Starting phenix.real_space_refine on Mon Mar 11 03:52:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cd0_16565/03_2024/8cd0_16565_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cd0_16565/03_2024/8cd0_16565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cd0_16565/03_2024/8cd0_16565.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cd0_16565/03_2024/8cd0_16565.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cd0_16565/03_2024/8cd0_16565_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cd0_16565/03_2024/8cd0_16565_updated.pdb" } resolution = 2.42 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= 0.015 sd= 0.025 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 2 5.49 5 S 26 5.16 5 C 4426 2.51 5 N 1162 2.21 5 O 1243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A ASP 317": "OD1" <-> "OD2" Residue "A ASP 320": "OD1" <-> "OD2" Residue "A PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 374": "OD1" <-> "OD2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "A TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 576": "OE1" <-> "OE2" Residue "A ASP 629": "OD1" <-> "OD2" Residue "A TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 656": "OD1" <-> "OD2" Residue "A PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 684": "OE1" <-> "OE2" Residue "A PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 784": "OE1" <-> "OE2" Residue "A PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 858": "OE1" <-> "OE2" Residue "C ASP 30": "OD1" <-> "OD2" Residue "C ASP 31": "OD1" <-> "OD2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 89": "OD1" <-> "OD2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6860 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5883 Classifications: {'peptide': 716} Link IDs: {'PCIS': 4, 'PTRANS': 32, 'TRANS': 679} Chain breaks: 6 Chain: "C" Number of atoms: 945 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 bond proxies already assigned to first conformer: 946 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'A3P': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1, 'water': 3} Link IDs: {None: 3} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.86, per 1000 atoms: 0.71 Number of scatterers: 6860 At special positions: 0 Unit cell: (78.11, 97.82, 102.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 26 16.00 P 2 15.00 O 1243 8.00 N 1162 7.00 C 4426 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS A 818 " - pdb=" SG CYS A 828 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 103 " distance=2.03 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: 2.69 Conformation dependent library (CDL) restraints added in 1.4 seconds 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 11 sheets defined 34.8% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 141 through 145 removed outlier: 3.665A pdb=" N VAL A 145 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 162 Processing helix chain 'A' and resid 288 through 301 Processing helix chain 'A' and resid 332 through 348 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 396 through 399 No H-bonds generated for 'chain 'A' and resid 396 through 399' Processing helix chain 'A' and resid 402 through 419 Processing helix chain 'A' and resid 441 through 450 removed outlier: 3.608A pdb=" N LYS A 448 " --> pdb=" O TYR A 444 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 502 through 509 Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.886A pdb=" N ARG A 548 " --> pdb=" O LYS A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 573 Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 589 through 594 Processing helix chain 'A' and resid 617 through 625 Processing helix chain 'A' and resid 649 through 652 removed outlier: 3.544A pdb=" N HIS A 652 " --> pdb=" O HIS A 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 649 through 652' Processing helix chain 'A' and resid 655 through 660 removed outlier: 3.561A pdb=" N GLU A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 680 No H-bonds generated for 'chain 'A' and resid 678 through 680' Processing helix chain 'A' and resid 686 through 693 Processing helix chain 'A' and resid 706 through 719 Processing helix chain 'A' and resid 723 through 727 Processing helix chain 'A' and resid 730 through 733 No H-bonds generated for 'chain 'A' and resid 730 through 733' Processing helix chain 'A' and resid 742 through 752 Processing helix chain 'A' and resid 757 through 767 removed outlier: 3.814A pdb=" N ARG A 763 " --> pdb=" O THR