Starting phenix.real_space_refine on Mon Mar 11 01:20:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxf_32877/03_2024/7wxf_32877.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxf_32877/03_2024/7wxf_32877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxf_32877/03_2024/7wxf_32877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxf_32877/03_2024/7wxf_32877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxf_32877/03_2024/7wxf_32877.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxf_32877/03_2024/7wxf_32877.pdb" } resolution = 3.6 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 30 5.16 5 C 4054 2.51 5 N 1172 2.21 5 O 1238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 349": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A ARG 411": "NH1" <-> "NH2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ASP 448": "OD1" <-> "OD2" Residue "A PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A ASP 530": "OD1" <-> "OD2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "A ASP 577": "OD1" <-> "OD2" Residue "A ASP 589": "OD1" <-> "OD2" Residue "A TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 609": "OD1" <-> "OD2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A ARG 766": "NH1" <-> "NH2" Residue "B GLU 349": "OE1" <-> "OE2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B ARG 411": "NH1" <-> "NH2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B ASP 448": "OD1" <-> "OD2" Residue "B PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 467": "OE1" <-> "OE2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B GLU 508": "OE1" <-> "OE2" Residue "B GLU 526": "OE1" <-> "OE2" Residue "B ASP 530": "OD1" <-> "OD2" Residue "B ARG 551": "NH1" <-> "NH2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 576": "NH1" <-> "NH2" Residue "B ASP 577": "OD1" <-> "OD2" Residue "B ASP 589": "OD1" <-> "OD2" Residue "B TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 609": "OD1" <-> "OD2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "B ARG 694": "NH1" <-> "NH2" Residue "B ARG 766": "NH1" <-> "NH2" 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: 6494 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3247 Classifications: {'peptide': 430} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 414} Chain: "B" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3247 Classifications: {'peptide': 430} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 414} Time building chain proxies: 3.97, per 1000 atoms: 0.61 Number of scatterers: 6494 At special positions: 0 Unit cell: (96.46, 94.34, 65.72, 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 30 16.00 O 1238 8.00 N 1172 7.00 C 4054 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.3 seconds 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1596 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 12 sheets defined 48.6% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 348 through 363 removed outlier: 3.862A pdb=" N ALA A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 384 removed outlier: 3.883A pdb=" N GLN A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG A 370 " --> pdb=" O THR A 366 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 403 removed outlier: 4.293A pdb=" N ILE A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 412 Processing helix chain 'A' and resid 415 through 433 Processing helix chain 'A' and resid 471 through 483 removed outlier: 4.157A pdb=" N GLN A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 512 removed outlier: 3.647A pdb=" N THR A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 534 Processing helix chain 'A' and resid 546 through 557 Processing helix chain 'A' and resid 579 through 592 Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'A' and resid 614 through 626 Processing helix chain 'A' and resid 633 through 640 removed outlier: 3.505A pdb=" N LEU A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 678 Processing helix chain 'A' and resid 689 through 700 Processing helix chain 'A' and resid 740 through 744 removed outlier: 3.671A pdb=" N LEU A 744 " --> pdb=" O GLU A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 761 removed outlier: 3.580A pdb=" N PHE A 760 " --> pdb=" O ALA A 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 363 removed outlier: 3.862A