Starting phenix.real_space_refine on Mon Dec 30 12:22:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ohb_12899/12_2024/7ohb_12899.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ohb_12899/12_2024/7ohb_12899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ohb_12899/12_2024/7ohb_12899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ohb_12899/12_2024/7ohb_12899.map" model { file = "/net/cci-nas-00/data/ceres_data/7ohb_12899/12_2024/7ohb_12899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ohb_12899/12_2024/7ohb_12899.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 290 5.49 5 S 18 5.16 5 C 7560 2.51 5 N 2501 2.21 5 O 3055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13424 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 756 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 171} Time building chain proxies: 7.98, per 1000 atoms: 0.59 Number of scatterers: 13424 At special positions: 0 Unit cell: (92.4, 116.55, 133.35, 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 18 16.00 P 290 15.00 O 3055 8.00 N 2501 7.00 C 7560 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: 3.33 Conformation dependent library (CDL) restraints added in 1.2 seconds 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 10 sheets defined 64.8% alpha, 7.2% beta 144 base pairs and 266 stacking pairs defined. Time for finding SS restraints: 7.16 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.991A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.807A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.318A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.144A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.400A 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 131 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.853A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.563A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.590A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.377A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'K' and resid 81 through 88 removed outlier: 3.649A pdb=" N VAL K 85 " --> pdb=" O ASP K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 147 Processing helix chain 'K' and resid 171 through 179 removed outlier: 3.599A pdb=" N LEU K 175 " --> pdb=" O ARG K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 219 through 236 removed outlier: 4.087A pdb=" N ILE K 223 " --> pdb=" O GLN K 219 " (cutoff:3.500A) Proline residue: K 232 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.004A 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 98 removed outlier: 6.471A 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: 7.132A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.998A 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: 7.512A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 92 through 93 removed outlier: 3.602A pdb=" N VAL K 102 " --> pdb=" O ILE K 115 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR K 124 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS K 120 " --> pdb=" O PHE K 116 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY K 125 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ILE K 70 " --> pdb=" O GLY K 125 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL K 161 " --> pdb=" O GLN K 68 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE K 70 " --> pdb=" O ASN K 159 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASN K 159 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA K 72 " --> pdb=" O ILE K 157 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE K 157 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL K 74 " --> pdb=" O PHE K 155 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE K 155 " --> pdb=" O VAL K 74 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE K 212 " --> pdb=" O CYS K 164 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL K 213 " --> pdb=" O LEU K 205 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU K 205 " --> pdb=" O VAL K 213 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR K 215 " --> pdb=" O VAL K 203 