Starting phenix.real_space_refine on Fri Jul 3 04:09:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jla_36390/07_2026/8jla_36390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jla_36390/07_2026/8jla_36390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jla_36390/07_2026/8jla_36390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jla_36390/07_2026/8jla_36390.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jla_36390/07_2026/8jla_36390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jla_36390/07_2026/8jla_36390.map" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.003 sd= 0.033 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 312 5.49 5 S 14 5.16 5 C 6761 2.51 5 N 2309 2.21 5 O 2918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12314 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3200 Classifications: {'DNA': 156} Link IDs: {'rna3p': 155} Chain: "J" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3196 Classifications: {'DNA': 156} Link IDs: {'rna3p': 155} Time building chain proxies: 2.26, per 1000 atoms: 0.18 Number of scatterers: 12314 At special positions: 0 Unit cell: (74.2, 121.9, 129.32, 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 14 16.00 P 312 15.00 O 2918 8.00 N 2309 7.00 C 6761 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: 0.95 Conformation dependent library (CDL) restraints added in 348.3 milliseconds 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1388 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 73.7% alpha, 2.7% beta 156 base pairs and 283 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.557A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.558A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) 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: 3.716A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.559A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.528A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.763A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.024A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.545A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.714A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.481A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 removed outlier: 3.761A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.854A 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 removed outlier: 3.500A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.334A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (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: 6.765A 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: 7.085A 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 77 through 78 403 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 401 hydrogen bonds 802 hydrogen bond angles 0 basepair planarities 156 basepair parallelities 283 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 1.24 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: 2149 1.33 - 1.45: 4573 1.45 - 1.57: 5804 1.57 - 1.69: 622 1.69 - 1.81: 24 Bond restraints: 13172 Sorted by residual: bond pdb=" C3' DG J -53 " pdb=" C2' DG J -53 " ideal model delta sigma weight residual 1.516 1.554 -0.038 8.00e-03 1.56e+04 2.26e+01 bond pdb=" C3' DT I -76 " pdb=" C2' DT I -76 " ideal model delta sigma weight residual 1.516 1.554 -0.038 8.00e-03 1.56e+04 2.21e+01 bond pdb=" C3' DG I -53 " pdb=" C2' DG I -53 " ideal model delta sigma weight residual 1.516 1.552 -0.036 8.00e-03 1.56e+04 2.00e+01 bond pdb=" C3' DT J 72 " pdb=" C2' DT J 72 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.82e+01 bond pdb=" C3' DC J -68 " pdb=" C2' DC J -68 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.75e+01 ... (remaining 13167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 16757 1.42 - 2.84: 1896 2.84 - 4.26: 372 4.26 - 5.68: 91 5.68 - 7.10: 14 Bond angle restraints: 19130 Sorted by residual: angle pdb=" O4' DA I 47 " pdb=" C1' DA I 47 " pdb=" N9 DA I 47 " ideal model delta sigma weight