pdb=" N ALA B 352 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 384 removed outlier: 3.883A pdb=" N GLN B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG B 370 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 403 removed outlier: 4.293A pdb=" N ILE B 388 " --> pdb=" O ARG B 384 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 412 Processing helix chain 'B' and resid 415 through 433 Processing helix chain 'B' and resid 471 through 483 removed outlier: 4.157A pdb=" N GLN B 475 " --> pdb=" O ASP B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 512 removed outlier: 3.647A pdb=" N THR B 512 " --> pdb=" O GLU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 534 Processing helix chain 'B' and resid 546 through 557 Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'B' and resid 614 through 626 Processing helix chain 'B' and resid 633 through 640 removed outlier: 3.505A pdb=" N LEU B 640 " --> pdb=" O LEU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 678 Processing helix chain 'B' and resid 689 through 700 Processing helix chain 'B' and resid 740 through 744 removed outlier: 3.671A pdb=" N LEU B 744 " --> pdb=" O GLU B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 761 removed outlier: 3.580A pdb=" N PHE B 760 " --> pdb=" O ALA B 757 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 771 through 772 removed outlier: 3.515A pdb=" N GLU A 771 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 445 " --> pdb=" O GLU A 771 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU A 451 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 751 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 455 " --> pdb=" O LYS A 747 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 745 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N VAL B 705 " --> pdb=" O THR A 746 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP A 748 " --> pdb=" O VAL B 705 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 487 through 488 removed outlier: 6.306A pdb=" N LEU A 462 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL A 461 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE A 542 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU A 463 " --> pdb=" O ILE A 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 571 through 574 removed outlier: 6.728A pdb=" N HIS A 571 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL A 686 " --> pdb=" O HIS A 571 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR A 573 " --> pdb=" O VAL A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 605 through 607 removed outlier: 6.103A pdb=" N ILE A 606 " --> pdb=" O VAL A 664 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 629 through 630 removed outlier: 6.871A pdb=" N LYS A 629 " --> pdb=" O CYS A 659 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 704 through 705 removed outlier: 3.527A pdb=" N THR B 745 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 455 " --> pdb=" O LYS B 747 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU B 751 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU B 451 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 445 " --> pdb=" O GLU B 771 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 771 " --> pdb=" O ARG B 445 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 726 through 728 removed outlier: 4.252A pdb=" N GLY A 726 " --> pdb=" O VAL A 738 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 487 through 488 removed outlier: 6.306A pdb=" N LEU B 462 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL B 461 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE B 542 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU B 463 " --> pdb=" O ILE B 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 571 through 574 removed outlier: 6.728A pdb=" N HIS B 571 " --> pdb=" O VAL B 684 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL B 686 " --> pdb=" O HIS B 571 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR B 573 " --> pdb=" O VAL B 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 605 through 607 removed outlier: 6.103A pdb=" N ILE B 606 " --> pdb=" O VAL B 664 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 629 through 630 removed outlier: 6.871A pdb=" N LYS B 629 " --> pdb=" O CYS B 659 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 726 through 728 removed outlier: 4.252A pdb=" N GLY B 726 " --> pdb=" O VAL B 738 " (cutoff:3.500A) 286 hydrogen bonds defined for protein. 