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL K 203 " --> pdb=" O THR K 215 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1389 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 266 stacking parallelities Total time for adding SS restraints: 6.09 Time building geometry restraints manager: 3.87 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: 2665 1.33 - 1.45: 4528 1.45 - 1.57: 6451 1.57 - 1.69: 578 1.69 - 1.82: 32 Bond restraints: 14254 Sorted by residual: bond pdb=" C3' DT I 60 " pdb=" O3' DT I 60 " ideal model delta sigma weight residual 1.422 1.519 -0.097 3.00e-02 1.11e+03 1.05e+01 bond pdb=" O5' DA I 61 " pdb=" C5' DA I 61 " ideal model delta sigma weight residual 1.423 1.468 -0.045 3.00e-02 1.11e+03 2.30e+00 bond pdb=" C5' DA I 61 " pdb=" C4' DA I 61 " ideal model delta sigma weight residual 1.518 1.548 -0.030 2.00e-02 2.50e+03 2.23e+00 bond pdb=" CB VAL A 46 " pdb=" CG1 VAL A 46 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.13e+00 bond pdb=" CB VAL E 46 " pdb=" CG1 VAL E 46 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.02e+00 ... (remaining 14249 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 19692 2.06 - 4.11: 711 4.11 - 6.17: 64 6.17 - 8.22: 16 8.22 - 10.28: 3 Bond angle restraints: 20486 Sorted by residual: angle pdb=" CB ARG B 40 " pdb=" CG ARG B 40 " pdb=" CD ARG B 40 " ideal model delta sigma weight residual 111.30 121.58 -10.28 2.30e+00 1.89e-01 2.00e+01 angle pdb=" C ASN G 73 " pdb=" N LYS G 74 " pdb=" CA LYS G 74 " ideal model delta sigma weight residual 122.40 127.54 -5.14 1.45e+00 4.76e-01 1.26e+01 angle pdb=" O3' DT I 60 " pdb=" C3' DT I 60 " pdb=" C2' DT I 60 " ideal model delta sigma weight residual 111.50 116.71 -5.21 1.50e+00 4.44e-01 1.21e+01 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 113.18 121.37 -8.19 2.37e+00 1.78e-01 1.19e+01 angle pdb=" CB LYS G 15 " pdb=" CG LYS G 15 " pdb=" CD LYS G 15 " ideal model delta sigma weight residual 111.30 119.22 -7.92 2.30e+00 1.89e-01 1.19e+01 ... (remaining 20481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.96: 5269 20.96 - 41.91: 1340 41.91 - 62.87: 1178 62.87 - 83.83: 66 83.83 - 104.78: 6 Dihedral angle restraints: 7859 sinusoidal: 5121 harmonic: 2738 Sorted by residual: dihedral pdb=" CA GLU K 108 " pdb=" C GLU K 108 " pdb=" N PRO K 109 " pdb=" CA PRO K 109 " ideal model delta harmonic sigma weight residual 0.00 -39.57 39.57 0 5.00e+00 4.00e-02 6.26e+01 dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual -180.00 -158.58 -21.42 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA LYS K 199 " pdb=" C LYS K 199 " pdb=" N PRO K 200 " pdb=" CA PRO K 200 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 7856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2073 0.080 - 0.161: 242 0.161 - 0.241: 17 0.241 - 0.321: 3 0.321 - 0.402: 1 Chirality restraints: 2336 Sorted by residual: chirality pdb=" C1' DT I 60 " pdb=" O4' DT I 60 " pdb=" C2' DT I 60 " pdb=" N1 DT I 60 " both_signs ideal model delta sigma weight residual False 2.47 2.07 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CB ILE K 212 " pdb=" CA ILE K 212 " pdb=" CG1 ILE K 212 " pdb=" CG2 ILE K 212 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB THR K 111 " pdb=" CA THR K 111 " pdb=" OG1 THR K 111 " pdb=" CG2 THR K 111 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 2333 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 27 " -0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C VAL G 27 " 0.058 2.00e-02 2.50e+03 pdb=" O VAL G 27 " -0.022 2.00e-02 2.50e+03 pdb=" N GLY G 28 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 60 " 0.006 2.00e-02 2.50e+03 1.84e-02 8.44e+00 pdb=" N1 DT I 60 " -0.037 2.00e-02 2.50e+03 pdb=" C2 DT I 60 " 0.041 2.00e-02 2.50e+03 pdb=" O2 DT I 60 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DT I 60 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DT I 60 " 0.004 2.00e-02 2.50e+03 pdb=" O4 DT I 60 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DT I 60 " 0.004 2.00e-02 2.50e+03 pdb=" C7 DT I 60 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DT I 60 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.046 