Starting phenix.real_space_refine on Thu Jan 18 05:37:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wge_32484/01_2024/7wge_32484_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wge_32484/01_2024/7wge_32484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wge_32484/01_2024/7wge_32484.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wge_32484/01_2024/7wge_32484.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wge_32484/01_2024/7wge_32484_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wge_32484/01_2024/7wge_32484_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1495 atoms to isotropic. 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 P 3 5.49 5 Mg 1 5.21 5 S 47 5.16 5 C 4099 2.51 5 N 1121 2.21 5 O 1189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 316": "OD1" <-> "OD2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 538": "OE1" <-> "OE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A GLU 683": "OE1" <-> "OE2" Residue "A GLU 717": "OE1" <-> "OE2" Residue "A GLU 724": "OE1" <-> "OE2" Residue "A GLU 739": "OE1" <-> "OE2" Residue "A ASP 871": "OD1" <-> "OD2" Residue "A PHE 874": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 944": "OE1" <-> "OE2" Residue "B ASP 26": "OD1" <-> "OD2" Residue "B GLU 44": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6460 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5600 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 698, 5563 Classifications: {'peptide': 698} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 30, 'TRANS': 667} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 698, 5563 Classifications: {'peptide': 698} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 30, 'TRANS': 667} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 5630 Chain: "B" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 828 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 102} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.25, per 1000 atoms: 0.97 Number of scatterers: 6460 At special positions: 0 Unit cell: (68.475, 92.13, 140.685, 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) S 47 16.00 P 3 15.00 Mg 1 11.99 O 1189 8.00 N 1121 7.00 C 4099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 32 " - pdb=" SG CYS B 35 " 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: 2.50 Conformation dependent library (CDL) restraints added in 2.0 seconds 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1542 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 4 sheets defined 41.9% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 300 through 306 removed outlier: 3.508A pdb=" N VAL A 304 " --> pdb=" O TRP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 369 through 374 removed outlier: 4.014A pdb=" N GLN A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 387 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 436 through 444 removed outlier: 3.663A pdb=" N GLY A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 493 Processing helix chain 'A' and resid 497 through 509 Processing helix chain 'A' and resid 511 through 518 removed outlier: 4.434A pdb=" N LEU A 518 " --> pdb=" O TRP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 535 Processing helix chain 'A' and resid 547 through 558 Processing helix chain 'A' and resid 566 through 580 Processing helix chain 'A' and resid 588 through 593 removed outlier: 3.764A pdb=" N ARG A 592 " --> pdb=" O PRO A 588 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 588 through 593' Processing helix chain 'A' and resid 598 through 607 Processing helix chain 'A' and resid 624 through 639 removed outlier: 3.558A pdb=" N SER A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 659 Processing helix chain 'A' and resid 669 through 678 removed outlier: 3.752A pdb=" N LEU A 678 " --> pdb=" O LEU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 689 removed outlier: 4.300A pdb=" N MET A 686 " --> pdb=" O GLY A 682 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLU A 687 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN A 688 " --> pdb=" O ARG A 684 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 689 " --> pdb=" O GLU A 685 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 682 through 689' Processing helix chain 'A' and resid 698 through 709 removed outlier: 4.026A pdb=" N TRP A 703 " --> pdb=" O ASN A 699 " (cutoff:3.500A) Proline residue: A 705 - end of helix Processing helix chain 'A' and resid 716 through 723 Processing helix chain 'A' and resid 748 through 759 Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 822 through 833 Processing helix chain 'A' and resid 851 through 863 removed outlier: 3.718A pdb=" N LYS A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP A 856 " --> pdb=" O GLU A 852 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA A 863 " --> pdb=" O PHE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 889 removed outlier: 3.563A pdb=" N LEU A 885 " --> pdb=" O GLY A 881 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 888 " --> pdb=" O HIS A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 920 removed outlier: 3.932A pdb=" N GLN A 912 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 946 Processing helix chain 'A' and resid 965 through 977 removed outlier: 3.806A pdb=" N GLN A 969 " --> pdb=" O ASP A 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 18 Processing helix chain 'B' and resid 33 through 48 Proline residue: B 40 - end of helix Processing helix chain 'B' and resid 64 through 70 Processing helix chain 'B' and resid 95 through 105 Processing sheet with id= A, first strand: chain 'A' and resid 283 through 286 removed outlier: 3.563A pdb=" N GLU A 477 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 286 " --> pdb=" O TRP A 475 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N TRP A 475 " --> pdb=" O ARG A 286 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE A 454 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU A 332 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ILE A 456 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER A 453 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N HIS A 363 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ILE A 408 " --> pdb=" O HIS A 363 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE A 365 " --> pdb=" O ILE A 408 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 783 through 787 removed outlier: 7.171A pdb=" N LYS A 766 " --> pdb=" O VAL A 784 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LEU A 786 " --> pdb=" O LYS A 766 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLN A 768 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLU A 812 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N LEU A 769 " --> pdb=" O GLU A 812 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASP A 814 " --> pdb=" O LEU A 769 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 841 through 843 removed outlier: 5.872A pdb=" N GLU A 869 " --> pdb=" O LEU A 842 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG A 898 " --> pdb=" O LEU A 870 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLU A 926 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG A 955 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A 982 " --> pdb=" O LEU A 956 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 2 through 5 removed outlier: 9.509A pdb=" N ILE B 3 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL B 55 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ILE B 5 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LYS B 57 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU B 22 " --> pdb=" O VAL B 54 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LEU B 56 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 24 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL B 58 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP B 26 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 77 " --> pdb=" O PHE B 27 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LYS B 82 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LYS B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) 193 hydrogen bonds defined for protein. 