Starting phenix.real_space_refine on Sat Nov 16 00:27:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcc_36157/11_2024/8jcc_36157.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcc_36157/11_2024/8jcc_36157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcc_36157/11_2024/8jcc_36157.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcc_36157/11_2024/8jcc_36157.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcc_36157/11_2024/8jcc_36157.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcc_36157/11_2024/8jcc_36157.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 232 5.49 5 S 16 5.16 5 C 5770 2.51 5 N 1958 2.21 5 O 2382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10358 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 766 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 710 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "E" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 626 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 766 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "H" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "I" Number of atoms: 2391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2391 Classifications: {'DNA': 116} Link IDs: {'rna3p': 115} Chain: "J" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2365 Classifications: {'DNA': 116} Link IDs: {'rna3p': 115} Time building chain proxies: 6.04, per 1000 atoms: 0.58 Number of scatterers: 10358 At special positions: 0 Unit cell: (83.74, 114.48, 115.54, 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 16 16.00 P 232 15.00 O 2382 8.00 N 1958 7.00 C 5770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.85 Conformation dependent library (CDL) restraints added in 721.6 milliseconds 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1316 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 75.7% alpha, 3.1% beta 114 base pairs and 199 stacking pairs defined. Time for finding SS restraints: 5.00 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.894A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.911A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 31 through 42 removed outlier: 4.044A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.968A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.650A pdb=" N ASN C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.343A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.608A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 58 through 68 Processing helix chain 'D' and resid 76 through 105 Processing helix chain 'D' and resid 111 through 123 removed outlier: 3.578A pdb=" N ALA D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU D 121 " --> pdb=" O MET D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.801A pdb=" N LYS D 129 " --> pdb=" O GLY D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 147 removed outlier: 3.729A pdb=" N ALA D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.005A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.611A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.843A pdb=" N TYR F 88 " --> pdb=" O MET F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 38 removed outlier: 3.683A pdb=" N ASN G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.275A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.628A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 58 through 71 Processing helix chain 'H' and resid 76 through 105 removed outlier: 3.523A pdb=" N THR H 105 " --> pdb=" O LEU H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 123 removed outlier: 3.598A pdb=" N VAL H 119 " --> pdb=" O THR H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 144 Processing helix chain 'H' and resid 145 through 147 No H-bonds generated for 'chain 'H' and resid 145 through 147' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.641A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.378A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.671A pdb=" N ARG C 42 " --> pdb=" O ILE D 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.839A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.385A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.443A pdb=" N ARG G 42 " --> pdb=" O ILE H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 379 hydrogen bonds defined for protein. 