residual 108.00 103.46 4.54 7.00e-01 2.04e+00 4.21e+01 angle pdb=" C4' DG J -53 " pdb=" O4' DG J -53 " pdb=" C1' DG J -53 " ideal model delta sigma weight residual 110.10 103.73 6.37 1.00e+00 1.00e+00 4.05e+01 angle pdb=" O4' DA I -54 " pdb=" C1' DA I -54 " pdb=" N9 DA I -54 " ideal model delta sigma weight residual 108.00 103.80 4.20 7.00e-01 2.04e+00 3.59e+01 angle pdb=" C4' DC J 37 " pdb=" O4' DC J 37 " pdb=" C1' DC J 37 " ideal model delta sigma weight residual 110.10 104.35 5.75 1.00e+00 1.00e+00 3.30e+01 angle pdb=" O4' DA J 71 " pdb=" C1' DA J 71 " pdb=" N9 DA J 71 " ideal model delta sigma weight residual 108.00 112.00 -4.00 7.00e-01 2.04e+00 3.27e+01 ... (remaining 19125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.00: 5506 33.00 - 65.99: 1547 65.99 - 98.99: 39 98.99 - 131.98: 0 131.98 - 164.98: 2 Dihedral angle restraints: 7094 sinusoidal: 4936 harmonic: 2158 Sorted by residual: dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sinusoidal sigma weight residual 220.00 55.02 164.98 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 68.92 151.08 1 3.50e+01 8.16e-04 1.47e+01 dihedral pdb=" C LYS C 74 " pdb=" N LYS C 74 " pdb=" CA LYS C 74 " pdb=" CB LYS C 74 " ideal model delta harmonic sigma weight residual -122.60 -131.76 9.16 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 7091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1684 0.069 - 0.138: 401 0.138 - 0.208: 83 0.208 - 0.277: 4 0.277 - 0.346: 2 Chirality restraints: 2174 Sorted by residual: chirality pdb=" C4' DG J -53 " pdb=" C5' DG J -53 " pdb=" O4' DG J -53 " pdb=" C3' DG J -53 " both_signs ideal model delta sigma weight residual False -2.53 -2.19 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C3' DT J 54 " pdb=" C4' DT J 54 " pdb=" O3' DT J 54 " pdb=" C2' DT J 54 " both_signs ideal model delta sigma weight residual False -2.73 -2.44 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C4' DC J 37 " pdb=" C5' DC J 37 " pdb=" O4' DC J 37 " pdb=" C3' DC J 37 " both_signs ideal model delta sigma weight residual False -2.53 -2.29 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 2171 not shown) Planarity restraints: 1340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 43 " 0.003 2.00e-02 2.50e+03 2.73e-02 2.05e+01 pdb=" N9 DA I 43 " -0.064 2.00e-02 2.50e+03 pdb=" C8 DA I 43 " 0.060 2.00e-02 2.50e+03 pdb=" N7 DA I 43 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DA I 43 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DA I 43 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 43 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I 43 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DA I 43 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DA I 43 " 0.010 2.00e-02 2.50e+03 pdb=" C4 DA I 43 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 42 " -0.059 2.00e-02 2.50e+03 3.14e-02 1.97e+01 pdb=" CG TYR H 42 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR H 42 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR H 42 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR H 42 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR H 42 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR H 42 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 42 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I -59 " 0.040 2.00e-02 2.50e+03 2.45e-02 1.51e+01 pdb=" N1 DT I -59 " -0.064 2.00e-02 2.50e+03 pdb=" C2 DT I -59 " 0.015 2.00e-02 2.50e+03 pdb=" O2 DT I -59 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DT I -59 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT I -59 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT I -59 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DT I -59 " 0.003 2.00e-02 2.50e+03 pdb=" C7 DT I -59 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DT I -59 " -0.001 2.00e-02 2.50e+03 ... (remaining 1337 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 4 2.27 - 2.92: 4692 2.92 - 3.58: 19109 3.58 - 4.24: 33457 4.24 - 4.90: 49191 Nonbonded interactions: 