Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 15:11:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb0_32391/04_2023/7wb0_32391.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb0_32391/04_2023/7wb0_32391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb0_32391/04_2023/7wb0_32391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb0_32391/04_2023/7wb0_32391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb0_32391/04_2023/7wb0_32391.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb0_32391/04_2023/7wb0_32391.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.054 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: 5 Type Number sf(0) Gaussians P 175 5.49 5 S 24 5.16 5 C 5765 2.51 5 N 1804 2.21 5 O 2328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "A ASP 522": "OD1" <-> "OD2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 605": "OE1" <-> "OE2" Residue "A GLU 630": "OE1" <-> "OE2" Residue "A TYR 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 781": "OD1" <-> "OD2" Residue "A GLU 790": "OE1" <-> "OE2" Residue "A PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 960": "OE1" <-> "OE2" Residue "A GLU 972": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 10096 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 674 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "C" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 547 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "D" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2446 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 8, 'rna3p_pur': 55, 'rna3p_pyr': 47} Link IDs: {'rna2p': 13, 'rna3p': 101} Chain breaks: 1 Chain: "A" Number of atoms: 6429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6429 Classifications: {'peptide': 797} Link IDs: {'PTRANS': 35, 'TRANS': 761} Chain breaks: 4 Time building chain proxies: 6.21, per 1000 atoms: 0.62 Number of scatterers: 10096 At special positions: 0 Unit cell: (104.34, 141, 125.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 175 15.00 O 2328 8.00 N 1804 7.00 C 5765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 810 " - pdb=" SG CYS A 912 " 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: 5.03 Conformation dependent library (CDL) restraints added in 994.8 milliseconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 10 sheets defined 40.8% alpha, 18.4% beta 55 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 60 through 92 Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.618A pdb=" N LEU A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.533A pdb=" N HIS A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 221 through 272 removed outlier: 3.662A pdb=" N VAL A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 309 Processing helix chain 'A' and resid 589 through 596 Processing helix chain 'A' and resid 647 through 650 removed outlier: 3.590A pdb=" N ILE A 650 " --> pdb=" O SER A 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 647 through 650' Processing helix chain 'A' and resid 697 through 717 removed outlier: 3.645A pdb=" N LYS A 701 " --> pdb=" O SER A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 724 Processing helix chain 'A' and resid 725 through 750 Processing helix chain 'A' and resid 770 through 774 removed outlier: 3.539A pdb=" N ARG A 774 " --> pdb=" O MET A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 790 removed outlier: 3.998A pdb=" N GLU A 790 " --> pdb=" O LYS A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 821 through 829 removed outlier: 3.681A pdb=" N VAL A 825 " --> pdb=" O ASP A 821 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 875 Processing helix chain 'A' and resid 881 through 885 removed outlier: 3.596A pdb=" N SER A 884 " --> pdb=" O ASP A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 898 Processing helix chain 'A' and resid 921 through 936 removed outlier: 3.569A pdb=" N ALA A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 951 removed outlier: 3.649A pdb=" N LYS A 942 " --> pdb=" O SER A 938 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 950 " --> pdb=" O THR A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 973 removed outlier: 3.708A pdb=" N VAL A 959 " --> pdb=" O LYS A 955 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 502 through 506 removed outlier: 3.928A pdb=" N GLY A 614 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU A 611 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU A 640 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN A 613 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU A 633 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.988A pdb=" N ILE A 114 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE A 128 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.988A pdb=" N ILE A 114 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 10.536A pdb=" N THR A 153 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR A 155 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 543 through 545 removed outlier: 3.671A pdb=" N LYS A 544 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 571 " --> pdb=" O LYS A 544 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE A 556 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N VAL A 559 " --> pdb=" O PHE A 517 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE A 517 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ASN A 561 " --> pdb=" O CYS A 515 " (cutoff:3.500A) removed outlier: 12.726A pdb=" N CYS A 515 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 516 " --> pdb=" O ILE A 532 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 691 through 694 removed outlier: 3.663A pdb=" N ALA A 666 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN A 654 " --> pdb=" O MET A 752 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE A 754 " --> pdb=" O ASN A 654 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE A 656 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ALA A 756 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N ILE A 658 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR A 801 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE A 755 " --> pdb=" O THR A 801 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 Processing sheet with id=AA8, first strand: chain 'A' and resid 831 through 832 removed outlier: 3.551A pdb=" N THR A 838 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 850 through 855 removed outlier: 3.583A pdb=" N TYR A 853 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 862 " --> pdb=" O TYR A 853 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 909 through 911 298 hydrogen bonds defined for protein. 849 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 137 hydrogen bonds 266 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 4.85 Time building geometry restraints manager: 5.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2062 1.33 - 1.45: 3183 1.45 - 1.57: 5025 1.57 - 1.69: 346 1.69 - 1.81: 36 Bond restraints: 10652 Sorted by residual: bond pdb=" CA ASP A 522 " pdb=" CB ASP A 522 " ideal model delta sigma weight residual 1.522 1.539 -0.017 1.27e-02 6.20e+03 1.88e+00 bond pdb=" C ALA A 320 " pdb=" N LYS A 321 " ideal model delta sigma weight residual 1.331 1.357 -0.026 2.07e-02 2.33e+03 1.63e+00 bond pdb=" C LYS A 210 " pdb=" O LYS A 210 " ideal model delta sigma weight residual 1.249 1.239 0.010 8.50e-03 1.38e+04 1.45e+00 bond pdb=" CG GLN A 702 " pdb=" CD GLN A 702 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.43e+00 bond pdb=" CA ASN A 528 " pdb=" C ASN A 528 " ideal model delta sigma weight residual 1.522 1.534 -0.013 1.08e-02 8.57e+03 1.35e+00 ... (remaining 10647 not shown) Histogram of bond angle deviations from ideal: 99.87 - 106.72: 1168 106.72 - 113.57: 5974 113.57 - 120.41: 4074 120.41 - 127.26: 3588 127.26 - 134.11: 371 Bond angle restraints: 15175 Sorted by residual: angle pdb=" C LYS A 899 " pdb=" N ARG A 900 " pdb=" CA ARG A 900 " ideal model delta sigma weight residual 121.54 127.66 -6.12 1.91e+00 2.74e-01 1.03e+01 angle pdb=" C LYS A 701 " pdb=" N GLN A 702 " pdb=" CA GLN A 702 " ideal model delta sigma weight residual 120.72 115.48 5.24 1.67e+00 3.59e-01 9.83e+00 angle pdb=" C LEU A 529 " pdb=" N TYR A 530 " pdb=" CA TYR A 530 " ideal model delta sigma weight residual 121.87 126.97 -5.10 1.64e+00 3.72e-01 9.67e+00 angle pdb=" C PHE A 901 " pdb=" N SER A 902 " pdb=" CA SER A 902 " ideal model delta sigma weight residual 122.56 117.92 4.64 1.50e+00 4.44e-01 9.58e+00 angle pdb=" N GLN A 702 " pdb=" CA GLN A 702 " pdb=" CB GLN A 702 " ideal model delta sigma weight residual 110.39 115.51 -5.12 1.66e+00 3.63e-01 9.53e+00 ... (remaining 15170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.54: 5515 29.54 - 59.07: 445 59.07 - 88.61: 42 88.61 - 118.14: 2 118.14 - 147.68: 1 Dihedral angle restraints: 6005 sinusoidal: 3679 harmonic: 2326 Sorted by residual: dihedral pdb=" O4' U D 17 " pdb=" C1' U D 17 " pdb=" N1 U D 17 " pdb=" C2 U D 17 " ideal model delta sinusoidal sigma weight residual 232.00 84.32 147.68 1 1.70e+01 3.46e-03 6.13e+01 dihedral pdb=" CA HIS A 903 " pdb=" C HIS A 903 " pdb=" N ARG A 904 " pdb=" CA ARG A 904 " ideal model delta harmonic sigma weight residual -180.00 -160.13 -19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA PRO A 333 " pdb=" C PRO A 333 " pdb=" N LEU A 334 " pdb=" CA LEU A 334 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 6002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1355 0.033 - 0.067: 313 0.067 - 0.100: 72 0.100 - 0.133: 36 0.133 - 0.166: 2 Chirality restraints: 1778 Sorted by residual: chirality pdb=" CB THR A 953 " pdb=" CA THR A 953 " pdb=" OG1 THR A 953 " pdb=" CG2 THR A 953 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CB ILE A 114 " pdb=" CA ILE A 114 " pdb=" CG1 ILE A 114 " pdb=" CG2 ILE A 114 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CA VAL A 667 " pdb=" N VAL A 667 " pdb=" C VAL A 667 " pdb=" CB VAL A 667 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 1775 not shown) Planarity restraints: 1303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 889 " 0.164 9.50e-02 1.11e+02 7.37e-02 3.41e+00 pdb=" NE ARG A 889 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 889 