Starting phenix.real_space_refine (version: dev) on Sun Dec 11 18:24:22 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxf_32877/12_2022/7wxf_32877.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxf_32877/12_2022/7wxf_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_32877/12_2022/7wxf_32877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxf_32877/12_2022/7wxf_32877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxf_32877/12_2022/7wxf_32877.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxf_32877/12_2022/7wxf_32877.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 4.31, per 1000 atoms: 0.66 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: 2.52 Conformation dependent library (CDL) restraints added in 1.5 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: 0.46 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: 1.78 Time building geometry restraints manager: 2.74 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 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. 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: 1.850 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: 6.310 Check model and map are aligned: 0.100 Convert atoms to be neutral: 0.060 Process input model: 20.870 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 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 : 13.55 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.62 % Favored : 87.15 % Rotamer Outliers : 0.29 % 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 *********************** 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 : 0.793 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 131 average time/residue: 0.1985 time to fit residues: 34.4407 Evaluate side-chains 92 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1189 ------------------------------------------------------------------------------- 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: 0.9980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.7798 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 6594 Z= 0.267 Angle : 0.669 7.090 8928 Z= 0.343 Chirality : 0.044 0.154 1046 Planarity : 0.004 0.032 1170 Dihedral : 4.999 16.600 918 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer Outliers : 2.75 % 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: -0.43 (0.27), residues: 372 sheet: -3.81 (0.38), residues: 118 loop : -3.80 (0.28), residues: 366 *********************** 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 123 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 0.809 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 120 average time/residue: 0.1549 time to fit residues: 25.9871 Evaluate side-chains 108 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.770 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0609 time to fit residues: 2.7330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0270 chunk 64 optimal weight: 0.0670 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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: 0.7734 moved from start: 0.2181 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= 0.175 Angle : 0.601 6.445 8928 Z= 0.302 Chirality : 0.042 0.214 1046 Planarity : 0.003 0.029 1170 Dihedral : 4.520 13.304 918 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer Outliers : 1.01 % 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: -2.60 (0.28), residues: 856 helix: 0.39 (0.28), residues: 374 sheet: -3.31 (0.41), residues: 122 loop : -3.53 (0.28), residues: 360 *********************** 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 135 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 133 average time/residue: 0.1588 time to fit residues: 29.3792 Evaluate side-chains 109 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 0.784 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0635 time to fit residues: 1.3512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 chunk 52 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 41 optimal weight: 0.0370 chunk 74 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- 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: 0.7753 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 6594 Z= 0.215 Angle : 0.617 7.201 8928 Z= 0.313 Chirality : 0.043 0.169 1046 Planarity : 0.003 0.025 1170 Dihedral : 4.470 14.002 918 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer Outliers : 1.88 % 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: -2.22 (0.29), residues: 856 helix: 0.68 (0.28), residues: 376 sheet: -3.11 (0.41), residues: 122 loop : -3.33 (0.29), residues: 358 *********************** 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 119 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 114 average time/residue: 0.1596 time to fit residues: 25.4883 Evaluate side-chains 104 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0719 time to fit residues: 1.9934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.3980 chunk 47 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN B 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2672 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= 0.184 Angle : 0.625 10.331 8928 Z= 0.308 Chirality : 0.041 0.163 1046 Planarity : 0.003 0.026 1170 Dihedral : 4.317 13.296 918 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer Outliers : 1.16 % 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: -1.89 (0.29), residues: 856 helix: 0.89 (0.29), residues: 376 sheet: -2.77 (0.40), residues: 134 loop : -3.13 (0.30), residues: 346 *********************** 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 129 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 0.842 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 125 average time/residue: 0.1593 time to fit residues: 27.5790 Evaluate side-chains 104 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 0.791 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0690 time to fit