106453 Sorted by model distance: nonbonded pdb=" O THR A 80 " pdb=" OD1 ASP A 81 " model vdw 1.607 3.040 nonbonded pdb=" O GLN G 24 " pdb=" CD1 TYR H 40 " model vdw 1.896 3.340 nonbonded pdb=" OH TYR H 40 " pdb=" OP1 DG I 48 " model vdw 1.950 3.040 nonbonded pdb=" OG1 THR F 82 " pdb=" OD2 ASP F 85 " model vdw 2.158 3.040 nonbonded pdb=" C THR A 80 " pdb=" OD1 ASP A 81 " model vdw 2.335 3.270 ... (remaining 106448 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' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid -77 through -1 or resid 1 through 77)) selection = (chain 'J' and (resid -77 through -1 or resid 1 through 77)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.770 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 13172 Z= 0.631 Angle : 1.002 7.104 19130 Z= 0.822 Chirality : 0.062 0.346 2174 Planarity : 0.010 0.135 1340 Dihedral : 28.206 164.979 5706 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.16 % Allowed : 11.94 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.27), residues: 732 helix: 0.81 (0.20), residues: 514 sheet: None (None), residues: 0 loop : -0.18 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 29 TYR 0.059 0.004 TYR H 42 PHE 0.027 0.002 PHE E 84 HIS 0.010 0.002 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00709 / 0.63 (13172) covalent geometry : angle 1.00195 / 0.82 (19130) hydrogen bonds : bond 0.10438 / 7.10 ( 804) hydrogen bonds : angle 3.79437 / 2.76 ( 1987) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8487 (mmm) cc_final: 0.8263 (mmm) REVERT: C 42 ARG cc_start: 0.8239 (mtp85) cc_final: 0.8034 (mtp85) REVERT: C 68 ASN cc_start: 0.8046 (m-40) cc_final: 0.7754 (m-40) REVERT: C 74 LYS cc_start: 0.7782 (mttt) cc_final: 0.7574 (mttt) REVERT: C 95 LYS cc_start: 0.8904 (ttmt) cc_final: 0.8650 (ttmm) REVERT: C 99 ARG cc_start: 0.7780 (mmm160) cc_final: 0.7569 (mmm160) REVERT: D 57 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8632 (mmmm) REVERT: E 59 GLU cc_start: 0.7810 (pm20) cc_final: 0.7477 (pm20) REVERT: F 25 ASN cc_start: 0.6886 (m-40) cc_final: 0.5998 (m-40) REVERT: G 13 LYS cc_start: 0.8298 (mmmm) cc_final: 0.8036 (mmmm) REVERT: G 18 SER cc_start: 0.8832 (m) cc_final: 0.8608 (p) REVERT: G 63 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8157 (mt) REVERT: G 73 ASN cc_start: 0.8198 (t0) cc_final: 0.7842 (t0) REVERT: H 57 LYS cc_start: 0.8680 (mmmm) cc_final: 0.8410 (mmmm) outliers start: 1 outliers final: 0 residues processed: 237 average time/residue: 0.1908 time to fit residues: 55.7867 Evaluate side-chains 207 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS C 73 ASN D 47 GLN D 82 HIS D 84 ASN E 68 GLN E 125 GLN F 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.102279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.086312 restraints weight = 21584.840| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.27 r_work: 0.2970 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13172 Z= 0.167 Angle : 0.675 11.202 19130 Z= 0.400 Chirality : 0.048 0.236 2174 Planarity : 0.005 0.057 1340 Dihedral : 30.885 165.452 4238 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.23 % Allowed : 15.65 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.96 (0.30), residues: 732 helix: 2.72 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -0.17 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 99 TYR 0.027 0.003 TYR H 42 PHE 0.007 0.001 PHE F 100 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.17 (13172) covalent geometry : angle 0.67487 / 0.40 (19130) hydrogen bonds : bond 0.05320 / 3.58 ( 804) hydrogen bonds : angle 2.92572 / 2.14 ( 1987) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8214 (pm20) cc_final: 0.7669 (pm20) REVERT: A 90 MET cc_start: 0.8570 (mmm) cc_final: 0.8306 (mmm) REVERT: A 96 CYS cc_start: 0.8559 (t) cc_final: 0.8184 (m) REVERT: C 50 TYR cc_start: 0.8611 (t80) cc_final: 0.8259 (t80) REVERT: C 57 TYR cc_start: 0.8890 (t80) cc_final: 0.8519 (t80) REVERT: C 68 ASN cc_start: 0.8681 (m-40) cc_final: 