A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 783 No H-bonds generated for 'chain 'A' and resid 780 through 783' Processing helix chain 'A' and resid 785 through 795 Processing helix chain 'A' and resid 804 through 807 No H-bonds generated for 'chain 'A' and resid 804 through 807' Processing helix chain 'A' and resid 842 through 851 Processing helix chain 'A' and resid 854 through 865 Processing helix chain 'A' and resid 872 through 879 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing sheet with id= A, first strand: chain 'A' and resid 111 through 114 removed outlier: 6.816A pdb=" N VAL A 85 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N GLU A 114 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL A 87 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU A 135 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N PHE A 88 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE A 137 " --> pdb=" O PHE A 88 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLY A 165 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N TYR A 138 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE A 167 " --> pdb=" O TYR A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 267 through 269 removed outlier: 3.715A pdb=" N ARG A 278 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 557 through 559 removed outlier: 3.680A pdb=" N ILE A 314 " --> pdb=" O GLN A 559 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 355 through 358 removed outlier: 7.203A pdb=" N TRP A 385 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N TYR A 358 " --> pdb=" O TRP A 385 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N PHE A 387 " --> pdb=" O TYR A 358 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 455 through 458 removed outlier: 6.271A pdb=" N MET A 479 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR A 458 " --> pdb=" O MET A 479 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU A 481 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 607 through 610 removed outlier: 3.530A pdb=" N GLU A 675 " --> pdb=" O LEU A 607 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 699 through 702 Processing sheet with id= H, first strand: chain 'A' and resid 809 through 811 removed outlier: 3.565A pdb=" N ALA A 809 " --> pdb=" O CYS A 818 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 811 " --> pdb=" O PHE A 816 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 816 " --> pdb=" O ASP A 811 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.584A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 35 through 38 removed outlier: 3.632A pdb=" N ALA C 91 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 121 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 49 through 51 195 hydrogen bonds defined for protein. 558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 2.95 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: 2039 1.34 - 1.46: 1607 1.46 - 1.58: 3357 1.58 - 1.70: 8 1.70 - 1.82: 40 Bond restraints: 7051 Sorted by residual: bond pdb=" C ALA A 430 " pdb=" N PRO A 431 " ideal model delta sigma weight residual 1.335 1.385 -0.050 1.30e-02 5.92e+03 1.48e+01 bond pdb=" CB PHE A 362 " pdb=" CG PHE A 362 " ideal model delta sigma weight residual 1.502 1.573 -0.071 2.30e-02 1.89e+03 9.64e+00 bond pdb=" C VAL A 429 " pdb=" N ALA A 430 " ideal model delta sigma weight residual 1.330 1.370 -0.040 1.37e-02 5.33e+03 8.51e+00 bond pdb=" CB PHE A 847 " pdb=" CG PHE A 847 " ideal model delta sigma weight residual 1.502 1.561 -0.059 2.30e-02 1.89e+03 6.53e+00 bond pdb=" C ALA A 686 " pdb=" N PRO A 687 " ideal model delta sigma weight residual 1.336 1.366 -0.031 1.23e-02 6.61e+03 6.16e+00 ... (remaining 7046 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.71: 247 106.71 - 113.61: 3606 113.61 - 120.50: 2855 120.50 - 127.40: 2750 127.40 - 134.29: 107 Bond angle restraints: 9565 Sorted by residual: angle pdb=" C THR A 485 " pdb=" N CYS A 486 " pdb=" CA CYS A 486 " ideal model delta sigma weight residual 121.54 132.61 -11.07 1.91e+00 2.74e-01 3.36e+01 angle pdb=" C PHE A 399 " pdb=" N HIS A 400 " pdb=" CA HIS A 400 " ideal model delta sigma weight residual 121.54 132.56 -11.02 1.91e+00 2.74e-01 3.33e+01 angle pdb=" CB GLU A 858 " pdb=" CG GLU A 858 " pdb=" CD GLU A 858 " ideal model delta sigma weight residual 112.60 121.92 -9.32 1.70e+00 3.46e-01 3.01e+01 angle pdb=" C SER A 213 " pdb=" N GLU A 214 " pdb=" CA GLU A 214 " ideal model delta sigma weight residual 121.70 131.18 -9.48 1.80e+00 3.09e-01 2.77e+01 angle pdb=" CG ARG C 74 " pdb=" CD ARG C 74 " pdb=" NE ARG C 74 " ideal model delta sigma weight residual 112.00 123.50 -11.50 2.20e+00 2.07e-01 2.73e+01 ... (remaining 9560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 3539 17.31 - 34.62: 433 34.62 - 51.93: 119 51.93 - 69.24: 41 69.24 - 86.55: 10 Dihedral angle restraints: 4142 sinusoidal: 1701 harmonic: 2441 Sorted by residual: dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 601 " pdb=" CB CYS A 601 " ideal model delta sinusoidal sigma weight residual 93.00 165.46 -72.46 1 1.00e+01 1.00e-02 6.71e+01 dihedral pdb=" CA ASN C 84 " pdb=" C ASN C 84 " pdb=" N LEU C 85 " pdb=" CA LEU C 85 " ideal model delta harmonic sigma weight residual 180.00 -153.96 -26.04 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA SER C 11 " pdb=" C SER C 11 " pdb=" N VAL C 12 " pdb=" CA VAL C 12 " ideal model delta harmonic sigma weight residual 180.00 159.00 21.00 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 4139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 858 0.080 - 0.161: 126 0.161 - 0.241: 24 0.241 - 0.322: 6 0.322 - 0.402: 2 Chirality restraints: 1016 Sorted by residual: chirality pdb=" CB ILE C 51 " pdb=" CA ILE C 51 " pdb=" CG1 ILE C 51 " pdb=" CG2 ILE C 51 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CB THR C 90 " pdb=" CA THR C 90 " pdb=" OG1 THR C 90 " pdb=" CG2 THR C 90 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CB ILE A 421 " pdb=" CA ILE A 421 " pdb=" CG1 ILE A 421 " pdb=" CG2 ILE A 421 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1013 not shown) Planarity restraints: 1212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 643 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C ILE A 643 " 0.059 2.00e-02 2.50e+03 pdb=" O ILE A 643 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN A 644 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 339 " 0.024 2.00e-02 2.50e+03 2.52e-02 1.11e+01 pdb=" CG PHE A 339 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 339 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 339 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE A 339 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 339 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 339 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 627 " -0.053 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO A 628 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 628 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 628 " -0.044 5.00e-02 4.00e+02 ... (remaining 1209 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 142 2.68 - 3.23: 5817 3.23 - 3.79: 11511 3.79 - 4.34: 15783 4.34 - 4.90: 25139 Nonbonded interactions: 58392 Sorted by model distance: nonbonded pdb="CA CA A 902 " pdb=" O HOH A1003 " model vdw 2.122 2.510 nonbonded pdb=" OD1 ASP A 320 " pdb="CA CA A 902 " model vdw 2.162 2.510 nonbonded pdb=" NE2 HIS A 393 " pdb="CA CA A 902 " model vdw 2.198 2.590 nonbonded pdb=" O GLU A 513 " pdb=" OG1 THR A 517 " model vdw 2.295 2.440 nonbonded pdb=" OG SER C 17 " pdb=" OD1 ASN C 83 " model vdw 2.335 2.440 ... (remaining 58387 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.560 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: 0.000 Extract box with map and model: 19.120 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 23.940 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:16.680 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 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 0.071 7051 Z= 0.428 Angle : 1.253 17.105 9565 Z= 0.680 Chirality : 0.065 0.402 1016 Planarity : 0.010 0.080 1212 Dihedral : 17.387 86.546 2564 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.03 % Allowed : 22.09 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -3.15 (0.25), residues: 820 helix: -3.33 (0.17), residues: 300 sheet: -1.35 (0.45), residues: 133 loop : -1.10 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 595 HIS 0.027 0.003 HIS A 400 PHE 0.058 0.004 PHE A 339 TYR 0.038 0.003 TYR A 680 ARG 0.010 0.001 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7859 (tp30) cc_final: 0.7576 (mm-30) REVERT: A 137 ILE cc_start: 0.6041 (OUTLIER) cc_final: 0.5649 (mt) REVERT: A 143 LYS cc_start: 0.6523 (mttp) cc_final: 0.6191 (mttm) REVERT: A 203 LYS cc_start: 0.7110 (mptt) cc_final: 0.6848 (mttm) REVERT: A 206 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6795 (mp) REVERT: A 208 TYR cc_start: 0.7867 (t80) cc_final: 0.7408 (t80) REVERT: A 308 LEU cc_start: 0.7927 (mt) cc_final: 0.7636 (tp) REVERT: A 400 HIS cc_start: 0.5718 (p-80) cc_final: 0.5414 (p90) REVERT: A 