822 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: 1.91 Time building geometry restraints manager: 2.61 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: 2258 1.34 - 1.46: 852 1.46 - 1.57: 3438 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 6594 Sorted by residual: bond pdb=" CA PHE A 719 " pdb=" C PHE A 719 " ideal model delta sigma weight residual 1.522 1.493 0.028 1.72e-02 3.38e+03 2.70e+00 bond pdb=" CA PHE B 719 " pdb=" C PHE B 719 " ideal model delta sigma weight residual 1.522 1.493 0.028 1.72e-02 3.38e+03 2.70e+00 bond pdb=" C ARG B 469 " pdb=" N PRO B 470 " ideal model delta sigma weight residual 1.337 1.321 0.015 9.80e-03 1.04e+04 2.40e+00 bond pdb=" C ARG A 469 " pdb=" N PRO A 470 " ideal model delta sigma weight residual 1.337 1.321 0.015 9.80e-03 1.04e+04 2.40e+00 bond pdb=" CB VAL A 738 " pdb=" CG1 VAL A 738 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.14e+00 ... (remaining 6589 not shown) Histogram of bond angle deviations from ideal: 99.93 - 106.74: 190 106.74 - 113.56: 3872 113.56 - 120.37: 2384 120.37 - 127.18: 2416 127.18 - 133.99: 66 Bond angle restraints: 8928 Sorted by residual: angle pdb=" C ALA B 518 " pdb=" N VAL B 519 " pdb=" CA VAL B 519 " ideal model delta sigma weight residual 121.95 127.85 -5.90 1.53e+00 4.27e-01 1.49e+01 angle pdb=" C ALA A 518 " pdb=" N VAL A 519 " pdb=" CA VAL A 519 " ideal model delta sigma weight residual 121.95 127.85 -5.90 1.53e+00 4.27e-01 1.49e+01 angle pdb=" N VAL B 519 " pdb=" CA VAL B 519 " pdb=" C VAL B 519 " ideal model delta sigma weight residual 108.06 103.51 4.55 1.28e+00 6.10e-01 1.26e+01 angle pdb=" N VAL A 519 " pdb=" CA VAL A 519 " pdb=" C VAL A 519 " ideal model delta sigma weight residual 108.06 103.51 4.55 1.28e+00 6.10e-01 1.26e+01 angle pdb=" C HIS B 571 " pdb=" N VAL B 572 " pdb=" CA VAL B 572 " ideal model delta sigma weight residual 122.96 120.00 2.96 9.50e-01 1.11e+00 9.72e+00 ... (remaining 8923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 3602 17.92 - 35.85: 342 35.85 - 53.77: 74 53.77 - 71.69: 10 71.69 - 89.61: 8 Dihedral angle restraints: 4036 sinusoidal: 1572 harmonic: 2464 Sorted by residual: dihedral pdb=" CA ARG A 469 " pdb=" C ARG A 469 " pdb=" N PRO A 470 " pdb=" CA PRO A 470 " ideal model delta harmonic sigma weight residual -180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ARG B 469 " pdb=" C ARG B 469 " pdb=" N PRO B 470 " pdb=" CA PRO B 470 " ideal model delta harmonic sigma weight residual -180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ASP B 754 " pdb=" C ASP B 754 " pdb=" N HIS B 755 " pdb=" CA HIS B 755 " ideal model delta harmonic sigma weight residual -180.00 -162.82 -17.18 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 4033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 628 0.036 - 0.071: 288 0.071 - 0.107: 106 0.107 - 0.143: 20 0.143 - 0.178: 4 Chirality restraints: 1046 Sorted by residual: chirality pdb=" CA VAL A 519 " pdb=" N VAL A 519 " pdb=" C VAL A 519 " pdb=" CB VAL A 519 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.96e-01 chirality pdb=" CA VAL B 519 " pdb=" N VAL B 519 " pdb=" C VAL B 519 " pdb=" CB VAL B 519 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.96e-01 chirality pdb=" CB THR A 524 " pdb=" CA THR A 524 " pdb=" OG1 THR A 524 " pdb=" CG2 THR A 524 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 1043 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 457 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO B 458 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 458 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 458 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 457 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO A 458 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 458 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 458 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 643 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO B 644 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 644 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 644 " 0.019 5.00e-02 4.00e+02 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 204 2.68 - 