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 889 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 889 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U D 20 " 0.020 2.00e-02 2.50e+03 1.04e-02 2.44e+00 pdb=" N1 U D 20 " -0.022 2.00e-02 2.50e+03 pdb=" C2 U D 20 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U D 20 " -0.001 2.00e-02 2.50e+03 pdb=" N3 U D 20 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U D 20 " 0.003 2.00e-02 2.50e+03 pdb=" O4 U D 20 " 0.006 2.00e-02 2.50e+03 pdb=" C5 U D 20 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U D 20 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 38 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO A 39 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " 0.021 5.00e-02 4.00e+02 ... (remaining 1300 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 394 2.69 - 3.24: 8735 3.24 - 3.79: 16669 3.79 - 4.35: 20645 4.35 - 4.90: 31638 Nonbonded interactions: 78081 Sorted by model distance: nonbonded pdb=" OD1 ASP A 733 " pdb=" ND2 ASN A 737 " model vdw 2.136 2.520 nonbonded pdb=" OG1 THR A 38 " pdb=" OD1 ASP A 40 " model vdw 2.198 2.440 nonbonded pdb=" O6 DG B 22 " pdb=" NZ LYS A 227 " model vdw 2.246 2.520 nonbonded pdb=" O2 U D 45 " pdb=" N4 C D 46 " model vdw 2.248 2.520 nonbonded pdb=" OD1 ASN A 737 " pdb=" NH2 ARG A 740 " model vdw 2.257 2.520 ... (remaining 78076 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.630 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 33.800 Find NCS groups from input model: 0.240 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: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 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 0.030 10652 Z= 0.155 Angle : 0.579 10.444 15175 Z= 0.323 Chirality : 0.034 0.166 1778 Planarity : 0.004 0.074 1303 Dihedral : 18.374 147.677 4498 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.31), residues: 787 helix: 2.01 (0.30), residues: 297 sheet: 0.14 (0.46), residues: 134 loop : -1.01 (0.33), residues: 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.953 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2459 time to fit residues: 22.9241 Evaluate side-chains 42 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 20.0000 chunk 55 optimal weight: 0.0000 chunk 86 optimal weight: 7.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN A 804 GLN A 812 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 10652 Z= 0.153 Angle : 0.525 6.597 15175 Z= 0.281 Chirality : 0.033 0.142 1778 Planarity : 0.004 0.045 1303 Dihedral : 19.496 149.045 2844 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.32 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.31), residues: 787 helix: 2.33 (0.30), residues: 304 sheet: 0.27 (0.47), residues: 123 loop : -0.89 (0.33), residues: 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.925 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 52 average time/residue: 0.2740 time to fit residues: 19.9687 Evaluate side-chains 40 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.934 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1372 time to fit residues: 1.4674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 chunk 93 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN A 924 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 10652 Z= 0.272 Angle : 0.597 7.492 15175 Z= 0.319 Chirality : 0.037 0.144 1778 Planarity : 0.004 0.041 1303 Dihedral : 19.592 139.100 2844 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.83 % Favored : 95.04 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.31), residues: 787 helix: 2.09 (0.30), residues: 304 sheet: -0.27 (0.45), residues: 135 loop : -1.04 (0.33), residues: 348 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.884 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 56 average time/residue: 0.2679 time to fit residues: 21.0438 Evaluate side-chains 42 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1078 time to fit residues: 1.5365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 10652 Z= 0.141 Angle : 0.507 7.056 15175 Z= 0.274 Chirality : 0.033 0.132 1778 Planarity : 0.004 0.054 1303 Dihedral : 19.492 142.802 2844 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.31), residues: 787 helix: 2.38 (0.30), residues: 304 sheet: -0.26 (0.46), residues: 133 loop : -0.92 (0.33), residues: 350 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.931 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 53 average time/residue: 0.3146 time to fit residues: 22.8098 Evaluate side-chains 48 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1297 time to fit residues: 1.9917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 10652 Z= 0.319 Angle : 0.643 8.083 15175 Z= 0.345 Chirality : 0.038 0.163 1778 Planarity : 0.006 0.141 1303 Dihedral : 19.714 135.198 2844 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.97 % Favored : 93.90 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.31), residues: 787 helix: 2.01 (0.31), residues: 297 sheet: -0.30 (0.46), residues: 133 loop : -1.30 (0.32), residues: 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 