1125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 297 hydrogen bonds 594 hydrogen bond angles 0 basepair planarities 114 basepair parallelities 199 stacking parallelities Total time for adding SS restraints: 4.29 Time building geometry restraints manager: 3.27 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: 1956 1.33 - 1.45: 3509 1.45 - 1.57: 5046 1.57 - 1.69: 462 1.69 - 1.81: 28 Bond restraints: 11001 Sorted by residual: bond pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.44e+00 bond pdb=" C3' DA I -38 " pdb=" O3' DA I -38 " ideal model delta sigma weight residual 1.422 1.452 -0.030 3.00e-02 1.11e+03 9.96e-01 bond pdb=" CB ILE A 74 " pdb=" CG2 ILE A 74 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.35e-01 bond pdb=" C3' DC J 4 " pdb=" O3' DC J 4 " ideal model delta sigma weight residual 1.422 1.450 -0.028 3.00e-02 1.11e+03 8.67e-01 bond pdb=" C4' DG I -35 " pdb=" C3' DG I -35 " ideal model delta sigma weight residual 1.523 1.504 0.019 2.00e-02 2.50e+03 8.61e-01 ... (remaining 10996 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 15524 1.88 - 3.76: 287 3.76 - 5.64: 24 5.64 - 7.52: 5 7.52 - 9.40: 3 Bond angle restraints: 15843 Sorted by residual: angle pdb=" O3' DG I 4 " pdb=" C3' DG I 4 " pdb=" C2' DG I 4 " ideal model delta sigma weight residual 111.50 105.19 6.31 1.50e+00 4.44e-01 1.77e+01 angle pdb=" O3' DA J -25 " pdb=" C3' DA J -25 " pdb=" C2' DA J -25 " ideal model delta sigma weight residual 111.50 106.11 5.39 1.50e+00 4.44e-01 1.29e+01 angle pdb=" O3' DA J 16 " pdb=" C3' DA J 16 " pdb=" C2' DA J 16 " ideal model delta sigma weight residual 111.50 106.50 5.00 1.50e+00 4.44e-01 1.11e+01 angle pdb=" CB MET H 117 " pdb=" CG MET H 117 " pdb=" SD MET H 117 " ideal model delta sigma weight residual 112.70 122.10 -9.40 3.00e+00 1.11e-01 9.81e+00 angle pdb=" O3' DC I -27 " pdb=" C3' DC I -27 " pdb=" C2' DC I -27 " ideal model delta sigma weight residual 111.50 106.87 4.63 1.50e+00 4.44e-01 9.54e+00 ... (remaining 15838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 4792 35.78 - 71.55: 1192 71.55 - 107.33: 16 107.33 - 143.10: 2 143.10 - 178.88: 1 Dihedral angle restraints: 6003 sinusoidal: 3967 harmonic: 2036 Sorted by residual: dihedral pdb=" C4' DT I -17 " pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " pdb=" P DT I -16 " ideal model delta sinusoidal sigma weight residual 220.00 41.12 178.88 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC J 4 " pdb=" C3' DC J 4 " pdb=" O3' DC J 4 " pdb=" P DC J 5 " ideal model delta sinusoidal sigma weight residual 220.00 88.74 131.26 1 3.50e+01 8.16e-04 1.30e+01 dihedral pdb=" C4' DA I -38 " pdb=" C3' DA I -38 " pdb=" O3' DA I -38 " pdb=" P DG I -37 " ideal model delta sinusoidal sigma weight residual 220.00 97.11 122.89 1 3.50e+01 8.16e-04 1.21e+01 ... (remaining 6000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1426 0.041 - 0.082: 322 0.082 - 0.122: 56 0.122 - 0.163: 8 0.163 - 0.204: 3 Chirality restraints: 1815 Sorted by residual: chirality pdb=" CB ILE H 110 " pdb=" CA ILE H 110 " pdb=" CG1 ILE H 110 " pdb=" CG2 ILE H 110 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C3' DA J -25 " pdb=" C4' DA J -25 " pdb=" O3' DA J -25 " pdb=" C2' DA J -25 " both_signs ideal model delta sigma weight residual False -2.66 -2.83 0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" C3' DG I 4 " pdb=" C4' DG I 4 " pdb=" O3' DG I 4 " pdb=" C2' DG I 4 " both_signs ideal model delta sigma weight residual False -2.66 -2.83 0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 1812 not shown) Planarity restraints: 1203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " 0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO A 43 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -5 " 0.025 2.00e-02 2.50e+03 1.08e-02 3.49e+00 pdb=" N9 DG I -5 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DG I -5 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I -5 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG I -5 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG I -5 " 0.005 2.00e-02 2.50e+03 pdb=" O6 DG I -5 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DG I -5 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I -5 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I -5 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I -5 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I -5 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -35 " -0.024 2.00e-02 2.50e+03 9.74e-03 2.84e+00 pdb=" N9 DG I -35 " 0.020 2.00e-02 2.50e+03 pdb=" C8 DG I -35 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DG I -35 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG I -35 " -0.002 2.00e-02 2.50e+03 pdb=" O6 DG I -35 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I -35 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I -35 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I -35 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG I -35 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG I -35 " 