3.23: 6872 3.23 - 3.79: 9631 3.79 - 4.34: 12156 4.34 - 4.90: 20843 Nonbonded interactions: 49706 Sorted by model distance: nonbonded pdb=" O ILE B 429 " pdb=" OG SER B 433 " model vdw 2.123 2.440 nonbonded pdb=" O ILE A 429 " pdb=" OG SER A 433 " model vdw 2.123 2.440 nonbonded pdb=" OG SER A 546 " pdb=" OD1 ASP A 548 " model vdw 2.162 2.440 nonbonded pdb=" OG SER B 546 " pdb=" OD1 ASP B 548 " model vdw 2.162 2.440 nonbonded pdb=" O CYS A 570 " pdb=" ND1 HIS A 571 " model vdw 2.245 2.520 ... (remaining 49701 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 5.460 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 21.100 Find NCS groups from input model: 0.380 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 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 : 0.007 0.048 6594 Z= 0.459 Angle : 0.789 8.746 8928 Z= 0.433 Chirality : 0.046 0.178 1046 Planarity : 0.004 0.042 1170 Dihedral : 15.049 89.614 2440 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.62 % Favored : 87.15 % Rotamer: Outliers : 0.29 % Allowed : 8.41 % Favored : 91.30 % 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: -4.85 (0.24), residues: 856 helix: -1.83 (0.24), residues: 362 sheet: -4.72 (0.30), residues: 120 loop : -4.11 (0.26), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 748 HIS 0.004 0.001 HIS B 607 PHE 0.015 0.002 PHE B 642 TYR 0.012 0.002 TYR B 631 ARG 0.006 0.001 ARG A 735 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 0.780 Fit side-chains REVERT: A 575 ASP cc_start: 0.8392 (t0) cc_final: 0.8191 (t70) REVERT: A 694 ARG cc_start: 0.8127 (mtm180) cc_final: 0.7878 (ttm170) REVERT: A 724 GLU cc_start: 0.8415 (pp20) cc_final: 0.7712 (pp20) REVERT: B 445 ARG cc_start: 0.6917 (ttp-170) cc_final: 0.6696 (ttm-80) REVERT: B 575 ASP cc_start: 0.8385 (t0) cc_final: 0.8167 (t70) REVERT: B 724 GLU cc_start: 0.8359 (pp20) cc_final: 0.7629 (pp20) outliers start: 2 outliers final: 0 residues processed: 131 average time/residue: 0.2002 time to fit residues: 34.7330 Evaluate side-chains 94 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 363 GLN A 375 ASN A 556 GLN A 559 HIS A 607 HIS A 652 HIS ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 ASN B 354 ASN B 363 GLN B 375 ASN B 392 ASN B 556 GLN B 559 HIS B 607 HIS B 652 HIS B 708 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6594 Z= 0.264 Angle : 0.667 7.017 8928 Z= 0.342 Chirality : 0.043 0.155 1046 Planarity : 0.004 0.032 1170 Dihedral : 4.969 16.510 918 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 2.75 % Allowed : 13.91 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.27), residues: 856 helix: -0.44 (0.27), residues: 372 sheet: -3.83 (0.38), residues: 118 loop : -3.79 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 748 HIS 0.006 0.001 HIS B 559 PHE 0.019 0.002 PHE B 387 TYR 0.005 0.001 TYR B 631 ARG 0.005 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 694 ARG cc_start: 0.8089 (mtm180) cc_final: 0.7812 (ttp-110) REVERT: A 712 ARG cc_start: 0.8666 (tpt90) cc_final: 0.8415 (tpt90) REVERT: A 724 GLU cc_start: 0.8539 (pp20) cc_final: 0.7765 (pp20) REVERT: B 450 LEU cc_start: 0.7943 (tt) cc_final: 0.7520 (tp) REVERT: B 575 ASP cc_start: 0.8179 (t0) cc_final: 0.7975 (t0) outliers start: 19 outliers final: 15 residues processed: 123 average time/residue: 0.1998 time to fit residues: 33.9403 Evaluate side-chains 109 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 745 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 0.0870 chunk 64 optimal weight: 0.0270 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 0.0980 chunk 84 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 overall best weight: 0.2818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6594 Z= 0.150 Angle : 0.592 6.463 8928 Z= 0.295 Chirality : 0.042 0.217 1046 Planarity : 0.003 0.030 1170 Dihedral : 4.426 13.140 918 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 1.88 % Allowed : 16.81 % Favored : 81.30 % 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: -2.50 (0.29), residues: 856 helix: 0.50 (0.28), residues: 374 sheet: -3.30 (0.41), residues: 122 loop : -3.50 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 768 HIS 0.003 0.001 HIS A 675 PHE 0.021 0.002 PHE A 387 TYR 0.005 0.001 TYR B 573 ARG 0.004 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 LYS