413 LYS cc_start: 0.4280 (ttmt) cc_final: 0.3836 (ttmm) REVERT: A 452 SER cc_start: 0.8106 (m) cc_final: 0.7894 (m) REVERT: A 536 ASP cc_start: 0.6909 (m-30) cc_final: 0.6348 (t0) REVERT: A 676 LYS cc_start: 0.7685 (tttt) cc_final: 0.7482 (tmtp) REVERT: A 688 ARG cc_start: 0.6999 (ttp-110) cc_final: 0.6556 (ptm160) REVERT: A 708 ASP cc_start: 0.6210 (t70) cc_final: 0.5944 (t70) REVERT: A 743 LYS cc_start: 0.7804 (mttt) cc_final: 0.7075 (mptt) REVERT: A 864 TYR cc_start: 0.5837 (OUTLIER) cc_final: 0.5160 (t80) REVERT: C 106 LYS cc_start: 0.7626 (pttt) cc_final: 0.7251 (tttm) outliers start: 15 outliers final: 7 residues processed: 132 average time/residue: 1.0877 time to fit residues: 152.8389 Evaluate side-chains 103 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 447 TRP Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 98 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.0770 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 343 ASN A 400 HIS A 408 GLN A 583 GLN A 731 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7051 Z= 0.177 Angle : 0.555 9.516 9565 Z= 0.285 Chirality : 0.041 0.153 1016 Planarity : 0.005 0.047 1212 Dihedral : 7.445 66.723 963 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.20 % Allowed : 21.14 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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 (0.27), residues: 820 helix: -1.38 (0.25), residues: 315 sheet: -0.98 (0.49), residues: 116 loop : -0.58 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 391 HIS 0.013 0.001 HIS A 400 PHE 0.014 0.001 PHE A 494 TYR 0.010 0.001 TYR A 852 ARG 0.006 0.001 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 100 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7841 (tp30) cc_final: 0.7526 (mm-30) REVERT: A 143 LYS cc_start: 0.6288 (mttp) cc_final: 0.5993 (mttm) REVERT: A 203 LYS cc_start: 0.7045 (mptt) cc_final: 0.6770 (mttp) REVERT: A 413 LYS cc_start: 0.4437 (ttmt) cc_final: 0.4143 (ttmm) REVERT: A 452 SER cc_start: 0.8000 (OUTLIER) cc_final: 0.7757 (m) REVERT: A 626 MET cc_start: 0.7227 (mtp) cc_final: 0.6934 (mtp) REVERT: A 634 TYR cc_start: 0.6902 (m-80) cc_final: 0.6612 (m-80) REVERT: A 688 ARG cc_start: 0.6932 (ttp-110) cc_final: 0.6476 (ptp90) REVERT: A 708 ASP cc_start: 0.6055 (t70) cc_final: 0.5775 (t70) REVERT: A 721 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.5259 (t0) REVERT: A 743 LYS cc_start: 0.7797 (mttt) cc_final: 0.7110 (mptt) REVERT: A 784 GLU cc_start: 0.6225 (pp20) cc_final: 0.5675 (pp20) REVERT: A 853 ARG cc_start: 0.4912 (OUTLIER) cc_final: 0.4584 (ttm170) REVERT: A 864 TYR cc_start: 0.5990 (OUTLIER) cc_final: 0.5632 (m-80) REVERT: C 106 LYS cc_start: 0.7565 (pttt) cc_final: 0.7179 (tttm) REVERT: C 115 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.6946 (m-30) outliers start: 31 outliers final: 11 residues processed: 122 average time/residue: 1.2418 time to fit residues: 160.9106 Evaluate side-chains 109 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 447 TRP Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 853 ARG Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 0.0770 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 400 HIS A 475 HIS ** A 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7051 Z= 0.172 Angle : 0.541 8.878 9565 Z= 0.277 Chirality : 0.041 0.149 1016 Planarity : 0.004 0.037 1212 Dihedral : 6.753 60.932 953 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.42 % Allowed : 20.05 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.29), residues: 820 helix: -0.44 (0.27), residues: 318 sheet: -0.69 (0.52), residues: 112 loop : -0.33 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 391 HIS 0.014 0.001 HIS A 400 PHE 0.020 0.002 PHE C 108 TYR 0.025 0.001 TYR A 680 ARG 0.003 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 103 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7531 (mm-30) REVERT: A 143 LYS cc_start: 0.6189 (mttp) cc_final: 0.5879 (mttm) REVERT: A 203 LYS cc_start: 0.6987 (mptt) cc_final: 0.6771 (mttm) REVERT: A 413 LYS cc_start: 0.4519 (ttmt) cc_final: 0.4138 (ttmm) REVERT: A 452 SER cc_start: 0.8096 (OUTLIER) cc_final: 0.7812 (m) REVERT: A 626 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.7051 (mtp) REVERT: A 634 TYR cc_start: 0.7108 (m-80) cc_final: 0.6778 (m-80) REVERT: A 688 ARG cc_start: 0.6926 (ttp-110) cc_final: 0.6407 (ptt-90) REVERT: A 743 LYS cc_start: 0.7774 (mttt) cc_final: 0.7093 (mptt) REVERT: A 782 ARG cc_start: 0.5261 (OUTLIER) cc_final: 0.4629 (mtp85) REVERT: A 784 GLU cc_start: 0.6217 (pp20) cc_final: 0.5628 (pp20) REVERT: A 864 TYR cc_start: 0.6112 (OUTLIER) cc_final: 0.5776 (m-80) REVERT: C 64 LYS cc_start: 0.6115 (OUTLIER) cc_final: 0.5870 (tppt) REVERT: C 106 LYS cc_start: 0.7643 (pttt) cc_final: 0.7250 (tttm) REVERT: C 115 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7311 (m-30) outliers start: 40 outliers final: 17 residues processed: 129 average time/residue: 0.9845 time to fit residues: 135.5035 Evaluate side-chains 117 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 93 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 559 GLN Chi-restraints excluded: chain A residue 583 GLN Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 782 ARG Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 400 HIS ** A 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7051 Z= 0.266 Angle : 0.618 8.293 9565 Z= 0.317 Chirality : 0.043 0.154 1016 Planarity : 0.005 0.036 1212 Dihedral : 6.909 58.227 951 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.42 % Allowed : 20.46 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.29), residues: 820 helix: -0.22 (0.28), residues: 310 sheet: -0.74 (0.50), residues: 120 loop : -0.21 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 391 HIS 0.013 0.002 HIS A 400 PHE 0.028 0.002 PHE A 339 TYR 0.031 0.002 TYR A 680 ARG 0.003 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 97 time to evaluate : 0.787 Fit side-chains REVERT: A 114 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7530 (mm-30) REVERT: A 138 TYR cc_start: 0.7544 (m-80) cc_final: 0.7273 (m-80) REVERT: A 143 LYS cc_start: 0.6226 (mttp) cc_final: 0.5748 (mttm) REVERT: A 330 MET cc_start: 0.5035 (mtp) cc_final: 0.4789 (mtt) REVERT: A 413 LYS cc_start: 0.4618 (ttmt) cc_final: 0.4184 (ttmm) REVERT: A 447 TRP cc_start: 0.8150 (OUTLIER) cc_final: 0.7827 (m-10) REVERT: A 452 SER cc_start: 0.8144 (OUTLIER) cc_final: 0.7822 (m) REVERT: A 516 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7459 (mm) REVERT: A 626 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.7062 (mtp) REVERT: A 688 ARG cc_start: 0.6952 (ttp-110) cc_final: 0.6454 (ptt-90) REVERT: A 743 LYS cc_start: 0.7775 (mttt) cc_final: 0.7118 (mptt) REVERT: A 782 ARG cc_start: 0.5218 (OUTLIER) cc_final: 0.4796 (mtp85) REVERT: A 784 GLU cc_start: 0.6415 (pp20) cc_final: 0.5741 (pp20) REVERT: C 106 LYS cc_start: 0.7683 (pttt) cc_final: 0.7250 (tttm) outliers start: 40 outliers final: 15 residues processed: 126 average time/residue: 0.9379 time to fit residues: 126.5342 Evaluate side-chains 110 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 447 TRP Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 559 GLN Chi-restraints excluded: chain A residue 583 GLN Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 782 ARG Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 140 ASN ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS A 475 HIS ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7051 Z= 0.280 Angle : 0.620 8.271 9565 Z= 0.319 Chirality : 0.044 0.157 1016 Planarity : 0.004 0.034 1212 Dihedral : 6.614 56.574 949 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.83 % Allowed : 20.60 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.29), residues: 820 helix: -0.22 (0.28), residues: 310 sheet: -0.92 (0.50), residues: 114 loop : -0.16 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 391 HIS 0.014 0.002 HIS A 400 PHE 0.019 0.002 PHE A 543 TYR 0.033 0.002 TYR A 680 ARG 0.003 0.000 ARG A 688 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 93 time to evaluate : 0.835 Fit side-chains REVERT: A 114 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7567 (mm-30) REVERT: A 330 MET cc_start: 0.5026 (mtp) cc_final: 0.4744 (mtt) REVERT: A 375 ASP cc_start: 0.7212 (m-30) cc_final: 0.6958 (m-30) REVERT: A 413 LYS cc_start: 0.4573 (ttmt) cc_final: 0.4190 (ttmm) REVERT: A 447 TRP cc_start: 0.8139 (OUTLIER) cc_final: 0.7565 (m-10) REVERT: A 452 SER cc_start: 0.8113 (OUTLIER) cc_final: 0.7828 (m) REVERT: A 626 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.7061 (mtp) REVERT: A 688 ARG cc_start: 0.6912 (ttp-110) cc_final: 0.6494 (ptt-90) REVERT: A 743 LYS cc_start: 0.7742 (mttt) cc_final: 0.7096 (mptt) REVERT: A 782 ARG cc_start: 0.5357 (OUTLIER) cc_final: 0.4856 (mtp85) REVERT: A 784 GLU cc_start: 0.6556 (pp20) cc_final: 0.5753 (pp20) REVERT: C 106 LYS cc_start: 0.7652 (pttt) cc_final: 0.7246 (tttm) outliers start: 43 outliers final: 20 residues processed: 122 average time/residue: 0.9988 time to fit residues: 130.0571 Evaluate side-chains 111 