5.00e-02 4.00e+02 7.00e-02 7.84e+00 pdb=" N PRO G 80 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.039 5.00e-02 4.00e+02 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2703 2.78 - 3.31: 11633 3.31 - 3.84: 27034 3.84 - 4.37: 31845 4.37 - 4.90: 45229 Nonbonded interactions: 118444 Sorted by model distance: nonbonded pdb=" OG1 THR D 29 " pdb=" OP1 DT I 30 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.276 3.040 nonbonded pdb=" O GLY K 174 " pdb=" OG SER K 178 " model vdw 2.278 3.040 nonbonded pdb=" NE2 GLN G 24 " pdb=" OE1 GLN H 44 " model vdw 2.302 3.120 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.322 3.120 ... (remaining 118439 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 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 24 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 27 through 121) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 38.280 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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 0.097 14254 Z= 0.291 Angle : 0.856 10.276 20486 Z= 0.496 Chirality : 0.053 0.402 2336 Planarity : 0.007 0.070 1584 Dihedral : 28.695 104.782 6091 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.89 % Allowed : 4.32 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.23), residues: 925 helix: -1.01 (0.18), residues: 588 sheet: -0.37 (0.82), residues: 41 loop : -1.97 (0.29), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.025 0.002 PHE K 99 TYR 0.039 0.002 TYR G 50 ARG 0.012 0.001 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 192 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7946 (t0) cc_final: 0.7504 (t70) REVERT: B 25 ASN cc_start: 0.8125 (m-40) cc_final: 0.7909 (m110) REVERT: C 74 LYS cc_start: 0.8764 (mppt) cc_final: 0.8530 (mptt) REVERT: E 106 ASP cc_start: 0.7443 (m-30) cc_final: 0.7181 (m-30) REVERT: F 74 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7766 (mt-10) REVERT: G 91 GLU cc_start: 0.8048 (tt0) cc_final: 0.7820 (tt0) REVERT: H 33 SER cc_start: 0.8880 (t) cc_final: 0.8491 (p) REVERT: H 34 TYR cc_start: 0.8858 (m-80) cc_final: 0.8614 (m-80) REVERT: K 69 ASN cc_start: 0.7863 (t0) cc_final: 0.6761 (m110) REVERT: K 121 MET cc_start: 0.7527 (tpt) cc_final: 0.7034 (mtm) outliers start: 7 outliers final: 1 residues processed: 196 average time/residue: 0.3414 time to fit residues: 90.3618 Evaluate side-chains 144 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS C 110 ASN D 92 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14254 Z= 0.204 Angle : 0.597 6.829 20486 Z= 0.355 Chirality : 0.037 0.169 2336 Planarity : 0.005 0.048 1584 Dihedral : 30.914 90.219 4227 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.02 % Allowed : 10.93 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.26), residues: 925 helix: 1.08 (0.20), residues: 599 sheet: -0.09 (0.71), residues: 47 loop : -1.69 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.014 0.001 PHE K 99 TYR 0.017 0.002 TYR K 231 ARG 0.008 0.001 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 163 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8769 (pm20) cc_final: 0.8425 (pm20) REVERT: A 81 ASP cc_start: 0.7994 (t0) cc_final: 0.7723 (t70) REVERT: B 25 ASN cc_start: 0.8133 (m-40) cc_final: 0.7925 (m110) REVERT: E 76 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7920 (tp-100) REVERT: F 74 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7695 (mt-10) REVERT: H 30 ARG cc_start: 0.8040 (mtp85) cc_final: 0.7742 (mtp85) REVERT: H 33 SER cc_start: 0.8858 (t) cc_final: 0.8571 (p) REVERT: H 42 LEU cc_start: 0.9359 (tp) cc_final: 0.9119 (tp) REVERT: H 90 GLU cc_start: 0.8406 (mp0) cc_final: 0.8205 (mp0) REVERT: K 69 ASN cc_start: 0.7722 (t0) cc_final: 0.6243 (m110) outliers start: 8 outliers final: 5 residues processed: 165 average time/residue: 0.3136 time to fit residues: 70.6954 Evaluate side-chains 146 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain K residue 164 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 106 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN F 93 