cc_start: 0.8433 (mppt) cc_final: 0.7900 (mmmt) REVERT: A 503 MET cc_start: 0.8217 (mmm) cc_final: 0.7904 (tpp) REVERT: A 508 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8414 (tm-30) REVERT: A 521 LEU cc_start: 0.8032 (tt) cc_final: 0.7819 (tt) REVERT: A 584 LEU cc_start: 0.9139 (tt) cc_final: 0.8704 (mt) REVERT: A 601 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7615 (tmm) REVERT: A 662 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7070 (tm-30) REVERT: A 694 ARG cc_start: 0.8069 (mtm180) cc_final: 0.7817 (ttp-110) REVERT: A 712 ARG cc_start: 0.8477 (tpt90) cc_final: 0.8206 (tpt90) REVERT: A 724 GLU cc_start: 0.8470 (pp20) cc_final: 0.7986 (pp20) REVERT: B 503 MET cc_start: 0.8229 (mmm) cc_final: 0.8020 (tpp) REVERT: B 508 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8459 (tm-30) REVERT: B 584 LEU cc_start: 0.9143 (tt) cc_final: 0.8720 (mt) REVERT: B 601 MET cc_start: 0.8006 (tmm) cc_final: 0.7628 (tmm) REVERT: B 654 TYR cc_start: 0.7706 (m-10) cc_final: 0.7485 (m-10) REVERT: B 662 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7249 (tm-30) REVERT: B 694 ARG cc_start: 0.8218 (ttm170) cc_final: 0.7798 (ttp-110) outliers start: 13 outliers final: 6 residues processed: 133 average time/residue: 0.2076 time to fit residues: 36.1760 Evaluate side-chains 115 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 74 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 HIS B 675 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6594 Z= 0.196 Angle : 0.597 8.740 8928 Z= 0.300 Chirality : 0.042 0.171 1046 Planarity : 0.003 0.026 1170 Dihedral : 4.370 13.510 918 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.61 % Allowed : 18.12 % Favored : 79.28 % 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: -2.06 (0.29), residues: 856 helix: 0.86 (0.29), residues: 374 sheet: -3.04 (0.41), residues: 122 loop : -3.29 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 768 HIS 0.002 0.001 HIS B 559 PHE 0.033 0.003 PHE B 616 TYR 0.005 0.001 TYR A 654 ARG 0.007 0.000 ARG B 625 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 LYS cc_start: 0.8301 (mppt) cc_final: 0.7880 (mmmt) REVERT: A 503 MET cc_start: 0.8377 (mmm) cc_final: 0.7794 (mmm) REVERT: A 508 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8461 (tm-30) REVERT: A 534 MET cc_start: 0.7818 (mtm) cc_final: 0.7498 (mtp) REVERT: A 573 TYR cc_start: 0.8802 (t80) cc_final: 0.8356 (t80) REVERT: A 584 LEU cc_start: 0.9164 (tt) cc_final: 0.8749 (mt) REVERT: A 601 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7629 (tmm) REVERT: A 662 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7109 (tm-30) REVERT: A 712 ARG cc_start: 0.8566 (tpt90) cc_final: 0.8281 (tpt90) REVERT: B 493 LYS cc_start: 0.8305 (mppt) cc_final: 0.7911 (mmmt) REVERT: B 503 MET cc_start: 0.8341 (mmm) cc_final: 0.7838 (mmm) REVERT: B 508 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8425 (tm-30) REVERT: B 573 TYR cc_start: 0.8825 (t80) cc_final: 0.8345 (t80) REVERT: B 601 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7626 (tmm) REVERT: B 624 LYS cc_start: 0.9003 (mmmt) cc_final: 0.8742 (pttp) REVERT: B 662 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7282 (tm-30) REVERT: B 694 ARG cc_start: 0.8194 (ttm170) cc_final: 0.7842 (ttp-110) outliers start: 18 outliers final: 11 residues processed: 122 average time/residue: 0.1709 time to fit residues: 28.5793 Evaluate side-chains 115 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 745 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 0.0370 chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 42 optimal weight: 0.0020 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.4266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 565 HIS ** A 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 565 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6594 Z= 0.156 Angle : 0.573 7.983 8928 Z= 0.287 Chirality : 0.041 0.163 1046 Planarity : 0.003 0.024 1170 Dihedral : 4.161 13.094 918 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.04 % Allowed : 18.26 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.30), residues: 856 helix: 0.98 (0.29), residues: 378 sheet: -2.65 (0.41), residues: 134 loop : -3.19 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 768 HIS 0.003 0.001 HIS B 559 PHE 0.026 0.002 PHE