0.002 2.00e-02 2.50e+03 ... (remaining 1200 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1893 2.78 - 3.31: 9631 3.31 - 3.84: 20427 3.84 - 4.37: 23005 4.37 - 4.90: 33585 Nonbonded interactions: 88541 Sorted by model distance: nonbonded pdb=" O ILE C 78 " pdb=" OG SER D 76 " model vdw 2.246 3.040 nonbonded pdb=" OG SER H 57 " pdb=" OD2 ASP H 84 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 89 " model vdw 2.274 3.040 nonbonded pdb=" O ILE A 119 " pdb=" OG SER B 47 " model vdw 2.284 3.040 nonbonded pdb=" OG SER D 85 " pdb=" O GLY F 101 " model vdw 2.290 3.040 ... (remaining 88536 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 15 through 105) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 56 through 147) } 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: 0.420 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.290 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 : 0.005 0.037 11001 Z= 0.274 Angle : 0.600 9.395 15843 Z= 0.346 Chirality : 0.036 0.204 1815 Planarity : 0.004 0.054 1203 Dihedral : 28.833 178.878 4687 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.34 % Allowed : 31.62 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.32), residues: 691 helix: 1.75 (0.23), residues: 525 sheet: None (None), residues: 0 loop : -1.39 (0.42), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 113 HIS 0.003 0.001 HIS H 70 PHE 0.007 0.001 PHE D 58 TYR 0.011 0.001 TYR D 145 ARG 0.005 0.000 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 325 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ASN cc_start: 0.7118 (t0) cc_final: 0.6514 (t0) REVERT: C 57 TYR cc_start: 0.7832 (t80) cc_final: 0.7582 (t80) REVERT: G 61 GLU cc_start: 0.6135 (tt0) cc_final: 0.5169 (tt0) REVERT: H 108 GLN cc_start: 0.7506 (pt0) cc_final: 0.6928 (pt0) outliers start: 2 outliers final: 1 residues processed: 326 average time/residue: 0.3259 time to fit residues: 134.5055 Evaluate side-chains 256 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 255 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN D 70 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11001 Z= 0.247 Angle : 0.630 5.988 15843 Z= 0.363 Chirality : 0.036 0.377 1815 Planarity : 0.005 0.053 1203 Dihedral : 30.321 178.452 3304 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 6.15 % Allowed : 34.70 % Favored : 59.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.33), residues: 691 helix: 1.93 (0.23), residues: 531 sheet: None (None), residues: 0 loop : -1.28 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 113 HIS 0.005 0.001 HIS E 113 PHE 0.022 0.002 PHE D 62 TYR 0.015 0.002 TYR B 98 ARG 0.012 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ASN cc_start: 0.7411 (t0) cc_final: 0.7172 (t0) REVERT: C 42 ARG cc_start: 0.8154 (mtp180) cc_final: 0.7736 (mmm-85) REVERT: C 61 GLU cc_start: 0.7183 (tt0) cc_final: 0.6865 (tt0) REVERT: C 77 ARG cc_start: 0.6588 (OUTLIER) cc_final: 0.6014 (mtt180) REVERT: C 104 GLN cc_start: 0.8128 (mp10) cc_final: 0.7871 (mp10) outliers start: 36 outliers final: 12 residues processed: 286 average time/residue: 0.2992 time to fit residues: 110.4188 Evaluate side-chains 247 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 234 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 68 GLN A 108 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 94 ASN G 112 GLN H 108 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11001 Z= 0.286 Angle : 0.650 9.688 15843 Z= 0.375 Chirality : 0.037 0.328 1815 Planarity : 0.005 0.052 1203 Dihedral : 30.403 177.993 3304 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.62 % Allowed : 36.24 % Favored : 59.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.32), residues: 691 helix: 1.76 (0.23), residues: 531 sheet: None (None), residues: 0 loop : -1.30 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 113 HIS 0.006 0.001 HIS E 113 PHE 0.014 0.001 PHE D 62 TYR 0.017 0.002 TYR C 57 ARG 0.011 0.001 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 246 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ASN cc_start: 0.7474 (t0) cc_final: 0.7136 (t0) REVERT: C 42 ARG cc_start: 0.8113 (mtp180) cc_final: 0.7793 (mmm-85) REVERT: C 57 TYR cc_start: 0.7744 (t80) cc_final: 0.7385 (t80) REVERT: D 126 GLN cc_start: 0.7152 (tp-100) cc_final: 0.6544 (tp-100) REVERT: F 97 LEU cc_start: 0.8994 (tp) cc_final: 0.8731 (tt) REVERT: H 84 ASP cc_start: 0.7054 (OUTLIER) cc_final: 0.6833 (m-30) outliers start: 27 outliers final: 16 residues processed: 256 average time/residue: 0.3048 time to fit residues: 100.6186 Evaluate side-chains 243 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 226 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN B 25 ASN C 84 GLN E 108 ASN E 113 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11001 Z= 0.213 Angle : 0.631 7.997 15843 Z= 0.364 Chirality : 0.036 0.262 1815 Planarity : 0.004 0.052 1203 Dihedral : 30.371 178.550 3302 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.79 % Allowed : 34.70 % Favored : 60.