544 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: 1.75 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 2183 1.37 - 1.52: 1846 1.52 - 1.66: 2499 1.66 - 1.80: 41 1.80 - 1.95: 24 Bond restraints: 6593 Sorted by residual: bond pdb=" CA GLY A 309 " pdb=" C GLY A 309 " ideal model delta sigma weight residual 1.514 1.531 -0.017 1.41e-02 5.03e+03 1.48e+00 bond pdb=" N GLY A 309 " pdb=" CA GLY A 309 " ideal model delta sigma weight residual 1.449 1.466 -0.017 1.45e-02 4.76e+03 1.34e+00 bond pdb=" CG ARG A 773 " pdb=" CD ARG A 773 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.51e-01 bond pdb=" CA ASP A 935 " pdb=" CB ASP A 935 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 8.60e-01 bond pdb=" CB PRO A 320 " pdb=" CG PRO A 320 " ideal model delta sigma weight residual 1.492 1.538 -0.046 5.00e-02 4.00e+02 8.33e-01 ... (remaining 6588 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.58: 188 106.58 - 113.45: 3660 113.45 - 120.33: 2383 120.33 - 127.21: 2626 127.21 - 134.09: 77 Bond angle restraints: 8934 Sorted by residual: angle pdb=" N MET A 741 " pdb=" CA MET A 741 " pdb=" C MET A 741 " ideal model delta sigma weight residual 114.56 109.17 5.39 1.27e+00 6.20e-01 1.80e+01 angle pdb=" C LEU A 934 " pdb=" N ASP A 935 " pdb=" CA ASP A 935 " ideal model delta sigma weight residual 121.54 127.02 -5.48 1.91e+00 2.74e-01 8.23e+00 angle pdb=" CA MET A 741 " pdb=" C MET A 741 " pdb=" N GLY A 742 " ideal model delta sigma weight residual 119.26 116.19 3.07 1.14e+00 7.69e-01 7.27e+00 angle pdb=" N HIS A 737 " pdb=" CA HIS A 737 " pdb=" C HIS A 737 " ideal model delta sigma weight residual 113.19 108.94 4.25 1.58e+00 4.01e-01 7.24e+00 angle pdb=" CG ARG A 773 " pdb=" CD ARG A 773 " pdb=" NE ARG A 773 " ideal model delta sigma weight residual 112.00 117.23 -5.23 2.20e+00 2.07e-01 5.64e+00 ... (remaining 8929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 3627 17.92 - 35.85: 330 35.85 - 53.77: 68 53.77 - 71.69: 21 71.69 - 89.61: 8 Dihedral angle restraints: 4054 sinusoidal: 1680 harmonic: 2374 Sorted by residual: dihedral pdb=" CA PRO A 616 " pdb=" C PRO A 616 " pdb=" N LEU A 617 " pdb=" CA LEU A 617 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ASP A 387 " pdb=" CB ASP A 387 " pdb=" CG ASP A 387 " pdb=" OD1 ASP A 387 " ideal model delta sinusoidal sigma weight residual -30.00 -86.71 56.71 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA LYS B 36 " pdb=" C LYS B 36 " pdb=" N MET B 37 " pdb=" CA MET B 37 " ideal model delta harmonic sigma weight residual 180.00 164.21 15.79 0 5.00e+00 4.00e-02 9.98e+00 ... (remaining 4051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 782 0.043 - 0.085: 183 0.085 - 0.128: 53 0.128 - 0.170: 2 0.170 - 0.213: 3 Chirality restraints: 1023 Sorted by residual: chirality pdb=" CB VAL A 296 " pdb=" CA VAL A 296 " pdb=" CG1 VAL A 296 " pdb=" CG2 VAL A 296 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CG LEU A 934 " pdb=" CB LEU A 934 " pdb=" CD1 LEU A 934 " pdb=" CD2 LEU A 934 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE A 615 " pdb=" N ILE A 615 " pdb=" C ILE A 615 " pdb=" CB ILE A 615 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 1020 not shown) Planarity restraints: 1133 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 319 " -0.052 5.00e-02 4.00e+02 7.83e-02 9.81e+00 pdb=" N PRO A 320 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 565 " 0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO A 566 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 566 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 566 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 712 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO A 713 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 713 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 713 " 0.024 5.00e-02 4.00e+02 ... (remaining 1130 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 281 2.73 - 3.27: 6671 3.27 - 3.81: 10340 3.81 - 4.36: 12430 4.36 - 4.90: 21046 Nonbonded interactions: 50768 Sorted by model distance: nonbonded pdb=" OG SER A 587 " pdb=" OD1 ASP A 589 " model vdw 2.182 2.440 nonbonded pdb=" OE1 GLU A 812 " pdb=" OG1 THR A 841 " model vdw 2.243 2.440 nonbonded pdb=" O ILE A 662 " pdb=" ND1 HIS A 663 " model vdw 2.248 2.520 nonbonded pdb=" OG SER A 341 " pdb="MG MG A1002 " model vdw 2.259 2.170 nonbonded pdb=" OE2 GLU A 683 " pdb=" ND2 ASN A 699 " model vdw 2.278 2.520 ... (remaining 50763 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=0.30 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 1.200 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.060 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6593 Z= 0.168 Angle : 0.631 7.401 8934 Z= 0.315 Chirality : 0.040 0.213 1023 Planarity : 0.005 0.078 1133 Dihedral : 15.024 89.613 2509 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 0.28 % Allowed : 0.56 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.30), residues: 