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN H 81 ASN H 92 GLN K 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.092 14254 Z= 0.517 Angle : 0.692 7.292 20486 Z= 0.401 Chirality : 0.043 0.190 2336 Planarity : 0.005 0.043 1584 Dihedral : 31.166 88.959 4226 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.41 % Allowed : 14.74 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.59 (0.26), residues: 925 helix: 1.33 (0.20), residues: 599 sheet: -0.00 (0.72), residues: 47 loop : -1.61 (0.32), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 82 PHE 0.013 0.002 PHE K 99 TYR 0.020 0.002 TYR G 39 ARG 0.006 0.001 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8804 (pm20) cc_final: 0.8429 (pm20) REVERT: A 81 ASP cc_start: 0.8077 (t0) cc_final: 0.7842 (t70) REVERT: B 25 ASN cc_start: 0.8316 (m-40) cc_final: 0.8082 (m110) REVERT: G 104 GLN cc_start: 0.8556 (mm110) cc_final: 0.8193 (mm110) REVERT: H 30 ARG cc_start: 0.8260 (mtp85) cc_final: 0.7952 (mtp85) REVERT: H 39 TYR cc_start: 0.7728 (t80) cc_final: 0.7131 (t80) REVERT: K 69 ASN cc_start: 0.7947 (t0) cc_final: 0.6187 (m110) outliers start: 19 outliers final: 11 residues processed: 145 average time/residue: 0.3095 time to fit residues: 62.0263 Evaluate side-chains 137 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 57 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 71 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 101 optimal weight: 40.0000 chunk 30 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14254 Z= 0.293 Angle : 0.602 7.684 20486 Z= 0.355 Chirality : 0.037 0.183 2336 Planarity : 0.004 0.043 1584 Dihedral : 30.687 87.919 4226 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.41 % Allowed : 16.77 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.17 (0.27), residues: 925 helix: 1.80 (0.21), residues: 605 sheet: 0.11 (0.73), residues: 47 loop : -1.48 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 46 PHE 0.009 0.001 PHE A 67 TYR 0.012 0.001 TYR G 57 ARG 0.005 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8834 (pm20) cc_final: 0.8407 (pm20) REVERT: A 81 ASP cc_start: 0.7952 (t0) cc_final: 0.7742 (t70) REVERT: B 25 ASN cc_start: 0.8272 (m-40) cc_final: 0.8036 (m110) REVERT: F 53 GLU cc_start: 0.7088 (tt0) cc_final: 0.6832 (tt0) REVERT: H 28 LYS cc_start: 0.7711 (ptmt) cc_final: 0.7408 (pttt) REVERT: H 30 ARG cc_start: 0.8167 (mtp85) cc_final: 0.7862 (mtp85) REVERT: H 39 TYR cc_start: 0.7626 (t80) cc_final: 0.7070 (t80) REVERT: H 42 LEU cc_start: 0.9388 (tp) cc_final: 0.9155 (tp) REVERT: H 90 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: K 159 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.8105 (t0) outliers start: 19 outliers final: 12 residues processed: 159 average time/residue: 0.3166 time to fit residues: 69.0024 Evaluate side-chains 150 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 159 ASN Chi-restraints excluded: chain K residue 205 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 101 optimal weight: 50.0000 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 159 ASN ** K 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14254 Z= 0.279 Angle : 0.596 7.117 20486 Z= 0.351 Chirality : 0.037 0.218 2336 Planarity : 0.004 0.040 1584 Dihedral : 30.601 87.881 4226 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.67 % Allowed : 18.55 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.27), residues: 925 helix: 2.01 (0.21), residues: 605 sheet: 0.19 (0.73), residues: 47 loop : -1.46 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 46 PHE 0.011 0.001 PHE E 67 TYR 0.023 0.002 TYR K 231 ARG 0.007 0.000 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8851 (pm20) cc_final: 0.8462 (pm20) REVERT: A 81 ASP cc_start: 0.7942 (t0) cc_final: 0.7728 (t70) REVERT: B 25 ASN cc_start: 0.8290 (m-40) cc_final: 0.8057 (m110) REVERT: E 94 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7641 (mt-10) REVERT: F 74 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7802 (mt-10) REVERT: H 30 ARG cc_start: 0.8152 (mtp85) cc_final: 0.7798 (mtp85) REVERT: H 42 LEU cc_start: 0.9371 (tp) cc_final: 0.9138 (tp) REVERT: H 65 ASP cc_start: 0.8857 (t0) cc_final: 0.8649 (t0) REVERT: K 64 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7650 (p) REVERT: K 195 TYR cc_start: 0.8094 (t80) cc_final: 0.7735 (t80) outliers start: 21 outliers final: 14 residues processed: 158 average time/residue: 0.3240 time to fit residues: 69.7396 Evaluate side-chains 152 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 205 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 50.0000 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 109 optimal weight: 50.