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.32), residues: 691 helix: 1.72 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -1.17 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 113 HIS 0.006 0.001 HIS E 113 PHE 0.011 0.001 PHE D 62 TYR 0.021 0.002 TYR F 98 ARG 0.007 0.001 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 251 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ASN cc_start: 0.7560 (t0) cc_final: 0.7220 (t0) REVERT: H 84 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.6782 (m-30) outliers start: 28 outliers final: 17 residues processed: 265 average time/residue: 0.2837 time to fit residues: 98.1862 Evaluate side-chains 243 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 225 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 59 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN C 94 ASN E 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11001 Z= 0.266 Angle : 0.660 11.389 15843 Z= 0.377 Chirality : 0.037 0.361 1815 Planarity : 0.005 0.052 1203 Dihedral : 30.431 178.142 3302 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 6.50 % Allowed : 35.90 % Favored : 57.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.32), residues: 691 helix: 1.61 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -1.28 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP H 113 HIS 0.003 0.001 HIS F 75 PHE 0.021 0.001 PHE D 62 TYR 0.022 0.002 TYR F 98 ARG 0.008 0.001 ARG H 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 242 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ASN cc_start: 0.7736 (t0) cc_final: 0.7426 (t0) REVERT: H 84 ASP cc_start: 0.7056 (OUTLIER) cc_final: 0.6810 (m-30) outliers start: 38 outliers final: 26 residues processed: 256 average time/residue: 0.2724 time to fit residues: 92.0698 Evaluate side-chains 258 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 231 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Chi-restraints excluded: chain H residue 147 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 9 optimal weight: 0.0870 chunk 49 optimal weight: 4.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 113 HIS C 24 GLN C 84 GLN E 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11001 Z= 0.233 Angle : 0.651 8.439 15843 Z= 0.374 Chirality : 0.036 0.318 1815 Planarity : 0.005 0.052 1203 Dihedral : 30.391 178.635 3302 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 5.47 % Allowed : 38.12 % Favored : 56.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.32), residues: 691 helix: 1.63 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -1.27 (0.43), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 113 HIS 0.003 0.001 HIS F 75 PHE 0.015 0.001 PHE D 62 TYR 0.021 0.002 TYR C 57 ARG 0.011 0.001 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 241 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ASN cc_start: 0.7682 (t0) cc_final: 0.7415 (t0) REVERT: C 57 TYR cc_start: 0.7769 (t80) cc_final: 0.7261 (t80) REVERT: C 104 GLN cc_start: 0.8145 (mp10) cc_final: 0.7945 (mp10) REVERT: H 84 ASP cc_start: 0.7025 (OUTLIER) cc_final: 0.6791 (m-30) outliers start: 32 outliers final: 24 residues processed: 253 average time/residue: 0.2856 time to fit residues: 94.2569 Evaluate side-chains 250 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 225 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 0.0870 chunk 72 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 52 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.0470 chunk 51 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 113 HIS B 75 HIS C 84 GLN E 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11001 Z= 0.207 Angle : 0.677 12.867 15843 Z= 0.381 Chirality : 0.036 0.340 1815 Planarity : 0.005 0.052 1203 Dihedral : 30.236 178.953 3302 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.96 % Allowed : 38.46 % Favored : 56.