A 616 TYR 0.005 0.001 TYR A 654 ARG 0.004 0.000 ARG B 625 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: A 349 GLU cc_start: 0.8219 (mm-30) cc_final: 0.8016 (mm-30) REVERT: A 375 ASN cc_start: 0.8270 (m-40) cc_final: 0.7915 (m110) REVERT: A 493 LYS cc_start: 0.8312 (mppt) cc_final: 0.7872 (mmmt) REVERT: A 503 MET cc_start: 0.8418 (mmm) cc_final: 0.8162 (mmm) REVERT: A 573 TYR cc_start: 0.8775 (t80) cc_final: 0.8399 (t80) REVERT: A 584 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8724 (mt) REVERT: A 594 TYR cc_start: 0.8260 (t80) cc_final: 0.7725 (t80) REVERT: A 601 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7670 (tmm) REVERT: A 662 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7171 (tm-30) REVERT: A 712 ARG cc_start: 0.8520 (tpt90) cc_final: 0.8244 (tpt90) REVERT: B 493 LYS cc_start: 0.8323 (mppt) cc_final: 0.7909 (mmmt) REVERT: B 503 MET cc_start: 0.8395 (mmm) cc_final: 0.7750 (mmm) REVERT: B 573 TYR cc_start: 0.8787 (t80) cc_final: 0.8318 (t80) REVERT: B 584 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8747 (mt) REVERT: B 601 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7693 (tmm) REVERT: B 624 LYS cc_start: 0.9017 (mmmt) cc_final: 0.8727 (pttp) REVERT: B 662 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7222 (tm-30) REVERT: B 694 ARG cc_start: 0.8140 (ttm170) cc_final: 0.7800 (ttp-110) outliers start: 21 outliers final: 10 residues processed: 127 average time/residue: 0.1670 time to fit residues: 28.8415 Evaluate side-chains 118 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.0670 chunk 43 optimal weight: 5.9990 chunk 80 optimal weight: 0.0770 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6594 Z= 0.186 Angle : 0.607 9.360 8928 Z= 0.298 Chirality : 0.042 0.159 1046 Planarity : 0.003 0.024 1170 Dihedral : 4.116 13.476 918 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 4.49 % Allowed : 17.68 % Favored : 77.83 % 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: -1.73 (0.29), residues: 856 helix: 0.96 (0.28), residues: 380 sheet: -2.45 (0.42), residues: 134 loop : -3.12 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 748 HIS 0.003 0.001 HIS B 559 PHE 0.030 0.002 PHE A 387 TYR 0.005 0.001 TYR A 654 ARG 0.003 0.000 ARG B 625 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 111 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 LYS cc_start: 0.8321 (mppt) cc_final: 0.7847 (mmmt) REVERT: A 503 MET cc_start: 0.8379 (mmm) cc_final: 0.8075 (mmm) REVERT: A 573 TYR cc_start: 0.8765 (t80) cc_final: 0.8407 (t80) REVERT: A 584 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8734 (mt) REVERT: A 594 TYR cc_start: 0.8270 (t80) cc_final: 0.7748 (t80) REVERT: A 601 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7682 (tmm) REVERT: A 662 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7206 (tm-30) REVERT: A 712 ARG cc_start: 0.8560 (tpt90) cc_final: 0.8271 (tpt90) REVERT: B 493 LYS cc_start: 0.8341 (mppt) cc_final: 0.7959 (mmmt) REVERT: B 573 TYR cc_start: 0.8786 (t80) cc_final: 0.8364 (t80) REVERT: B 584 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8606 (mt) REVERT: B 601 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7695 (tmm) REVERT: B 624 LYS cc_start: 0.9034 (mmmt) cc_final: 0.8703 (pttp) REVERT: B 662 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7311 (tm-30) REVERT: B 694 ARG cc_start: 0.8119 (ttm170) cc_final: 0.7773 (ttp-110) outliers start: 31 outliers final: 19 residues processed: 129 average time/residue: 0.1726 time to fit residues: 30.2266 Evaluate side-chains 122 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 745 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 0.0070 chunk 70 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 33 optimal weight: 0.0030 chunk 49 optimal weight: 4.9990 overall best weight: 0.3608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6594 Z= 0.155 Angle : 0.600 10.024 8928 Z= 0.290 Chirality : 0.041 0.158 1046 Planarity : 0.003 0.023 1170 Dihedral : 3.956 12.965 918 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.06 % Allowed : 18.84 % Favored : 77.10 % 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: -1.61 (0.29), residues: 856 helix: 0.97 (0.28), residues: 380 sheet: -2.21 (0.43), residues: 134 loop : -3.04 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 