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 225 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14254 Z= 0.290 Angle : 0.606 8.987 20486 Z= 0.354 Chirality : 0.037 0.240 2336 Planarity : 0.004 0.039 1584 Dihedral : 30.554 88.362 4226 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.05 % Allowed : 18.68 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.27), residues: 925 helix: 2.04 (0.21), residues: 605 sheet: 0.28 (0.74), residues: 47 loop : -1.42 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 106 PHE 0.010 0.001 PHE E 67 TYR 0.016 0.002 TYR K 139 ARG 0.006 0.000 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8837 (pm20) cc_final: 0.8423 (pm20) REVERT: A 76 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8278 (mm-40) REVERT: D 90 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: E 90 MET cc_start: 0.7954 (mmm) cc_final: 0.7666 (mmp) REVERT: F 74 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7809 (mt-10) REVERT: H 30 ARG cc_start: 0.8157 (mtp85) cc_final: 0.7807 (mtp85) REVERT: H 42 LEU cc_start: 0.9379 (tp) cc_final: 0.9142 (tp) REVERT: H 65 ASP cc_start: 0.8864 (t0) cc_final: 0.8642 (t0) REVERT: H 90 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: K 64 VAL cc_start: 0.7919 (OUTLIER) cc_final: 0.7649 (p) REVERT: K 159 ASN cc_start: 0.7979 (t0) cc_final: 0.7765 (t0) outliers start: 24 outliers final: 16 residues processed: 158 average time/residue: 0.3112 time to fit residues: 68.1051 Evaluate side-chains 153 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 205 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 0.0270 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14254 Z= 0.191 Angle : 0.587 9.567 20486 Z= 0.344 Chirality : 0.035 0.189 2336 Planarity : 0.004 0.041 1584 Dihedral : 30.218 89.491 4226 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.78 % Allowed : 21.09 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.69 (0.27), residues: 925 helix: 2.29 (0.21), residues: 605 sheet: -0.06 (0.74), residues: 42 loop : -1.41 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.014 0.001 PHE K 99 TYR 0.043 0.002 TYR K 224 ARG 0.007 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8805 (pm20) cc_final: 0.8457 (pm20) REVERT: F 74 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7708 (mt-10) REVERT: H 30 ARG cc_start: 0.8092 (mtp85) cc_final: 0.7736 (mtp85) REVERT: H 42 LEU cc_start: 0.9308 (tp) cc_final: 0.9094 (tp) REVERT: H 90 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: H 92 GLN cc_start: 0.8813 (tt0) cc_final: 0.8545 (tt0) REVERT: K 159 ASN cc_start: 0.7814 (t0) cc_final: 0.7411 (m-40) outliers start: 14 outliers final: 8 residues processed: 157 average time/residue: 0.3129 time to fit residues: 67.2924 Evaluate side-chains 144 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 205 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14254 Z= 0.256 Angle : 0.599 9.556 20486 Z= 0.350 Chirality : 0.036 0.185 2336 Planarity : 0.004 0.041 1584 Dihedral : 30.343 87.494 4226 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.52 % Allowed : 21.98 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.27), residues: 925 helix: 2.21 (0.21), residues: 605 sheet: 0.01 (0.75), residues: 42 loop : -1.43 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 46 PHE 0.011 0.001 PHE E 67 TYR 0.014 0.001 TYR G 57 ARG 0.006 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8772 (pm20) cc_final: 0.8429 (pm20) REVERT: F 74 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7733 (mt-10) REVERT: H 30 ARG cc_start: 