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 86 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 447 TRP Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 559 GLN Chi-restraints excluded: chain A residue 583 GLN Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 782 ARG Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 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 95 GLN A 140 ASN ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS A 408 GLN ** A 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7051 Z= 0.182 Angle : 0.554 8.271 9565 Z= 0.283 Chirality : 0.042 0.146 1016 Planarity : 0.004 0.045 1212 Dihedral : 6.193 54.351 949 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 5.56 % Allowed : 21.68 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.30), residues: 820 helix: 0.05 (0.29), residues: 314 sheet: -0.84 (0.52), residues: 107 loop : -0.10 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 391 HIS 0.014 0.001 HIS A 400 PHE 0.014 0.001 PHE A 543 TYR 0.029 0.002 TYR A 680 ARG 0.004 0.000 ARG A 709 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 97 time to evaluate : 0.762 Fit side-chains REVERT: A 114 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7540 (mm-30) REVERT: A 330 MET cc_start: 0.5001 (mtp) cc_final: 0.4763 (mtt) REVERT: A 413 LYS cc_start: 0.4524 (ttmt) cc_final: 0.4135 (ttmm) REVERT: A 447 TRP cc_start: 0.8130 (OUTLIER) cc_final: 0.7737 (m-10) REVERT: A 452 SER cc_start: 0.8057 (OUTLIER) cc_final: 0.7751 (m) REVERT: A 504 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7444 (mm-30) REVERT: A 626 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7063 (mtp) REVERT: A 688 ARG cc_start: 0.6912 (ttp-110) cc_final: 0.6541 (ptt-90) REVERT: A 743 LYS cc_start: 0.7751 (mttt) cc_final: 0.7108 (mptt) REVERT: A 782 ARG cc_start: 0.5324 (OUTLIER) cc_final: 0.4610 (mtp85) REVERT: A 784 GLU cc_start: 0.6527 (pp20) cc_final: 0.5590 (pp20) REVERT: C 106 LYS cc_start: 0.7630 (pttt) cc_final: 0.7236 (tttm) outliers start: 41 outliers final: 16 residues processed: 126 average time/residue: 1.0587 time to fit residues: 141.7421 Evaluate side-chains 113 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 447 TRP Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 521 ASN Chi-restraints excluded: chain A residue 559 GLN Chi-restraints excluded: chain A residue 583 GLN Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 782 ARG Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 58 optimal weight: 0.0170 chunk 67 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 140 ASN ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS A 408 GLN ** A 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7051 Z= 0.201 Angle : 0.572 7.704 9565 Z= 0.292 Chirality : 0.042 0.146 1016 Planarity : 0.004 0.046 1212 Dihedral : 6.167 53.988 949 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.69 % Allowed : 21.82 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.30), residues: 820 helix: 0.11 (0.29), residues: 314 sheet: -0.82 (0.53), residues: 105 loop : -0.04 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 391 HIS 0.015 0.001 HIS A 400 PHE 0.014 0.001 PHE A 543 TYR 0.033 0.002 TYR A 680 ARG 0.005 0.000 ARG A 709 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 95 time to evaluate : 0.870 Fit side-chains REVERT: A 88 PHE cc_start: 0.6530 (OUTLIER) cc_final: 0.6197 (m-10) REVERT: A 114 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7505 (mm-30) REVERT: A 330 MET cc_start: 0.4991 (mtp) cc_final: 0.4707 (mtt) REVERT: A 375 ASP cc_start: 0.7139 (m-30) cc_final: 0.6893 (m-30) REVERT: A 413 LYS cc_start: 0.4529 (ttmt) cc_final: 0.4134 (ttmm) REVERT: A 447 TRP cc_start: 0.8149 (OUTLIER) cc_final: 0.7681 (m-10) REVERT: A 452 SER cc_start: 0.8046 (OUTLIER) cc_final: 0.7743 (m) REVERT: A 504 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7466 (mm-30) REVERT: A 626 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.7031 (mtp) REVERT: A 688 ARG cc_start: 0.6903 (ttp-110) cc_final: 0.6551 (ptt-90) REVERT: A 743 LYS cc_start: 0.7754 (mttt) cc_final: 0.7113 (mptt) REVERT: A 782 ARG cc_start: 0.5398 (OUTLIER) cc_final: 0.4771 (mtp85) REVERT: A 784 GLU cc_start: 0.6523 (pp20) cc_final: 0.5962 (pp20) REVERT: C 106 LYS cc_start: 0.7627 (pttt) cc_final: 0.7233 (tttm) outliers start: 42 outliers final: 19 residues processed: 121 average time/residue: 1.0491 time to fit residues: 136.0493 Evaluate side-chains 116 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 90 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 