238 1.34 - 1.46: 3223 1.46 - 1.58: 5948 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 13491 Sorted by residual: bond pdb=" CB THR B 20 " pdb=" CG2 THR B 20 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.44e+00 bond pdb=" C5 BGC D 1 " pdb=" O5 BGC D 1 " ideal model delta sigma weight residual 1.411 1.434 -0.023 2.00e-02 2.50e+03 1.37e+00 bond pdb=" C5 BGC D 2 " pdb=" O5 BGC D 2 " ideal model delta sigma weight residual 1.411 1.434 -0.023 2.00e-02 2.50e+03 1.37e+00 bond pdb=" C5 BGC C 1 " pdb=" O5 BGC C 1 " ideal model delta sigma weight residual 1.411 1.434 -0.023 2.00e-02 2.50e+03 1.35e+00 bond pdb=" C5 BGC C 2 " pdb=" O5 BGC C 2 " ideal model delta sigma weight residual 1.411 1.433 -0.022 2.00e-02 2.50e+03 1.25e+00 ... (remaining 13486 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.48: 310 106.48 - 113.38: 6910 113.38 - 120.29: 5082 120.29 - 127.19: 5804 127.19 - 134.09: 146 Bond angle restraints: 18252 Sorted by residual: angle pdb=" N TRP B 716 " pdb=" CA TRP B 716 " pdb=" CB TRP B 716 " ideal model delta sigma weight residual 114.17 109.82 4.35 1.14e+00 7.69e-01 1.46e+01 angle pdb=" N TRP A 716 " pdb=" CA TRP A 716 " pdb=" CB TRP A 716 " ideal model delta sigma weight residual 114.17 109.82 4.35 1.14e+00 7.69e-01 1.45e+01 angle pdb=" N VAL A 686 " pdb=" CA VAL A 686 " pdb=" C VAL A 686 " ideal model delta sigma weight residual 111.88 107.91 3.97 1.06e+00 8.90e-01 1.40e+01 angle pdb=" N VAL B 686 " pdb=" CA VAL B 686 " pdb=" C VAL B 686 " ideal model delta sigma weight residual 111.88 107.96 3.92 1.06e+00 8.90e-01 1.37e+01 angle pdb=" N GLY A 741 " pdb=" CA GLY A 741 " pdb=" C GLY A 741 " ideal model delta sigma weight residual 110.38 114.95 -4.57 1.28e+00 6.10e-01 1.27e+01 ... (remaining 18247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6947 17.88 - 35.75: 711 35.75 - 53.63: 235 53.63 - 71.50: 48 71.50 - 89.38: 25 Dihedral angle restraints: 7966 sinusoidal: 3270 harmonic: 4696 Sorted by residual: dihedral pdb=" CA PHE B 413 " pdb=" C PHE B 413 " pdb=" N ASN B 414 " pdb=" CA ASN B 414 " ideal model delta harmonic sigma weight residual -180.00 -156.04 -23.96 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA PHE A 413 " pdb=" C PHE A 413 " pdb=" N ASN A 414 " pdb=" CA ASN A 414 " ideal model delta harmonic sigma weight residual 180.00 -157.15 -22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ILE A 330 " pdb=" C ILE A 330 " pdb=" N TRP A 331 " pdb=" CA TRP A 331 " ideal model delta harmonic sigma weight residual 180.00 -158.92 -21.08 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 7963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 928 0.029 - 0.058: 578 0.058 - 0.087: 220 0.087 - 0.116: 121 0.116 - 0.145: 33 Chirality restraints: 1880 Sorted by residual: chirality pdb=" CA ILE B 262 " pdb=" N ILE B 262 " pdb=" C ILE B 262 " pdb=" CB ILE B 262 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA ILE A 262 " pdb=" N ILE A 262 " pdb=" C ILE A 262 " pdb=" CB ILE A 262 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA VAL B 441 " pdb=" N VAL B 441 " pdb=" C VAL B 441 " pdb=" CB VAL B 441 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 1877 not shown) Planarity restraints: 2369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 493 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO A 494 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 494 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 494 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 480 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C ASP B 480 " 0.024 2.00e-02 2.50e+03 pdb=" O ASP B 480 " -0.009 2.00e-02 2.50e+03 pdb=" N TRP B 481 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 480 " 0.007 2.00e-02 2.50e+03 1.32e-02 1.75e+00 pdb=" C ASP A 480 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP A 480 " 0.008 2.00e-02 2.50e+03 pdb=" N TRP A 481 " 0.008 2.00e-02 2.50e+03 ... (remaining 2366 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3618 2.80 - 3.33: 12039 3.33 - 3.85: 26208 3.85 - 4.38: 32487 4.38 - 4.90: 50151 Nonbonded interactions: 124503 Sorted by model distance: nonbonded pdb=" OD2 ASP B 321 " pdb=" OH TYR B 682 " model vdw 2.278 2.440 nonbonded pdb=" O MET A 67 " pdb=" O HOH A 901 " model vdw 2.301 2.440 nonbonded pdb=" O MET B 67 " pdb=" O HOH B 901 " model vdw 2.304 2.440 nonbonded pdb=" OE2 GLU B 247 " pdb=" O HOH B 902 " model vdw 2.305 2.440 nonbonded pdb=" OE2 GLU A 247 " pdb=" O HOH A 902 " model vdw 2.307 2.440 ... (remaining 124498 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 2 through 461 or (resid 462 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ or name OH )) or resid 463 through 810)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 3.210 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: 13.800 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 37.750 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 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:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 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 : 0.003 0.061 13491 Z= 0.221 Angle : 0.590 6.392 18252 Z= 0.333 Chirality : 0.046 0.145 1880 Planarity : 0.004 0.036 2369 Dihedral : 17.233 89.378 4990 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.30 % Allowed : 16.98 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.44 (0.21), residues: 1614 helix: 0.99 (0.24), residues: 477 sheet: 1.02 (0.28), residues: 281 loop : -0.31 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 331 HIS 0.005 0.001 HIS B 653 PHE 0.017 0.002 PHE B 119 TYR 0.015 0.002 TYR A 13 ARG 0.002 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 1.424 Fit side-chains REVERT: A 355 ARG cc_start: 0.8232 (mtt-85) cc_final: 0.7902 (mtt90) REVERT: A 605 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8447 (ttpt) REVERT: B 229 LYS cc_start: 0.8332 (ttmt) cc_final: 0.7907 (tttt) outliers start: 18 outliers final: 14 residues processed: 144 average time/residue: 1.8411 time to fit residues: 283.6208 Evaluate side-chains 141 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN B 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.0353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 13491 Z= 0.326 Angle : 0.654 6.847 18252 Z= 0.362 Chirality : 0.050 0.166 1880 Planarity : 0.005 0.053 2369 Dihedral : 7.317 56.888 1894 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.46 % Allowed : 15.68 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.41 (0.21), residues: 1614 helix: 0.94 (0.23), residues: 498 sheet: 1.01 (0.28), residues: 281 loop : -0.35 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 331 HIS 0.007 0.002 HIS B 653 PHE 0.020 0.003 PHE A 369 TYR 0.019 0.002 TYR A 13 ARG 0.004 0.000 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 123 time to evaluate : 1.547 Fit side-chains REVERT: A 379 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: A 802 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8506 (mtpt) REVERT: A 807 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7645 (tm-30) REVERT: B 379 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7493 (tt0) REVERT: B 523 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8143 (ttmm) REVERT: B 599 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: B 605 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8422 (ttpt) outliers start: 34 outliers final: 19 residues processed: 144 average time/residue: 1.8425 time to fit residues: 283.8763 Evaluate side-chains 147 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 718 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 144 optimal weight: 0.0570 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 overall best weight: 1.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.0388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 13491 Z= 0.295 Angle : 0.632 6.620 18252 Z= 0.350 Chirality : 0.049 0.152 1880 Planarity : 0.005 0.046 2369 Dihedral : 6.891 58.248 1884 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.03 % Allowed : 14.52 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.43 (0.21), residues: 1614 helix: 1.03 (0.23), residues: 492 sheet: 1.00 (0.28), residues: 281 loop : -0.38 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 331 HIS 0.007 0.002 HIS B 653 PHE 0.020 0.002 PHE A 369 TYR 0.018 0.002 TYR A 13 ARG 0.003 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 128 time to evaluate : 1.523 Fit side-chains REVERT: A 376 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7886 (mtp85) REVERT: A 379 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: A 802 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8521 (mtpt) REVERT: A 807 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: B 379 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: B 523 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8164 (ttmm) REVERT: B 560 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7772 (mm-30) REVERT: B 599 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8139 (mp0) REVERT: B 605 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8241 (ttpt) outliers start: 42 outliers final: 22 residues processed: 153 average time/residue: 1.7544 time to fit residues: 287.4211 Evaluate side-chains 156 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 125 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 652 CYS Chi-restraints excluded: chain B residue 670 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.0450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 13491 Z= 0.355 Angle : 0.674 7.208 18252 Z= 0.373 Chirality : 0.051 0.179 1880 Planarity : 0.005 0.056 2369 Dihedral : 7.001 58.360 1884 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.96 % Allowed : 14.45 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.40 (0.21), residues: 1614 helix: 1.00 (0.23), residues: 491 sheet: 0.97 (0.28), residues: 282 loop : -0.37 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 331 HIS 0.007 0.002 HIS B 653 PHE 0.020 0.003 PHE A 369 TYR 0.019 0.002 TYR A 13 ARG 0.004 0.001 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 128 time to evaluate : 1.554 Fit side-chains REVERT: A 376 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7919 (mtp85) REVERT: A 379 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7714 (tt0) REVERT: A 802 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8514 (mtpt) REVERT: A 807 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: B 188 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7414 (tt0) REVERT: B 379 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: B 523 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8167 (ttmm) REVERT: B 560 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7747 (mm-30) REVERT: B 599 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: B 605 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8225 (ttpt) REVERT: B 794 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8714 (mm) outliers start: 41 outliers final: 24 residues processed: 152 average time/residue: 1.8272 time to fit residues: 296.8573 Evaluate side-chains 162 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 127 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 652 CYS Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 794 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.0470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 13491 Z= 0.355 Angle : 0.672 7.098 18252 Z= 0.372 Chirality : 0.051 0.180 1880 Planarity : 0.005 0.054 2369 Dihedral : 6.967 58.512 1883 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.11 % Allowed : 14.23 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.39 (0.21), residues: 1614 helix: 0.99 (0.23), residues: 491 sheet: 0.96 (0.28), residues: 282 loop : -0.38 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 331 HIS 0.007 0.002 HIS B 653 PHE 0.020 0.003 PHE A 369 TYR 0.019 0.002 TYR A 13 ARG 0.004 0.001 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 128 time to evaluate : 1.579 Fit side-chains REVERT: A 376 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7924 (mtp85) REVERT: A 379 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: A 802 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8514 (mtpt) REVERT: A 807 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7742 (tm-30) REVERT: B 188 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7363 (tt0) REVERT: B 379 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: B 523 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8167 (ttmm) REVERT: B 560 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.7770 (mm-30) REVERT: B 599 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: B 605 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8218 (ttpt) REVERT: B 794 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8710 (mm) outliers start: 43 outliers final: 26 residues processed: 156 average time/residue: 1.8376 time to fit residues: 306.1497 Evaluate side-chains 164 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 127 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 652 CYS Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 794 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.0535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13491 Z= 0.153 Angle : 0.533 5.872 18252 Z= 0.295 Chirality : 0.045 0.145 1880 Planarity : 0.004 0.040 2369 Dihedral : 6.309 58.235 1881 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.38 % Allowed : 15.32 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.60 (0.21), residues: 1614 helix: 1.30 (0.24), residues: 486 sheet: 1.04 (0.29), residues: 280 loop : -0.32 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 331 HIS 0.005 0.001 HIS A 653 PHE 0.021 0.002 PHE A 369 TYR 0.014 0.001 TYR A 462 ARG 0.001 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 127 time to evaluate : 1.532 Fit side-chains REVERT: A 376 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7817 (mtp85) REVERT: A 379 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7705 (tt0) REVERT: A 802 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8511 (mtpt) REVERT: B 379 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7541 (tt0) REVERT: B 605 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8354 (ttpt) outliers start: 33 outliers final: 18 residues processed: 146 average time/residue: 1.8873 time to fit residues: 294.4331 Evaluate side-chains 148 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.0503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13491 Z= 0.213 Angle : 0.572 6.393 18252 Z= 0.317 Chirality : 0.047 0.143 1880 Planarity : 0.004 0.038 2369 Dihedral : 6.323 57.077 1879 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.53 % Allowed : 15.10 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.62 (0.21), residues: 1614 helix: 1.30 (0.24), residues: 487 sheet: 1.06 (0.29), residues: 280 loop : -0.31 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 331 HIS 0.006 0.001 HIS A 653 PHE 0.019 0.002 PHE A 369 TYR 0.016 0.002 TYR A 13 ARG 0.002 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 125 time to evaluate : 1.692 Fit side-chains REVERT: A 376 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7860 (mtp85) REVERT: A 379 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: A 802 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8509 (mtpt) REVERT: B 379 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7544 (tt0) REVERT: B 605 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8357 (ttpt) REVERT: B 670 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8322 (mtt) outliers start: 35 outliers final: 19 residues processed: 147 average time/residue: 1.8194 time to fit residues: 286.9410 Evaluate side-chains 149 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 652 CYS Chi-restraints excluded: chain B residue 670 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 4.9990 chunk 61 optimal weight: 0.1980 