807 helix: 1.54 (0.28), residues: 344 sheet: -0.37 (0.52), residues: 111 loop : -2.23 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 351 HIS 0.006 0.001 HIS A 553 PHE 0.011 0.001 PHE A 454 TYR 0.007 0.001 TYR A 723 ARG 0.016 0.001 ARG A 773 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.722 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1846 time to fit residues: 33.5115 Evaluate side-chains 96 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 0.0870 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 HIS ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6593 Z= 0.189 Angle : 0.638 8.593 8934 Z= 0.312 Chirality : 0.041 0.219 1023 Planarity : 0.005 0.057 1133 Dihedral : 5.953 53.122 902 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.27 % Favored : 92.48 % Rotamer: Outliers : 1.94 % Allowed : 9.58 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.74 (0.30), residues: 807 helix: 0.90 (0.28), residues: 362 sheet: -0.20 (0.52), residues: 111 loop : -2.22 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 703 HIS 0.003 0.001 HIS A 594 PHE 0.046 0.002 PHE A 673 TYR 0.011 0.001 TYR A 796 ARG 0.010 0.001 ARG A 773 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 0.727 Fit side-chains REVERT: A 313 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6972 (tt0) REVERT: A 680 ASP cc_start: 0.7606 (m-30) cc_final: 0.7397 (m-30) REVERT: A 717 GLU cc_start: 0.6662 (pm20) cc_final: 0.6386 (mt-10) REVERT: B 41 LYS cc_start: 0.7676 (mmmm) cc_final: 0.7130 (mmtp) outliers start: 12 outliers final: 6 residues processed: 119 average time/residue: 0.1867 time to fit residues: 29.7895 Evaluate side-chains 99 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 HIS ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 GLN ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 HIS ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 6593 Z= 0.406 Angle : 0.822 8.218 8934 Z= 0.406 Chirality : 0.048 0.238 1023 Planarity : 0.006 0.048 1133 Dihedral : 7.031 64.943 902 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.02 % Favored : 91.73 % Rotamer: Outliers : 3.47 % Allowed : 10.14 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.46 (0.29), residues: 807 helix: 0.06 (0.26), residues: 382 sheet: -0.52 (0.51), residues: 113 loop : -2.44 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.004 TRP A 789 HIS 0.007 0.001 HIS A 720 PHE 0.024 0.003 PHE A 738 TYR 0.020 0.003 TYR A 303 ARG 0.010 0.001 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 0.829 Fit side-chains REVERT: A 313 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7171 (tt0) REVERT: A 488 GLU cc_start: 0.6359 (mt-10) cc_final: 0.6155 (mt-10) REVERT: A 714 HIS cc_start: 0.6440 (OUTLIER) cc_final: 0.5501 (t-90) REVERT: A 967 MET cc_start: 0.6739 (mmp) cc_final: 0.6456 (tpp) outliers start: 23 outliers final: 14 residues processed: 129 average time/residue: 0.2251 time to fit residues: 36.9787 Evaluate side-chains 110 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 714 HIS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6593 Z= 0.211 Angle : 0.638 9.885 8934 Z= 0.311 Chirality : 0.041 0.207 1023 Planarity : 0.005 0.048 1133 Dihedral : 6.665 64.342 902 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.89 % Favored : 92.98 % Rotamer: Outliers : 2.50 % Allowed : 13.47 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.32 (0.29), residues: 807 helix: 0.20 (0.26), residues: 381 sheet: -0.40 (0.53), residues: 110 loop : -2.41 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 789 HIS 0.003 0.001 HIS A 594 PHE 0.034 0.002 PHE A 738 TYR 0.018 0.002 TYR A 489 ARG 0.008 0.001 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 0.747 Fit side-chains REVERT: A 313 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7173 (tt0) REVERT: A 542 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7859 (mp) REVERT: A 799 ILE cc_start: 0.8603 (tp) cc_final: 0.8373 (tp) REVERT: B 12 LYS cc_start: 0.7330 (mttm) cc_final: 0.6989 (mmtp) outliers start: 16 outliers final: 12 residues processed: 113 average time/residue: 0.2139 time to fit residues: 31.1914 Evaluate side-chains 111 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 714 HIS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 106 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.0470 chunk 65 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.0980 chunk 44 optimal weight: 2.