447 TRP Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 521 ASN Chi-restraints excluded: chain A residue 559 GLN Chi-restraints excluded: chain A residue 583 GLN Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 782 ARG Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 140 ASN ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS A 408 GLN ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7051 Z= 0.263 Angle : 0.606 7.719 9565 Z= 0.313 Chirality : 0.044 0.162 1016 Planarity : 0.004 0.044 1212 Dihedral : 6.359 54.296 949 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.15 % Allowed : 22.36 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.30), residues: 820 helix: -0.00 (0.28), residues: 313 sheet: -0.89 (0.52), residues: 105 loop : -0.10 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 391 HIS 0.015 0.002 HIS A 400 PHE 0.016 0.002 PHE A 543 TYR 0.034 0.002 TYR A 680 ARG 0.003 0.000 ARG A 709 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 91 time to evaluate : 0.795 Fit side-chains REVERT: A 88 PHE cc_start: 0.6539 (OUTLIER) cc_final: 0.6169 (m-10) REVERT: A 114 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7501 (mm-30) REVERT: A 330 MET cc_start: 0.5047 (mtp) cc_final: 0.4772 (mtt) REVERT: A 375 ASP cc_start: 0.7282 (m-30) cc_final: 0.6692 (m-30) REVERT: A 413 LYS cc_start: 0.4540 (ttmt) cc_final: 0.4113 (ttmm) REVERT: A 447 TRP cc_start: 0.8194 (OUTLIER) cc_final: 0.7751 (m-10) REVERT: A 452 SER cc_start: 0.8071 (OUTLIER) cc_final: 0.7781 (m) REVERT: A 504 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7562 (mm-30) REVERT: A 626 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.7054 (mtp) REVERT: A 688 ARG cc_start: 0.6894 (ttp-110) cc_final: 0.6527 (ptt-90) REVERT: A 743 LYS cc_start: 0.7761 (mttt) cc_final: 0.7136 (mptt) REVERT: A 782 ARG cc_start: 0.5451 (OUTLIER) cc_final: 0.4864 (mtp85) REVERT: A 784 GLU cc_start: 0.6573 (pp20) cc_final: 0.5902 (pp20) REVERT: A 858 GLU cc_start: 0.6463 (mp0) cc_final: 0.6062 (mp0) REVERT: C 106 LYS cc_start: 0.7642 (pttt) cc_final: 0.7220 (tttm) outliers start: 38 outliers final: 20 residues processed: 116 average time/residue: 1.0298 time to fit residues: 127.1813 Evaluate side-chains 114 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 87 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 447 TRP Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 521 ASN Chi-restraints excluded: chain A residue 559 GLN Chi-restraints excluded: chain A residue 583 GLN Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 782 ARG Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 70 optimal weight: 0.0070 chunk 48 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 140 ASN ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS A 408 GLN A 769 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7051 Z= 0.224 Angle : 0.585 7.959 9565 Z= 0.301 Chirality : 0.043 0.148 1016 Planarity : 0.004 0.040 1212 Dihedral : 6.226 52.768 949 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.88 % Allowed : 22.49 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.30), residues: 820 helix: 0.10 (0.29), residues: 313 sheet: -0.87 (0.52), residues: 105 loop : -0.07 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 391 HIS 0.014 0.001 HIS A 400 PHE 0.015 0.002 PHE A 543 TYR 0.032 0.002 TYR A 680 ARG 0.003 0.000 ARG A 709 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 91 time to evaluate : 0.788 Fit side-chains REVERT: A 88 PHE cc_start: 0.6553 (OUTLIER) cc_final: 0.6142 (m-10) REVERT: A 114 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7495 (mm-30) REVERT: A 330 MET cc_start: 0.5047 (mtp) cc_final: 0.4742 (mtt) REVERT: A 375 ASP cc_start: 0.7223 (m-30) cc_final: 0.6634 (m-30) REVERT: A 413 LYS cc_start: 0.4481 (ttmt) cc_final: 0.4062 (ttmm) REVERT: A 447 TRP cc_start: 0.8161 (OUTLIER) cc_final: 0.7638 (m-10) REVERT: A 452 SER cc_start: 0.8082 (OUTLIER) cc_final: 0.7800 (m) REVERT: A 504 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7477 (mm-30) REVERT: A 626 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.7076 (mtp) REVERT: A 688 ARG cc_start: 0.6882 (ttp-110) cc_final: 0.6406 (ptt-90) REVERT: A 717 GLN cc_start: 0.6247 (OUTLIER) cc_final: 0.5116 (mp10) REVERT: A 743 LYS cc_start: 0.7766 (mttt) cc_final: 0.7144 (mptt) REVERT: A 782 ARG cc_start: 0.5402 (OUTLIER) cc_final: 0.4748 (mtp85) REVERT: A 784 GLU cc_start: 0.6571 (pp20) cc_final: 0.5939 (pp20) REVERT: A 858 GLU cc_start: 0.6477 (mp0) cc_final: 0.6087 (mp0) REVERT: C 106 LYS cc_start: 0.7635 (pttt) cc_final: 0.7225 (tttm) outliers start: 36 outliers final: 21 residues processed: 115 average time/residue: 1.0450 time to fit residues: 127.8725 Evaluate side-chains 117 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 88 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 447 TRP Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 521 ASN Chi-restraints excluded: chain A residue 559 GLN Chi-restraints excluded: chain A residue 583 GLN Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 749 ASN Chi-restraints excluded: chain A residue 782 ARG Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 140 ASN ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS A 408 GLN ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7051 Z= 0.194 Angle : 0.576 7.946 9565 Z= 0.297 Chirality : 0.042 0.148 1016 Planarity : 0.004 0.039 1212 Dihedral : 6.140 51.965 949 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.20 % Allowed : 23.17 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.30), residues: 820 helix: 0.16 (0.29), residues: 314 sheet: -0.83 (0.52), residues: 105 loop : -0.03 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 447 HIS 0.014 0.001 HIS A 400 PHE 0.014 0.001 PHE A 543 TYR 0.039 0.002 TYR A 680 ARG 0.003 0.000 ARG A 709 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 92 time to evaluate : 0.782 Fit side-chains REVERT: A 88 PHE cc_start: 0.6536 (OUTLIER) cc_final: 0.6157 (m-10) REVERT: A 114 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7461 (mm-30) REVERT: A 308 LEU cc_start: 0.7985 (mt) cc_final: 0.7770 (tp) REVERT: A 330 MET cc_start: 0.5031 (mtp) cc_final: 0.4727 (mtt) REVERT: A 375 ASP cc_start: 0.7181 (m-30) cc_final: 0.6935 (m-30) REVERT: A 413 LYS cc_start: 0.4502 (ttmt) cc_final: 0.4060 (ttmm) REVERT: A 447 TRP cc_start: 0.8128 (OUTLIER) cc_final: 0.7582 (m-10) REVERT: A 452 SER cc_start: 0.8035 (OUTLIER) cc_final: 0.7802 (m) REVERT: A 504 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7466 (mm-30) REVERT: A 626 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.7074 (mtp) REVERT: A 688 ARG cc_start: 0.6813 (ttp-110) cc_final: 0.6396 (ptt-90) REVERT: A 717 GLN cc_start: 0.6251 (OUTLIER) cc_final: 0.5103 (mp10) REVERT: A 743 LYS cc_start: 0.7755 (mttt) cc_final: 0.7133 (mptt) REVERT: A 782 ARG cc_start: 0.5368 (OUTLIER) cc_final: 0.4705 (mtp85) REVERT: A 784 GLU cc_start: 0.6559 (pp20) cc_final: 0.5936 (pp20) REVERT: A 858 GLU cc_start: 0.6463 (mp0) cc_final: 0.6066 (mp0) REVERT: C 106 LYS cc_start: 0.7626 (pttt) cc_final: 0.7239 (tttm) outliers start: 31 outliers final: 18 residues processed: 114 average time/residue: 1.0555 time to fit residues: 127.9108 Evaluate side-chains 118 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 92 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 447 TRP Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 521 ASN Chi-restraints excluded: chain A residue 559 GLN Chi-restraints excluded: chain A residue 583 GLN Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 749 ASN Chi-restraints excluded: chain A residue 782 ARG Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 27 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 8 optimal weight: 0.0030 chunk 12 optimal weight: 0.0870 chunk 57 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 overall best weight: 0.4568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 140 ASN A 277 GLN ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS ** A 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.174370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.152765 restraints weight = 17631.242| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 2.84 r_work: 0.3978 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3982 r_free = 0.3982 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3982 r_free = 0.3982 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7051 Z= 0.157 Angle : 0.547 7.741 9565 Z= 0.281 Chirality : 0.041 0.146 1016 Planarity : 0.004 0.034 1212 Dihedral : 5.916 50.756 949 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.66 % Allowed : 24.25 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.30), residues: 820 helix: 0.41 (0.29), residues: 310 sheet: -0.81 (0.52), residues: 105 loop : 0.01 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 447 HIS 0.016 0.001 HIS A 400 PHE 0.046 0.002 PHE A 339 TYR 0.031 0.001 TYR A 680 ARG 0.004 0.000 ARG A 709 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3256.71 seconds wall clock time: 58 minutes 55.66 seconds (3535.66 seconds total)