residues: 1.3122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 0.0570 chunk 43 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 HIS B 565 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2819 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 : 0.634 9.386 8928 Z= 0.313 Chirality : 0.042 0.187 1046 Planarity : 0.003 0.025 1170 Dihedral : 4.271 13.092 918 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer Outliers : 2.03 % 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 (0.29), residues: 856 helix: 0.84 (0.28), residues: 380 sheet: -2.57 (0.41), residues: 134 loop : -3.07 (0.30), residues: 342 *********************** 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 119 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 0.739 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 114 average time/residue: 0.1625 time to fit residues: 25.7082 Evaluate side-chains 101 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.811 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0624 time to fit residues: 1.6240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 0.0270 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 82 optimal weight: 0.0050 chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.5052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 6594 Z= 0.180 Angle : 0.639 8.944 8928 Z= 0.313 Chirality : 0.043 0.176 1046 Planarity : 0.003 0.024 1170 Dihedral : 4.172 13.374 918 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer Outliers : 1.16 % 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: -1.63 (0.29), residues: 856 helix: 0.90 (0.28), residues: 380 sheet: -2.30 (0.42), residues: 134 loop : -2.94 (0.31), residues: 342 *********************** 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 121 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 121 average time/residue: 0.1526 time to fit residues: 26.0006 Evaluate side-chains 101 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 0.749 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0653 time to fit residues: 1.4772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.0470 chunk 16 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 79 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3229 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= 0.189 Angle : 0.689 10.751 8928 Z= 0.328 Chirality : 0.044 0.288 1046 Planarity : 0.003 0.024 1170 Dihedral : 4.102 14.100 918 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer Outliers : 1.16 % 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: -1.52 (0.29), residues: 856 helix: 0.97 (0.28), residues: 378 sheet: -2.24 (0.41), residues: 144 loop : -2.81 (0.31), residues: 334 *********************** 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 121 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 116 average time/residue: 0.1562 time to fit residues: 25.5788 Evaluate side-chains 106 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 0.779 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0644 time to fit residues: 1.4522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 0.1980 chunk 60 optimal weight: 0.0170 chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 76 optimal weight: 0.0040 chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 0.0870 chunk 49 optimal weight: 4.9990 overall best weight: 0.2608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN A 559 HIS ** A 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6594 Z= 0.165 Angle : 0.670 10.631 8928 Z= 0.321 Chirality : 0.042 0.158 1046 Planarity : 0.003 0.025 1170 Dihedral : 3.961 13.708 918 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.30), residues: 856 helix: 1.12 (0.28), residues: 376 sheet: -1.97 (0.43), residues: 144 loop : -2.73 (0.32), residues: 336 *********************** 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 122 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 121 average time/residue: 0.1644 time to fit residues: 27.5478 Evaluate side-chains 104 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.773 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0620 time to fit residues: 1.4043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.0000 chunk 54 optimal weight: 0.3980 chunk 72 optimal weight: 0.0030 chunk 20 optimal weight: 0.6980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7667 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6594 Z= 0.180 Angle : 0.707 11.401 8928 Z= 0.335 Chirality : 0.043 0.201 1046 Planarity : 0.003 0.027 1170 Dihedral : 3.910 13.655 918 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.30), residues: 856 helix: 1.07 (0.28), residues: 376 sheet: -1.88 (0.43), residues: 144 loop : -2.69 (0.32), residues: 336 ********************** 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 113 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.1599 time to fit residues: 25.4227 Evaluate side-chains 105 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN B 637 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.153080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.116143 restraints weight = 8801.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.121425 restraints weight = 4990.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.125199 restraints weight = 3493.691| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 6594 Z= 0.298 Angle : 0.764 10.379 8928 Z= 0.370 Chirality : 0.046 0.376 1046 Planarity : 0.003 0.027 1170 Dihedral : 4.296 13.897 918 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer Outliers : 0.58 % 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: -1.54 (0.29), residues: 856 helix: 0.82 (0.28), residues: 378 sheet: -2.10 (0.42), residues: 142 loop : -2.72 (0.31), residues: 336 =============================================================================== Job complete usr+sys time: 1504.47 seconds wall clock time: 28 minutes 8.44 seconds (1688.44 seconds total)