52 time to evaluate : 0.967 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 65 average time/residue: 0.2829 time to fit residues: 25.4668 Evaluate side-chains 48 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1069 time to fit residues: 2.3623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN A 520 GLN ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 10652 Z= 0.167 Angle : 0.538 7.778 15175 Z= 0.292 Chirality : 0.035 0.178 1778 Planarity : 0.004 0.046 1303 Dihedral : 19.599 138.138 2844 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.94 % Favored : 95.93 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.31), residues: 787 helix: 2.11 (0.31), residues: 304 sheet: -0.36 (0.46), residues: 131 loop : -1.08 (0.33), residues: 352 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.937 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.2976 time to fit residues: 21.0729 Evaluate side-chains 44 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0955 time to fit residues: 1.5621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 77 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 10652 Z= 0.261 Angle : 0.591 8.453 15175 Z= 0.318 Chirality : 0.037 0.145 1778 Planarity : 0.004 0.049 1303 Dihedral : 19.693 135.958 2844 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.34 % Favored : 94.54 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.31), residues: 787 helix: 2.00 (0.31), residues: 304 sheet: -0.54 (0.45), residues: 135 loop : -1.19 (0.34), residues: 348 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.949 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 55 average time/residue: 0.3398 time to fit residues: 24.9285 Evaluate side-chains 51 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1189 time to fit residues: 2.6068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 87 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 10652 Z= 0.230 Angle : 0.578 8.747 15175 Z= 0.314 Chirality : 0.036 0.151 1778 Planarity : 0.004 0.052 1303 Dihedral : 19.665 136.626 2844 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.34 % Favored : 94.54 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.31), residues: 787 helix: 1.94 (0.31), residues: 304 sheet: -0.57 (0.45), residues: 135 loop : -1.14 (0.34), residues: 348 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.957 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 47 average time/residue: 0.3528 time to fit residues: 22.1130 Evaluate side-chains 47 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1249 time to fit residues: 1.4642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 0.0270 chunk 80 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 10652 Z= 0.172 Angle : 0.546 8.936 15175 Z= 0.296 Chirality : 0.034 0.133 1778 Planarity : 0.004 0.051 1303 Dihedral : 19.584 139.175 2844 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.83 % Favored : 95.04 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.31), residues: 787 helix: 2.19 (0.31), residues: 299 sheet: -0.47 (0.45), residues: 135 loop : -1.10 (0.33), residues: 353 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.842 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 52 average time/residue: 0.3198 time to fit residues: 22.3554 Evaluate side-chains 49 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.976 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 10652 Z= 0.259 Angle : 0.603 8.999 15175 Z= 0.324 Chirality : 0.037 0.144 1778 Planarity : 0.004 0.048 1303 Dihedral : 19.642 136.797 2844 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.10 % Favored : 93.77 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.31), residues: 787 helix: 2.05 (0.31), residues: 299 sheet: -0.65 (0.45), residues: 135 loop : -1.21 (0.33), residues: 353 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.956 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 47 average time/residue: 0.3489 time to fit residues: 22.0053 Evaluate side-chains 44 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1191 time to fit residues: 1.6611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 20 optimal weight: 0.0980 chunk 75 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 66 optimal weight: 0.4980 chunk 4 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.169813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.123257 restraints weight = 21963.258| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.88 r_work: 0.3564 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 10652 Z= 0.167 Angle : 0.556 9.886 15175 Z= 0.299 Chirality : 0.034 0.134 1778 Planarity : 0.004 0.047 1303 Dihedral : 19.589 138.946 2844 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.19 % Favored : 95.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.31), residues: 787 helix: 2.21 (0.31), residues: 299 sheet: -0.60 (0.45), residues: 135 loop : -1.14 (0.33), residues: 353 =============================================================================== Job complete usr+sys time: 1893.06 seconds wall clock time: 35 minutes 11.44 seconds (2111.44 seconds total)