0.8324 (m-40) REVERT: C 71 ARG cc_start: 0.7003 (ttp-110) cc_final: 0.6535 (ttp-110) REVERT: D 54 ILE cc_start: 0.8887 (tt) cc_final: 0.8451 (pt) REVERT: D 120 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8552 (mtpp) REVERT: E 59 GLU cc_start: 0.8080 (pm20) cc_final: 0.7779 (pm20) REVERT: F 35 ARG cc_start: 0.8772 (mmm-85) cc_final: 0.8533 (mmm-85) REVERT: G 63 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8654 (mt) REVERT: G 73 ASN cc_start: 0.8460 (t0) cc_final: 0.8119 (t0) REVERT: H 35 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7609 (mt-10) REVERT: H 64 SER cc_start: 0.8947 (m) cc_final: 0.8737 (t) outliers start: 20 outliers final: 10 residues processed: 229 average time/residue: 0.1536 time to fit residues: 45.0962 Evaluate side-chains 217 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 206 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 85 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 31 optimal weight: 0.0570 chunk 77 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 47 GLN D 82 HIS D 84 ASN H 49 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.100575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.084485 restraints weight = 21522.033| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.29 r_work: 0.2935 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13172 Z= 0.161 Angle : 0.633 9.839 19130 Z= 0.381 Chirality : 0.046 0.218 2174 Planarity : 0.005 0.056 1340 Dihedral : 30.741 164.764 4238 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.71 % Allowed : 18.71 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.50 (0.30), residues: 732 helix: 3.13 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -0.03 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 99 TYR 0.035 0.002 TYR D 83 PHE 0.026 0.002 PHE F 100 HIS 0.005 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.16 (13172) covalent geometry : angle 0.63292 / 0.38 (19130) hydrogen bonds : bond 0.05022 / 3.37 ( 804) hydrogen bonds : angle 2.69429 / 1.96 ( 1987) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8187 (pm20) cc_final: 0.7613 (pm20) REVERT: A 90 MET cc_start: 0.8557 (mmm) cc_final: 0.8346 (mmm) REVERT: B 100 PHE cc_start: 0.8374 (m-10) cc_final: 0.8102 (m-10) REVERT: C 57 TYR cc_start: 0.8905 (t80) cc_final: 0.8530 (t80) REVERT: C 61 GLU cc_start: 0.7883 (tp30) cc_final: 0.7622 (tp30) REVERT: C 68 ASN cc_start: 0.8777 (m-40) cc_final: 0.8115 (m-40) REVERT: C 71 ARG cc_start: 0.7223 (ttp-110) cc_final: 0.6386 (ttp-110) REVERT: C 99 ARG cc_start: 0.7763 (mmm160) cc_final: 0.7514 (mmm160) REVERT: C 110 ASN cc_start: 0.8321 (t0) cc_final: 0.8083 (p0) REVERT: D 120 LYS cc_start: 0.8826 (ttmm) cc_final: 0.8588 (mmmm) REVERT: E 42 ARG cc_start: 0.7760 (mtm-85) cc_final: 0.7537 (ttm-80) REVERT: E 59 GLU cc_start: 0.7970 (pm20) cc_final: 0.7594 (pm20) REVERT: G 63 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8622 (mt) REVERT: G 73 ASN cc_start: 0.8497 (t0) cc_final: 0.8172 (t0) REVERT: H 83 TYR cc_start: 0.8151 (m-10) cc_final: 0.7807 (m-10) outliers start: 23 outliers final: 15 residues processed: 227 average time/residue: 0.1554 time to fit residues: 45.0944 Evaluate side-chains 221 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 44 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 82 HIS F 75 HIS G 31 HIS H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.098614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.082817 restraints weight = 21492.527| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.28 r_work: 0.2900 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13172 Z= 0.164 Angle : 0.625 8.370 19130 Z= 0.375 Chirality : 0.046 0.211 2174 Planarity : 0.005 0.061 1340 Dihedral : 30.719 165.164 4238 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 4.35 % Allowed : 18.87 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.55 (0.30), residues: 732 helix: 3.20 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -0.05 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 