768 HIS 0.004 0.001 HIS B 559 PHE 0.026 0.002 PHE A 387 TYR 0.005 0.001 TYR A 654 ARG 0.002 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 LYS cc_start: 0.8337 (mppt) cc_final: 0.7837 (mmmt) REVERT: A 573 TYR cc_start: 0.8720 (t80) cc_final: 0.8316 (t80) REVERT: A 584 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8702 (mt) REVERT: A 594 TYR cc_start: 0.8232 (t80) cc_final: 0.7738 (t80) REVERT: A 601 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7678 (tmm) REVERT: A 662 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7239 (tm-30) REVERT: A 694 ARG cc_start: 0.8183 (ttm170) cc_final: 0.7887 (ttp-110) REVERT: A 712 ARG cc_start: 0.8527 (tpt90) cc_final: 0.8236 (tpt90) REVERT: B 493 LYS cc_start: 0.8348 (mppt) cc_final: 0.8020 (mmmt) REVERT: B 503 MET cc_start: 0.7847 (mmm) cc_final: 0.7638 (mmm) REVERT: B 563 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8035 (tt) REVERT: B 573 TYR cc_start: 0.8748 (t80) cc_final: 0.8387 (t80) REVERT: B 584 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8730 (mt) REVERT: B 601 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7692 (tmm) REVERT: B 624 LYS cc_start: 0.9046 (mmmt) cc_final: 0.8699 (pttp) REVERT: B 662 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7292 (tm-30) REVERT: B 694 ARG cc_start: 0.8120 (ttm170) cc_final: 0.7769 (ttp-110) outliers start: 28 outliers final: 17 residues processed: 136 average time/residue: 0.1570 time to fit residues: 29.4940 Evaluate side-chains 130 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 745 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.0870 chunk 16 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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: 0.7552 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6594 Z= 0.191 Angle : 0.638 9.087 8928 Z= 0.305 Chirality : 0.043 0.270 1046 Planarity : 0.003 0.023 1170 Dihedral : 4.028 13.484 918 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.77 % Allowed : 19.28 % Favored : 76.96 % 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: -1.58 (0.29), residues: 856 helix: 0.96 (0.28), residues: 378 sheet: -2.28 (0.41), residues: 144 loop : -2.91 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 748 HIS 0.004 0.001 HIS B 559 PHE 0.020 0.002 PHE A 387 TYR 0.006 0.001 TYR A 654 ARG 0.002 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 109 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 584 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8741 (mt) REVERT: A 594 TYR cc_start: 0.8225 (t80) cc_final: 0.7746 (t80) REVERT: A 601 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7657 (tmm) REVERT: A 662 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7273 (tm-30) REVERT: A 694 ARG cc_start: 0.8202 (ttm170) cc_final: 0.7903 (ttp-110) REVERT: B 563 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8071 (tt) REVERT: B 573 TYR cc_start: 0.8757 (t80) cc_final: 0.8391 (t80) REVERT: B 601 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7694 (tmm) REVERT: B 624 LYS cc_start: 0.9021 (mmmt) cc_final: 0.8669 (pttp) REVERT: B 662 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7359 (tm-30) REVERT: B 694 ARG cc_start: 0.8129 (ttm170) cc_final: 0.7776 (ttp-110) outliers start: 26 outliers final: 16 residues processed: 126 average time/residue: 0.1703 time to fit residues: 29.6324 Evaluate side-chains 128 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 745 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 HIS B 369 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6594 Z= 0.207 Angle : 0.651 9.467 8928 Z= 0.310 Chirality : 0.044 0.240 1046 Planarity : 0.003 0.024 1170 Dihedral : 4.111 13.261 918 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.48 % Allowed : 20.00 % Favored : 76.52 % 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: -1.57 (0.29), residues: 856 helix: 0.92 (0.28), residues: 378 sheet: -2.11 (0.44), residues: 134 loop : -2.90 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 748 HIS 0.005 0.001 HIS A 559 PHE 0.021 0.002 PHE A 387 TYR 0.021 0.001 TYR A 573 ARG 0.002 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 111 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 ASN cc_start: 0.8227 (m-40) cc_final: 0.7891 (m110) REVERT: A 503 MET cc_start: 0.8487 (tpp) cc_final: 0.8101 (mmm) REVERT: A 563 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8045 (tt) REVERT: A 584 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8750 (mt) REVERT: A 594 TYR cc_start: 0.8225 (t80) cc_final: 0.7735 (t80) REVERT: A 601 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7641 (tmm) REVERT: A 662 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7310 (tm-30) REVERT: A 694 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7911 (ttp-110) REVERT: B 573 TYR cc_start: 0.8758 (t80) cc_final: 0.8393 (t80) REVERT: B 601 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7649 (tmm) REVERT: B 624 LYS cc_start: 0.9053 (mmmt) cc_final: 0.8688 (pttp) REVERT: B 662 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7398 (tm-30) REVERT: B 694 ARG cc_start: 0.8084 (ttm170) cc_final: 0.7747 (ttp-110) outliers start: 24 outliers final: 15 residues processed: 126 average time/residue: 0.1534 time to fit residues: 27.2936 Evaluate side-chains 125 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 745 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.0770 chunk 56 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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: 0.7542 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6594 Z= 0.177 Angle : 0.632 8.552 8928 Z= 0.304 Chirality : 0.043 0.228 1046 Planarity : 0.003 0.023 1170 Dihedral : 4.006 13.228 918 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.19 % Allowed : 20.43 % Favored : 76.38 % 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: -1.48 (0.30), residues: 856 helix: 0.92 (0.28), residues: 380 sheet: -1.98 (0.44), residues: 134 loop : -2.82 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 768 HIS 0.002 0.001 HIS B 559 PHE 0.036 0.002 PHE B 616 TYR 0.018 0.001 TYR A 573 ARG 0.002 0.000 ARG A 445 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 ASN cc_start: 0.8197 (m-40) cc_final: 0.7844 (m110) REVERT: A 563 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8041 (tt) REVERT: A 584 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8750 (mt) REVERT: A 594 TYR cc_start: 0.8228 (t80) cc_final: 0.7779 (t80) REVERT: A 601 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7650 (tmm) REVERT: A 662 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7291 (tm-30) REVERT: A 694 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7909 (ttp-110) REVERT: B 503 MET cc_start: 0.8553 (tpp) cc_final: 0.8211 (mmm) REVERT: B 563 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8020 (tt) REVERT: B 573 TYR cc_start: 0.8739 (t80) cc_final: 0.8380 (t80) REVERT: B 601 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7679 (tmm) REVERT: B 624 LYS cc_start: 0.9055 (mmmt) cc_final: 0.8684 (pttp) REVERT: B 662 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7376 (tm-30) REVERT: B 694 ARG cc_start: 0.8078 (ttm170) cc_final: 0.7743 (ttp-110) outliers start: 22 outliers final: 13 residues processed: 123 average time/residue: 0.1905 time to fit residues: 32.3713 Evaluate side-chains 124 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 745 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 0.0070 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 70 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.2980 chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.155357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.119489 restraints weight = 8416.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.124965 restraints weight = 4781.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.128733 restraints weight = 3344.971| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6594 Z= 0.175 Angle : 0.637 8.324 8928 Z= 0.308 Chirality : 0.043 0.219 1046 Planarity : 0.003 0.023 1170 Dihedral : 3.941 13.187 918 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.61 % Allowed : 21.59 % Favored : 75.80 % 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: -1.37 (0.30), residues: 856 helix: 0.94 (0.28), residues: 380 sheet: -1.73 (0.45), residues: 130 loop : -2.77 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 768 HIS 0.002 0.001 HIS B 559 PHE 0.019 0.002 PHE A 387 TYR 0.018 0.001 TYR A 573 ARG 0.002 0.000 ARG A 445 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1651.71 seconds wall clock time: 30 minutes 52.15 seconds (1852.15 seconds total)