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.32), residues: 691 helix: 1.56 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -1.18 (0.43), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 113 HIS 0.003 0.001 HIS F 75 PHE 0.036 0.002 PHE D 62 TYR 0.017 0.002 TYR H 61 ARG 0.015 0.001 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 245 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ASN cc_start: 0.7579 (t0) cc_final: 0.7358 (t0) REVERT: C 57 TYR cc_start: 0.7884 (t80) cc_final: 0.7556 (t80) REVERT: H 84 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6665 (m-30) outliers start: 29 outliers final: 16 residues processed: 258 average time/residue: 0.2750 time to fit residues: 92.7580 Evaluate side-chains 245 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 228 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 67 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 75 HIS E 68 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN E 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11001 Z= 0.274 Angle : 0.691 8.607 15843 Z= 0.392 Chirality : 0.037 0.312 1815 Planarity : 0.005 0.049 1203 Dihedral : 30.370 178.016 3302 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.30 % Allowed : 39.49 % Favored : 55.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.32), residues: 691 helix: 1.55 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -1.22 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 113 HIS 0.003 0.001 HIS F 75 PHE 0.028 0.002 PHE D 62 TYR 0.019 0.002 TYR C 57 ARG 0.012 0.001 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 216 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 TYR cc_start: 0.7872 (t80) cc_final: 0.7515 (t80) REVERT: H 84 ASP cc_start: 0.7017 (OUTLIER) cc_final: 0.6740 (m-30) outliers start: 31 outliers final: 21 residues processed: 232 average time/residue: 0.2714 time to fit residues: 83.5202 Evaluate side-chains 228 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN C 38 ASN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN E 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11001 Z= 0.216 Angle : 0.700 11.324 15843 Z= 0.391 Chirality : 0.037 0.323 1815 Planarity : 0.005 0.049 1203 Dihedral : 30.264 178.900 3302 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.42 % Allowed : 41.37 % Favored : 55.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.32), residues: 691 helix: 1.43 (0.23), residues: 531 sheet: None (None), residues: 0 loop : -1.28 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 113 HIS 0.003 0.001 HIS B 75 PHE 0.026 0.001 PHE D 62 TYR 0.018 0.002 TYR H 61 ARG 0.008 0.001 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 GLU cc_start: 0.7055 (pp20) cc_final: 0.6835 (pp20) REVERT: G 94 ASN cc_start: 0.7061 (t0) cc_final: 0.6815 (t0) REVERT: H 84 ASP cc_start: 0.6960 (OUTLIER) cc_final: 0.6669 (m-30) outliers start: 20 outliers final: 16 residues processed: 234 average time/residue: 0.2780 time to fit residues: 85.5182 Evaluate side-chains 237 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 220 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN C 38 ASN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN E 108 ASN G 38 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 11001 Z= 0.399 Angle : 0.766 9.345 15843 Z= 0.432 Chirality : 0.041 0.305 1815 Planarity : 0.006 0.049 1203 Dihedral : 30.616 177.084 3302 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.27 % Allowed : 40.51 % Favored : 55.21 % 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: 691 helix: 1.20 (0.23), residues: 531 sheet: None (None), residues: 0 loop : -1.48 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 113 HIS 0.008 0.001 HIS B 75 PHE 0.047 0.003 PHE D 62 TYR 0.039 0.003 TYR C 57 ARG 0.010 0.001 ARG D 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 TYR cc_start: 0.7772 (t80) cc_final: 0.7503 (t80) REVERT: F 24 ASP cc_start: 0.7388 (p0) cc_final: 0.6867 (p0) outliers start: 25 outliers final: 24 residues processed: 218 average time/residue: 0.2675 time to fit residues: 77.7684 Evaluate side-chains 222 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN C 38 ASN ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.047835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.034377 restraints weight = 57057.206| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 3.77 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11001 Z= 0.249 Angle : 0.753 12.645 15843 Z= 0.416 Chirality : 0.038 0.295 1815 Planarity : 0.005 0.049 1203 Dihedral : 30.567 178.677 3302 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.59 % Allowed : 42.74 % Favored : 53.68 % 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: 0.78 (0.31), residues: 691 helix: 1.14 (0.23), residues: 531 sheet: None (None), residues: 0 loop : -1.49 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 113 HIS 0.003 0.001 HIS F 75 PHE 0.056 0.002 PHE D 62 TYR 0.033 0.002 TYR C 57 ARG 0.008 0.001 ARG D 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2287.31 seconds wall clock time: 42 minutes 5.82 seconds (2525.82 seconds total)