99 TYR 0.055 0.002 TYR D 83 PHE 0.007 0.001 PHE E 84 HIS 0.006 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.16 (13172) covalent geometry : angle 0.62512 / 0.37 (19130) hydrogen bonds : bond 0.04929 / 3.33 ( 804) hydrogen bonds : angle 2.60551 / 1.91 ( 1987) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.8680 (OUTLIER) cc_final: 0.8001 (t) REVERT: A 59 GLU cc_start: 0.8136 (pm20) cc_final: 0.7166 (pm20) REVERT: A 117 VAL cc_start: 0.8956 (m) cc_final: 0.8690 (t) REVERT: B 88 TYR cc_start: 0.8660 (m-80) cc_final: 0.8274 (m-80) REVERT: C 57 TYR cc_start: 0.8922 (t80) cc_final: 0.8559 (t80) REVERT: C 68 ASN cc_start: 0.8789 (m-40) cc_final: 0.7987 (m-40) REVERT: C 71 ARG cc_start: 0.7125 (ttp-110) cc_final: 0.6231 (ttp-110) REVERT: D 42 TYR cc_start: 0.8153 (t80) cc_final: 0.7942 (t80) REVERT: D 91 SER cc_start: 0.8686 (p) cc_final: 0.8433 (p) REVERT: D 120 LYS cc_start: 0.8837 (ttmm) cc_final: 0.8583 (mtpp) REVERT: E 59 GLU cc_start: 0.7912 (pm20) cc_final: 0.7563 (pm20) REVERT: G 73 ASN cc_start: 0.8513 (t0) cc_final: 0.8188 (t0) REVERT: H 83 TYR cc_start: 0.8119 (m-10) cc_final: 0.7898 (m-10) outliers start: 27 outliers final: 20 residues processed: 229 average time/residue: 0.1409 time to fit residues: 41.6373 Evaluate side-chains 235 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 11 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 82 HIS H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.093091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.077679 restraints weight = 21944.616| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.32 r_work: 0.2805 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13172 Z= 0.276 Angle : 0.736 8.449 19130 Z= 0.420 Chirality : 0.052 0.242 2174 Planarity : 0.006 0.064 1340 Dihedral : 30.835 164.764 4236 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 5.65 % Allowed : 19.19 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.30), residues: 732 helix: 2.75 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -0.35 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 99 TYR 0.043 0.003 TYR D 83 PHE 0.014 0.002 PHE B 100 HIS 0.013 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.28 (13172) covalent geometry : angle 0.73567 / 0.42 (19130) hydrogen bonds : bond 0.06401 / 4.33 ( 804) hydrogen bonds : angle 2.82408 / 2.07 ( 1987) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 239 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.8724 (OUTLIER) cc_final: 0.7976 (t) REVERT: A 59 GLU cc_start: 0.8156 (pm20) cc_final: 0.7221 (pm20) REVERT: A 60 LEU cc_start: 0.8838 (mp) cc_final: 0.8542 (mt) REVERT: A 117 VAL cc_start: 0.9085 (m) cc_final: 0.8852 (t) REVERT: B 25 ASN cc_start: 0.7388 (m-40) cc_final: 0.7119 (m-40) REVERT: B 40 ARG cc_start: 0.9262 (ttm110) cc_final: 0.8928 (ttm-80) REVERT: B 88 TYR cc_start: 0.8846 (m-10) cc_final: 0.8377 (m-10) REVERT: C 61 GLU cc_start: 0.7877 (tp30) cc_final: 0.7384 (tp30) REVERT: D 42 TYR cc_start: 0.8159 (t80) cc_final: 0.7940 (t80) REVERT: D 91 SER cc_start: 0.8880 (p) cc_final: 0.8648 (p) REVERT: E 59 GLU cc_start: 0.8041 (pm20) cc_final: 0.7718 (pm20) REVERT: G 73 ASN cc_start: 0.8514 (t0) cc_final: 0.8129 (t0) REVERT: H 83 TYR cc_start: 0.8213 (m-10) cc_final: 0.7703 (m-10) outliers start: 35 outliers final: 27 residues processed: 249 average time/residue: 0.1528 time to fit residues: 48.3580 Evaluate side-chains 258 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 230 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 120 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 28 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN B 75 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 82 HIS H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.095987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.080628 restraints weight = 21647.699| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.28 r_work: 0.2865 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13172 Z= 