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6593 Z= 0.226 Angle : 0.656 9.457 8934 Z= 0.322 Chirality : 0.041 0.235 1023 Planarity : 0.004 0.048 1133 Dihedral : 6.534 64.527 902 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.39 % Favored : 92.48 % Rotamer: Outliers : 3.19 % Allowed : 14.58 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.18 (0.30), residues: 807 helix: 0.35 (0.27), residues: 381 sheet: -0.34 (0.53), residues: 110 loop : -2.40 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 789 HIS 0.002 0.001 HIS A 594 PHE 0.024 0.002 PHE A 738 TYR 0.016 0.001 TYR A 796 ARG 0.008 0.001 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 0.569 Fit side-chains REVERT: A 313 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7145 (tt0) REVERT: A 531 MET cc_start: 0.6963 (tpt) cc_final: 0.6690 (tpt) REVERT: A 691 HIS cc_start: 0.5402 (m-70) cc_final: 0.5116 (m90) REVERT: B 15 LEU cc_start: 0.7164 (mt) cc_final: 0.6822 (pp) outliers start: 21 outliers final: 16 residues processed: 112 average time/residue: 0.2046 time to fit residues: 29.8742 Evaluate side-chains 115 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 714 HIS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 106 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 73 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6593 Z= 0.330 Angle : 0.737 9.683 8934 Z= 0.364 Chirality : 0.045 0.210 1023 Planarity : 0.005 0.045 1133 Dihedral : 7.272 73.946 902 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.65 % Favored : 91.23 % Rotamer: Outliers : 3.19 % Allowed : 15.97 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.53 (0.29), residues: 807 helix: -0.01 (0.26), residues: 382 sheet: -0.60 (0.53), residues: 112 loop : -2.43 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP A 789 HIS 0.004 0.001 HIS A 594 PHE 0.021 0.002 PHE A 673 TYR 0.013 0.002 TYR A 796 ARG 0.008 0.001 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 0.732 Fit side-chains REVERT: A 680 ASP cc_start: 0.7997 (m-30) cc_final: 0.7607 (m-30) REVERT: B 15 LEU cc_start: 0.7163 (mt) cc_final: 0.6803 (pp) REVERT: B 75 MET cc_start: 0.8353 (mpp) cc_final: 0.7640 (ptp) outliers start: 21 outliers final: 15 residues processed: 113 average time/residue: 0.2058 time to fit residues: 30.6275 Evaluate side-chains 103 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 714 HIS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 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 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6593 Z= 0.207 Angle : 0.669 8.930 8934 Z= 0.330 Chirality : 0.041 0.231 1023 Planarity : 0.005 0.046 1133 Dihedral : 7.069 69.983 902 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.02 % Favored : 91.85 % Rotamer: Outliers : 2.64 % Allowed : 18.33 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.39 (0.30), residues: 807 helix: 0.11 (0.27), residues: 382 sheet: -0.50 (0.54), residues: 110 loop : -2.36 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 789 HIS 0.002 0.001 HIS A 594 PHE 0.016 0.002 PHE A 738 TYR 0.016 0.001 TYR A 796 ARG 0.009 0.001 ARG A 592 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 0.863 Fit side-chains REVERT: A 313 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7052 (tt0) REVERT: A 680 ASP cc_start: 0.7779 (m-30) cc_final: 0.7453 (m-30) REVERT: A 967 MET cc_start: 0.8071 (mmm) cc_final: 0.7665 (tpp) REVERT: B 15 LEU cc_start: 0.7094 (mt) cc_final: 0.6839 (pp) REVERT: B 75 MET cc_start: 0.8317 (mpp) cc_final: 0.7699 (ptp) outliers start: 17 outliers final: 12 residues processed: 102 average time/residue: 0.2202 time to fit residues: 30.4826 Evaluate side-chains 102 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 714 HIS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.0070 chunk 48 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6593 Z= 0.330 Angle : 0.739 9.681 8934 Z= 0.363 Chirality : 0.044 0.210 1023 Planarity : 0.005 0.046 1133 Dihedral : 7.198 72.814 902 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.65 % Favored : 91.23 % Rotamer: Outliers : 3.33 % Allowed : 18.19 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.29), residues: 807 helix: -0.01 (0.27), residues: 377 sheet: -0.56 (0.54), residues: 109 loop : -2.55 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP A 789 