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.0496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 13491 Z= 0.309 Angle : 0.641 6.675 18252 Z= 0.355 Chirality : 0.050 0.155 1880 Planarity : 0.005 0.051 2369 Dihedral : 6.588 57.722 1879 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.60 % Allowed : 15.10 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.49 (0.21), residues: 1614 helix: 1.11 (0.23), residues: 492 sheet: 1.02 (0.28), residues: 281 loop : -0.35 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 331 HIS 0.007 0.002 HIS B 653 PHE 0.018 0.003 PHE B 119 TYR 0.019 0.002 TYR A 13 ARG 0.004 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 122 time to evaluate : 1.357 Fit side-chains REVERT: A 376 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7876 (mtp85) REVERT: A 379 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: A 802 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8501 (mtpt) REVERT: B 188 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7398 (tt0) REVERT: B 379 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: B 605 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8360 (ttpt) outliers start: 36 outliers final: 20 residues processed: 146 average time/residue: 1.6904 time to fit residues: 264.7645 Evaluate side-chains 149 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 652 CYS Chi-restraints excluded: chain B residue 670 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 135 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.0572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13491 Z= 0.162 Angle : 0.538 5.994 18252 Z= 0.298 Chirality : 0.045 0.145 1880 Planarity : 0.004 0.039 2369 Dihedral : 6.065 57.179 1876 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.02 % Allowed : 15.75 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.62 (0.21), residues: 1614 helix: 1.29 (0.24), residues: 492 sheet: 1.04 (0.29), residues: 280 loop : -0.30 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 331 HIS 0.006 0.001 HIS A 653 PHE 0.020 0.002 PHE A 369 TYR 0.014 0.001 TYR A 462 ARG 0.002 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 123 time to evaluate : 1.448 Fit side-chains REVERT: A 376 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7819 (mtp85) REVERT: A 379 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7697 (tt0) REVERT: A 802 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8507 (mtpt) REVERT: B 379 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: B 560 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7749 (mm-30) REVERT: B 605 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8210 (ttpt) outliers start: 28 outliers final: 17 residues processed: 140 average time/residue: 1.7892 time to fit residues: 268.0239 Evaluate side-chains 146 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 605 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 159 optimal weight: 0.4980 chunk 146 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.0522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 13491 Z= 0.346 Angle : 0.658 6.777 18252 Z= 0.365 Chirality : 0.051 0.172 1880 Planarity : 0.005 0.055 2369 Dihedral : 6.507 57.315 1876 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.02 % Allowed : 15.61 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.48 (0.21), residues: 1614 helix: 1.08 (0.23), residues: 492 sheet: 1.01 (0.28), residues: 281 loop : -0.34 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 331 HIS 0.007 0.002 HIS B 653 PHE 0.019 0.003 PHE B 119 TYR 0.019 0.002 TYR A 462 ARG 0.004 0.001 ARG B 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 119 time to evaluate : 1.606 Fit side-chains REVERT: A 376 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7884 (mtp85) REVERT: A 379 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: A 802 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8501 (mtpt) REVERT: B 379 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7543 (tt0) REVERT: B 560 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7800 (mm-30) REVERT: B 605 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8245 (ttpt) outliers start: 28 outliers final: 19 residues processed: 138 average time/residue: 1.8076 time to fit residues: 267.7494 Evaluate side-chains 144 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN A 407 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.097758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.085665 restraints weight = 13762.916| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.03 r_work: 0.2811 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.0489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13491 Z= 0.218 Angle : 0.584 6.306 18252 Z= 0.324 Chirality : 0.047 0.145 1880 Planarity : 0.004 0.038 2369 Dihedral : 6.301 57.957 1876 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.95 % Allowed : 15.61 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.57 (0.21), residues: 1614 helix: 1.23 (0.24), residues: 487 sheet: 1.02 (0.28), residues: 281 loop : -0.31 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 331 HIS 0.006 0.001 HIS A 653 PHE 0.019 0.002 PHE A 369 TYR 0.016 0.002 TYR A 462 ARG 0.002 0.000 ARG A 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5032.35 seconds wall clock time: 90 minutes 10.77 seconds (5410.77 seconds total)