0.148 Angle : 0.631 10.639 19130 Z= 0.376 Chirality : 0.045 0.227 2174 Planarity : 0.005 0.063 1340 Dihedral : 30.646 165.916 4236 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.55 % Allowed : 22.58 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.38 (0.30), residues: 732 helix: 3.15 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.28 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 99 TYR 0.025 0.002 TYR D 83 PHE 0.018 0.002 PHE E 78 HIS 0.007 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.15 (13172) covalent geometry : angle 0.63076 / 0.38 (19130) hydrogen bonds : bond 0.04831 / 3.27 ( 804) hydrogen bonds : angle 2.59578 / 1.90 ( 1987) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.8661 (OUTLIER) cc_final: 0.7886 (t) REVERT: A 59 GLU cc_start: 0.8174 (pm20) cc_final: 0.7205 (pm20) REVERT: A 60 LEU cc_start: 0.8795 (mp) cc_final: 0.8496 (mt) REVERT: B 25 ASN cc_start: 0.7349 (m-40) cc_final: 0.7080 (m-40) REVERT: B 88 TYR cc_start: 0.8788 (m-10) cc_final: 0.8445 (m-10) REVERT: C 57 TYR cc_start: 0.8927 (t80) cc_final: 0.8428 (t80) REVERT: D 42 TYR cc_start: 0.8099 (t80) cc_final: 0.7814 (t80) REVERT: D 91 SER cc_start: 0.8731 (p) cc_final: 0.8463 (p) REVERT: E 55 GLN cc_start: 0.9100 (mt0) cc_final: 0.8896 (mt0) REVERT: E 59 GLU cc_start: 0.7956 (pm20) cc_final: 0.7647 (pm20) REVERT: G 73 ASN cc_start: 0.8538 (t0) cc_final: 0.8189 (t0) REVERT: H 83 TYR cc_start: 0.8159 (m-10) cc_final: 0.7860 (m-10) outliers start: 22 outliers final: 15 residues processed: 236 average time/residue: 0.1406 time to fit residues: 42.8167 Evaluate side-chains 240 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 224 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 48 optimal weight: 0.9980 chunk 15 optimal weight: 0.2980 chunk 89 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.097022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.081624 restraints weight = 21549.786| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.28 r_work: 0.2884 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13172 Z= 0.147 Angle : 0.608 11.079 19130 Z= 0.365 Chirality : 0.044 0.213 2174 Planarity : 0.005 0.048 1340 Dihedral : 30.585 165.486 4236 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.55 % Allowed : 23.39 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.55 (0.31), residues: 732 helix: 3.25 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -0.19 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 99 TYR 0.021 0.002 TYR D 83 PHE 0.011 0.001 PHE B 100 HIS 0.005 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.15 (13172) covalent geometry : angle 0.60803 / 0.37 (19130) hydrogen bonds : bond 0.04609 / 3.09 ( 804) hydrogen bonds : angle 2.52177 / 1.85 ( 1987) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 225 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 57 SER cc_start: 0.8585 (OUTLIER) cc_final: 0.7756 (t) REVERT: A 59 GLU cc_start: 0.8116 (pm20) cc_final: 0.7196 (pm20) REVERT: B 25 ASN cc_start: 0.7325 (m-40) cc_final: 0.7060 (m-40) REVERT: B 35 ARG cc_start: 0.9067 (ttm-80) cc_final: 0.8664 (ttm-80) REVERT: B 88 TYR cc_start: 0.8808 (m-10) cc_final: 0.8357 (m-10) REVERT: C 64 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7820 (tp30) REVERT: D 42 TYR cc_start: 0.8056 (t80) cc_final: 0.7853 (t80) REVERT: D 45 LEU cc_start: 0.8819 (tp) cc_final: 0.8584 (tp) REVERT: D 91 SER cc_start: 0.8755 (p) cc_final: 0.8495 (p) REVERT: E 59 GLU cc_start: 0.7927 (pm20) cc_final: 0.7590 (pm20) REVERT: E 73 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8115 (tm-30) REVERT: G 73 ASN cc_start: 0.8524 (t0) cc_final: 0.8180 (t0) REVERT: H 62 MET cc_start: 0.8252 (mmm) cc_final: 0.7792 (mmm) REVERT: H 83 TYR cc_start: 0.8137 (m-10) cc_final: 0.7841 (m-10) outliers start: 22 outliers final: 17 residues processed: 235 average time/residue: 0.1403 time to fit residues: 42.5029 Evaluate side-chains 243 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 224 