HIS 0.004 0.001 HIS A 594 PHE 0.018 0.002 PHE A 673 TYR 0.012 0.002 TYR A 796 ARG 0.008 0.001 ARG A 592 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 0.789 Fit side-chains REVERT: A 313 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7103 (tt0) REVERT: A 314 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7557 (tt) REVERT: A 432 GLN cc_start: 0.5827 (mm110) cc_final: 0.5309 (tt0) REVERT: A 680 ASP cc_start: 0.7917 (m-30) cc_final: 0.7573 (m-30) REVERT: B 15 LEU cc_start: 0.7012 (mt) cc_final: 0.6779 (pp) REVERT: B 75 MET cc_start: 0.8265 (mpp) cc_final: 0.7615 (ptp) outliers start: 22 outliers final: 18 residues processed: 108 average time/residue: 0.1902 time to fit residues: 27.5493 Evaluate side-chains 106 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 714 HIS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 818 ASN Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 45 optimal weight: 0.0470 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6593 Z= 0.185 Angle : 0.658 12.573 8934 Z= 0.323 Chirality : 0.041 0.234 1023 Planarity : 0.005 0.046 1133 Dihedral : 7.025 67.934 902 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.02 % Favored : 92.86 % Rotamer: Outliers : 2.50 % Allowed : 19.31 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.30), residues: 807 helix: 0.20 (0.27), residues: 379 sheet: -0.40 (0.55), residues: 107 loop : -2.45 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 789 HIS 0.002 0.001 HIS A 737 PHE 0.013 0.001 PHE A 738 TYR 0.014 0.001 TYR A 796 ARG 0.008 0.001 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.752 Fit side-chains REVERT: A 432 GLN cc_start: 0.5774 (mm110) cc_final: 0.5218 (tt0) REVERT: B 75 MET cc_start: 0.8168 (mpp) cc_final: 0.7794 (ptp) outliers start: 16 outliers final: 14 residues processed: 99 average time/residue: 0.1732 time to fit residues: 23.3975 Evaluate side-chains 98 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 818 ASN Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.0770 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 HIS ** A 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.6013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 6593 Z= 0.355 Angle : 0.757 13.081 8934 Z= 0.370 Chirality : 0.045 0.226 1023 Planarity : 0.005 0.047 1133 Dihedral : 7.156 72.664 902 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.65 % Favored : 91.23 % Rotamer: Outliers : 2.64 % Allowed : 19.58 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.70 (0.29), residues: 807 helix: -0.16 (0.26), residues: 380 sheet: -0.55 (0.53), residues: 109 loop : -2.54 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP A 789 HIS 0.005 0.001 HIS A 720 PHE 0.018 0.002 PHE A 673 TYR 0.012 0.002 TYR A 796 ARG 0.008 0.001 ARG A 592 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.766 Fit side-chains REVERT: A 432 GLN cc_start: 0.5862 (mm110) cc_final: 0.5380 (tt0) REVERT: B 75 MET cc_start: 0.8350 (mpp) cc_final: 0.7799 (ptp) outliers start: 17 outliers final: 17 residues processed: 100 average time/residue: 0.1948 time to fit residues: 25.9163 Evaluate side-chains 98 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 818 ASN Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.0970 chunk 62 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 64 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 42 optimal weight: 0.0370 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 GLN ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.195229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.169812 restraints weight = 30476.406| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 4.76 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6593 Z= 0.194 Angle : 0.689 13.111 8934 Z= 0.338 Chirality : 0.041 0.232 1023 Planarity : 0.005 0.055 1133 Dihedral : 7.105 68.172 902 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 2.22 % Allowed : 19.58 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.45 (0.29), residues: 807 helix: 0.14 (0.27), residues: 378 sheet: -0.49 (0.54), residues: 109 loop : -2.51 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 789 HIS 0.002 0.001 HIS A 720 PHE 0.023 0.001 PHE A 738 TYR 0.014 0.001 TYR A 796 ARG 0.007 0.001 ARG A 592 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1599.72 seconds wall clock time: 29 minutes 44.53 seconds (1784.53 seconds total)