0.8149 (mtp85) cc_final: 0.7788 (mtp85) REVERT: H 42 LEU cc_start: 0.9364 (tp) cc_final: 0.9146 (tp) REVERT: H 90 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: K 95 ASN cc_start: 0.8044 (p0) cc_final: 0.7825 (p0) outliers start: 12 outliers final: 10 residues processed: 145 average time/residue: 0.2953 time to fit residues: 59.5987 Evaluate side-chains 146 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 205 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 108 optimal weight: 40.0000 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 82 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 0.0670 overall best weight: 1.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14254 Z= 0.290 Angle : 0.621 10.845 20486 Z= 0.358 Chirality : 0.037 0.200 2336 Planarity : 0.004 0.040 1584 Dihedral : 30.362 87.976 4226 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.78 % Allowed : 22.11 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.49 (0.27), residues: 925 helix: 2.10 (0.21), residues: 605 sheet: -0.03 (0.75), residues: 42 loop : -1.43 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 106 PHE 0.010 0.001 PHE E 67 TYR 0.018 0.002 TYR K 139 ARG 0.007 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8836 (pm20) cc_final: 0.8449 (pm20) REVERT: E 90 MET cc_start: 0.8125 (mmm) cc_final: 0.7762 (mmp) REVERT: F 74 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7796 (mt-10) REVERT: H 30 ARG cc_start: 0.8204 (mtp85) cc_final: 0.7852 (mtp85) REVERT: H 90 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7787 (mp0) REVERT: K 95 ASN cc_start: 0.8070 (p0) cc_final: 0.7848 (p0) REVERT: K 121 MET cc_start: 0.8436 (tpt) cc_final: 0.7542 (mpp) REVERT: K 159 ASN cc_start: 0.9095 (t0) cc_final: 0.8775 (t0) outliers start: 14 outliers final: 12 residues processed: 145 average time/residue: 0.3142 time to fit residues: 62.4833 Evaluate side-chains 141 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 205 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 116 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 14254 Z= 0.464 Angle : 0.681 9.228 20486 Z= 0.389 Chirality : 0.041 0.189 2336 Planarity : 0.005 0.056 1584 Dihedral : 30.797 89.129 4226 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.41 % Allowed : 21.73 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.13 (0.27), residues: 925 helix: 1.81 (0.21), residues: 606 sheet: -0.19 (0.73), residues: 42 loop : -1.54 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 106 PHE 0.010 0.002 PHE E 104 TYR 0.013 0.002 TYR G 39 ARG 0.008 0.001 ARG B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8876 (pm20) cc_final: 0.8488 (pm20) REVERT: D 90 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: G 104 GLN cc_start: 0.8530 (mm110) cc_final: 0.8181 (mm110) REVERT: H 30 ARG cc_start: 0.8287 (mtp85) cc_final: 0.7928 (mtp85) REVERT: K 95 ASN cc_start: 0.8116 (p0) cc_final: 0.7899 (p0) REVERT: K 159 ASN cc_start: 0.8992 (t0) cc_final: 0.8247 (t0) outliers start: 19 outliers final: 15 residues processed: 145 average time/residue: 0.3191 time to fit residues: 63.7350 Evaluate side-chains 143 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain K residue 205 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.090600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.054114 restraints weight = 38117.702| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.99 r_work: 0.2633 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14254 Z= 0.208 Angle : 0.618 9.684 20486 Z= 0.356 Chirality : 0.036 0.191 2336 Planarity : 0.004 0.041 1584 Dihedral : 30.151 88.536 4226 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.27 % Allowed : 23.38 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.49 (0.27), residues: 925 helix: 2.14 (0.21), residues: 604 sheet: -0.20 (0.72), residues: 42 loop : -1.49 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.011 0.001 PHE E 67 TYR 0.015 0.002 TYR G 57 ARG 0.007 0.000 ARG D 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2504.33 seconds wall clock time: 46 minutes 28.65 seconds (2788.65 seconds total)