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 52 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 73 ASN D 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.094204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.077235 restraints weight = 21245.602| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.37 r_work: 0.2794 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13172 Z= 0.262 Angle : 0.707 12.597 19130 Z= 0.403 Chirality : 0.049 0.239 2174 Planarity : 0.005 0.059 1340 Dihedral : 30.725 165.113 4236 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.71 % Allowed : 23.55 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.31), residues: 732 helix: 2.92 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.37 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 99 TYR 0.025 0.002 TYR D 83 PHE 0.014 0.002 PHE B 100 HIS 0.007 0.002 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.26 (13172) covalent geometry : angle 0.70659 / 0.40 (19130) hydrogen bonds : bond 0.05822 / 3.94 ( 804) hydrogen bonds : angle 2.73172 / 2.00 ( 1987) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 0.243 Fit side-chains REVERT: A 57 SER cc_start: 0.8683 (OUTLIER) cc_final: 0.7865 (t) REVERT: A 59 GLU cc_start: 0.8094 (pm20) cc_final: 0.7177 (pm20) REVERT: B 25 ASN cc_start: 0.7456 (m-40) cc_final: 0.7170 (m-40) REVERT: B 35 ARG cc_start: 0.9089 (ttm-80) cc_final: 0.8872 (ttm-80) REVERT: B 88 TYR cc_start: 0.8876 (m-10) cc_final: 0.7841 (m-10) REVERT: C 64 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7834 (tp30) REVERT: D 80 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8306 (tt) REVERT: D 83 TYR cc_start: 0.8346 (m-10) cc_final: 0.7681 (m-80) REVERT: D 91 SER cc_start: 0.8848 (p) cc_final: 0.8595 (p) REVERT: E 59 GLU cc_start: 0.8040 (pm20) cc_final: 0.7739 (pm20) REVERT: E 73 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8147 (tm-30) REVERT: G 73 ASN cc_start: 0.8527 (t0) cc_final: 0.8173 (t0) REVERT: H 71 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8238 (tm-30) REVERT: H 83 TYR cc_start: 0.8200 (m-10) cc_final: 0.7624 (m-10) REVERT: H 113 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8001 (mm-30) outliers start: 23 outliers final: 18 residues processed: 232 average time/residue: 0.1356 time to fit residues: 40.6370 Evaluate side-chains 243 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 222 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 118 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 60 optimal weight: 0.0980 chunk 94 optimal weight: 8.9990 chunk 47 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 73 ASN D 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.096940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.080049 restraints weight = 21202.544| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.36 r_work: 0.2845 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13172 Z= 0.146 Angle : 0.622 12.901 19130 Z= 0.369 Chirality : 0.044 0.208 2174 Planarity : 0.005 0.055 1340 Dihedral : 30.606 166.437 4236 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.23 % Allowed : 24.35 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.41 (0.31), residues: 732 helix: 3.16 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -0.30 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 99 TYR 0.016 0.001 TYR D 83 PHE 0.012 0.001 PHE B 100 HIS 0.006 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.15 (13172) covalent geometry : angle 0.62154 / 0.37 (19130) hydrogen bonds : bond 0.04649 / 3.13 ( 804) hydrogen bonds : angle 2.55587 / 1.87 ( 1987) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 221 time to evaluate : 0.281 Fit side-chains REVERT: A 57 SER cc_start: 0.8563 (OUTLIER) cc_final: 0.7755 (t) REVERT: A 59 GLU cc_start: 0.8069 (pm20) cc_final: 0.7122 (pm20) REVERT: B 25 ASN cc_start: 0.7355 (m-40) cc_final: 0.7072 (m-40) REVERT: B 35 ARG cc_start: 0.9069 (ttm-80) cc_final: 0.8828 (ttm-80) REVERT: C 57 TYR cc_start: 0.8923 (t80) cc_final: 0.8332 (t80) REVERT: C 64 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7798 (tp30) REVERT: D 80 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8095 (tt) REVERT: D 83 TYR cc_start: 0.8243 (m-10) cc_final: 0.8007 (m-80) REVERT: D 91 SER cc_start: 0.8762 (p) cc_final: 0.8498 (p) REVERT: E 59 GLU cc_start: 0.7983 (pm20) cc_final: 0.7658 (pm20) REVERT: E 73 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8106 (tm-30) REVERT: G 73 ASN cc_start: 0.8532 (t0) cc_final: 0.8206 (t0) REVERT: H 83 TYR cc_start: 0.8172 (m-10) cc_final: 0.7852 (m-10) outliers start: 20 outliers final: 13 residues processed: 230 average time/residue: 0.1357 time to fit residues: 40.4386 Evaluate side-chains 236 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 220 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.091944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.076413 restraints weight = 21945.766| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.34 r_work: 0.2773 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13172 Z= 0.301 Angle : 0.767 14.372 19130 Z= 0.427 Chirality : 0.052 0.271 2174 Planarity : 0.006 0.058 1340 Dihedral : 30.801 166.094 4236 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.03 % Allowed : 24.03 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.30), residues: 732 helix: 2.70 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.47 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 99 TYR 0.034 0.003 TYR D 83 PHE 0.020 0.002 PHE B 100 HIS 0.009 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.30 (13172) covalent geometry : angle 0.76684 / 0.43 (19130) hydrogen bonds : bond 0.06425 / 4.36 ( 804) hydrogen bonds : angle 2.82613 / 2.06 ( 1987) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 226 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.7885 (t) REVERT: A 59 GLU cc_start: 0.8135 (pm20) cc_final: 0.7176 (pm20) REVERT: B 25 ASN cc_start: 0.7509 (m-40) cc_final: 0.7225 (m-40) REVERT: B 35 ARG cc_start: 0.9107 (ttm-80) cc_final: 0.8888 (ttm-80) REVERT: B 88 TYR cc_start: 0.8946 (m-10) cc_final: 0.8601 (m-10) REVERT: C 64 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7792 (tp30) REVERT: D 45 LEU cc_start: 0.8782 (tp) cc_final: 0.8577 (tt) REVERT: D 51 ASP cc_start: 0.8547 (p0) cc_final: 0.8098 (p0) REVERT: D 52 THR cc_start: 0.9026 (t) cc_final: 0.8739 (p) REVERT: D 91 SER cc_start: 0.8886 (p) cc_final: 0.8636 (p) REVERT: E 59 GLU cc_start: 0.8089 (pm20) cc_final: 0.7816 (pm20) REVERT: E 73 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8152 (tm-30) REVERT: G 73 ASN cc_start: 0.8567 (t0) cc_final: 0.8189 (t0) REVERT: H 113 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8063 (mm-30) outliers start: 25 outliers final: 17 residues processed: 237 average time/residue: 0.1443 time to fit residues: 44.0856 Evaluate side-chains 244 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 0.1980 chunk 28 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.095192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.079779 restraints weight = 21625.006| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.27 r_work: 0.2848 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13172 Z= 0.156 Angle : 0.656 12.645 19130 Z= 0.382 Chirality : 0.044 0.211 2174 Planarity : 0.005 0.055 1340 Dihedral : 30.656 167.337 4236 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.58 % Allowed : 25.81 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.23 (0.31), residues: 732 helix: 3.05 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -0.42 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 99 TYR 0.017 0.002 TYR D 83 PHE 0.010 0.001 PHE E 78 HIS 0.005 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.16 (13172) covalent geometry : angle 0.65563 / 0.38 (19130) hydrogen bonds : bond 0.04844 / 3.27 ( 804) hydrogen bonds : angle 2.61296 / 1.91 ( 1987) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2361.73 seconds wall clock time: 41 minutes 0.49 seconds (2460.49 seconds total)