Starting phenix.real_space_refine on Wed Aug 5 22:06:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3o_46542/08_2026/9d3o_46542.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3o_46542/08_2026/9d3o_46542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d3o_46542/08_2026/9d3o_46542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3o_46542/08_2026/9d3o_46542.map" model { file = "/net/cci-nas-00/data/ceres_data/9d3o_46542/08_2026/9d3o_46542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3o_46542/08_2026/9d3o_46542.cif" } resolution = 3.0 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= 0.001 sd= 0.052 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 14 5.16 5 C 6651 2.51 5 N 2274 2.21 5 O 2808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12037 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 652 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "D" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 750 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "H" Number of atoms: 736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 734 Chain: "I" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2978 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2967 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Time building chain proxies: 2.78, per 1000 atoms: 0.23 Number of scatterers: 12037 At special positions: 0 Unit cell: (118.745, 84.15, 117.81, 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 290 15.00 O 2808 8.00 N 2274 7.00 C 6651 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: 1.04 Conformation dependent library (CDL) restraints added in 460.3 milliseconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 70.9% alpha, 3.1% beta 140 base pairs and 251 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.756A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.617A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.935A pdb=" N VAL B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'D' and resid 39 through 49 removed outlier: 3.502A pdb=" N LYS D 43 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.536A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.760A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.055A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.710A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.555A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 47 removed outlier: 3.747A pdb=" N TYR H 40 " --> pdb=" O SER H 36 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS H 41 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS H 44 " --> pdb=" O TYR H 40 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN H 45 " --> pdb=" O LYS H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 82 Processing helix chain 'H' and resid 88 through 100 removed outlier: 3.531A pdb=" N ILE H 92 " --> pdb=" O THR H 88 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR H 94 " --> pdb=" O ARG H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.639A pdb=" N GLU C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.698A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.821A pdb=" N GLU G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (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 removed outlier: 3.782A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.171A 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: 6.873A 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 'D' and resid 53 through 54 removed outlier: 7.321A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.904A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 98 Processing sheet with id=AA9, first strand: chain 'H' and resid 51 through 52 removed outlier: 7.014A pdb=" N GLY H 51 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 86 through 87 386 hydrogen bonds defined for protein. 1151 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 364 hydrogen bonds 728 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 251 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2438 1.33 - 1.45: 3983 1.45 - 1.57: 5816 1.57 - 1.69: 578 1.69 - 1.81: 26 Bond restraints: 12841 Sorted by residual: bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DA J -17 " pdb=" C2' DA J -17 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DC I -18 " pdb=" C2' DC I -18 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DC I -22 " pdb=" C2' DC I -22 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.84e+00 bond pdb=" C3' DA I -30 " pdb=" C2' DA I -30 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.79e+00 ... (remaining 12836 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 18369 2.54 - 5.08: 202 5.08 - 7.63: 2 7.63 - 10.17: 1 10.17 - 12.71: 1 Bond angle restraints: 18575 Sorted by residual: angle pdb=" C LEU D 101 " pdb=" N LEU D 102 " pdb=" CA LEU D 102 " ideal model delta sigma weight residual 123.15 110.44 12.71 2.23e+00 2.01e-01 3.25e+01 angle pdb=" N3 DT J 30 " pdb=" C4 DT J 30 " pdb=" O4 DT J 30 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT J 49 " pdb=" C4 DT J 49 " pdb=" O4 DT J 49 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT J 8 " pdb=" C4 DT J 8 " pdb=" O4 DT J 8 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT J 39 " pdb=" C4 DT J 39 " pdb=" O4 DT J 39 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 ... (remaining 18570 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 5496 35.15 - 70.30: 1444 70.30 - 105.45: 25 105.45 - 140.60: 0 140.60 - 175.75: 2 Dihedral angle restraints: 6967 sinusoidal: 4744 harmonic: 2223 Sorted by residual: dihedral pdb=" C4' DA J -17 " pdb=" C3' DA J -17 " pdb=" O3' DA J -17 " pdb=" P DG J -16 " ideal model delta sinusoidal sigma weight residual -140.00 35.75 -175.75 1 3.50e+01 8.16e-04 1.57e+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 72.43 147.57 1 3.50e+01 8.16e-04 1.45e+01 dihedral pdb=" CA ASN G 38 " pdb=" CB ASN G 38 " pdb=" CG ASN G 38 " pdb=" OD1 ASN G 38 " ideal model delta sinusoidal sigma weight residual 120.00 -169.48 -70.52 2 2.00e+01 2.50e-03 1.07e+01 ... (remaining 6964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 958 0.027 - 0.053: 728 0.053 - 0.080: 244 0.080 - 0.107: 137 0.107 - 0.133: 41 Chirality restraints: 2108 Sorted by residual: chirality pdb=" CA ILE F 46 " pdb=" N ILE F 46 " pdb=" C ILE F 46 " pdb=" CB ILE F 46 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" C3' DA J 38 " pdb=" C4' DA J 38 " pdb=" O3' DA J 38 " pdb=" C2' DA J 38 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 2105 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.79e+00 pdb=" N PRO D 103 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO G 80 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 24 " -0.010 2.00e-02 2.50e+03 2.00e-02 3.98e+00 pdb=" C ASP F 24 " 0.035 2.00e-02 2.50e+03 pdb=" O ASP F 24 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN F 25 " -0.011 2.00e-02 2.50e+03 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1844 2.77 - 3.30: 10302 3.30 - 3.83: 23637 3.83 - 4.37: 28133 4.37 - 4.90: 40446 Nonbonded interactions: 104362 Sorted by model distance: nonbonded pdb=" O LEU G 55 " pdb=" OG1 THR G 59 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR H 88 " pdb=" OE1 GLU H 91 " model vdw 2.277 3.040 nonbonded pdb=" NH2 ARG E 53 " pdb=" OP1 DT I -65 " model vdw 2.298 3.120 nonbonded pdb=" NH1 ARG A 72 " pdb=" OP1 DC I -23 " model vdw 2.302 3.120 ... (remaining 104357 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' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = (chain 'C' and resid 11 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 123)) selection = (chain 'H' and (resid 29 through 105 or resid 107 through 121)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.850 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.006 0.086 12841 Z= 0.511 Angle : 0.777 12.708 18575 Z= 0.681 Chirality : 0.044 0.133 2108 Planarity : 0.005 0.065 1346 Dihedral : 28.617 175.748 5535 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 20.69 % Favored : 79.31 % 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: 0.20 (0.30), residues: 752 helix: 0.73 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.21 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 45 TYR 0.031 0.002 TYR H 40 PHE 0.012 0.002 PHE B 61 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.51 (12841) covalent geometry : angle 0.77694 / 0.68 (18575) hydrogen bonds : bond 0.13028 / 8.72 ( 750) hydrogen bonds : angle 4.90339 / 3.75 ( 1879) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.318 Fit side-chains REVERT: A 40 ARG cc_start: 0.7782 (tpp80) cc_final: 0.7547 (tpp80) REVERT: E 42 ARG cc_start: 0.7875 (mmt90) cc_final: 0.6606 (mmm160) REVERT: E 120 MET cc_start: 0.9097 (mtt) cc_final: 0.8842 (mtt) REVERT: F 95 ARG cc_start: 0.8194 (mtt-85) cc_final: 0.7972 (mtt-85) REVERT: G 51 MET cc_start: 0.8890 (tpp) cc_final: 0.8638 (ttt) REVERT: G 74 LYS cc_start: 0.8570 (mmtt) cc_final: 0.8218 (mppt) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.7729 time to fit residues: 79.0278 Evaluate side-chains 85 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 40.0000 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 40.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 30.0000 chunk 45 optimal weight: 30.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN D 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.194054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.124902 restraints weight = 28534.619| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.15 r_work: 0.3324 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12841 Z= 0.232 Angle : 0.712 6.872 18575 Z= 0.403 Chirality : 0.049 0.246 2108 Planarity : 0.006 0.057 1346 Dihedral : 31.119 171.648 4001 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.76 % Allowed : 20.22 % Favored : 76.02 % 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: 0.59 (0.30), residues: 752 helix: 1.10 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.43 (0.36), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 72 TYR 0.013 0.002 TYR C 57 PHE 0.012 0.002 PHE B 100 HIS 0.006 0.001 HIS H 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.23 (12841) covalent geometry : angle 0.71215 / 0.40 (18575) hydrogen bonds : bond 0.05565 / 3.73 ( 750) hydrogen bonds : angle 3.20681 / 2.31 ( 1879) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.308 Fit side-chains REVERT: A 40 ARG cc_start: 0.7623 (tpp80) cc_final: 0.7344 (tpp80) REVERT: B 35 ARG cc_start: 0.8112 (mtp180) cc_final: 0.7773 (mtm110) REVERT: B 92 ARG cc_start: 0.8640 (ptm-80) cc_final: 0.8393 (ptm-80) REVERT: D 76 GLU cc_start: 0.8545 (tp30) cc_final: 0.8339 (tp30) REVERT: E 65 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7926 (tp) REVERT: E 120 MET cc_start: 0.8745 (mtt) cc_final: 0.8052 (mtt) REVERT: H 40 TYR cc_start: 0.8207 (t80) cc_final: 0.7954 (t80) REVERT: G 72 ASP cc_start: 0.8054 (m-30) cc_final: 0.7608 (m-30) REVERT: G 74 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8285 (mppt) outliers start: 24 outliers final: 9 residues processed: 100 average time/residue: 0.7310 time to fit residues: 78.2466 Evaluate side-chains 95 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 29 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 39 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 62 optimal weight: 30.0000 chunk 27 optimal weight: 5.9990 chunk 54 optimal weight: 30.0000 chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 52 optimal weight: 50.0000 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN D 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.195181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.130417 restraints weight = 24988.654| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.33 r_work: 0.3320 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12841 Z= 0.141 Angle : 0.627 6.835 18575 Z= 0.366 Chirality : 0.046 0.241 2108 Planarity : 0.005 0.052 1346 Dihedral : 31.189 172.143 4001 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.66 % Allowed : 22.10 % Favored : 75.24 % 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: 1.11 (0.30), residues: 752 helix: 1.53 (0.23), residues: 541 sheet: None (None), residues: 0 loop : -1.36 (0.36), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 72 TYR 0.010 0.001 TYR H 38 PHE 0.017 0.002 PHE H 63 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 (12841) covalent geometry : angle 0.62733 / 0.37 (18575) hydrogen bonds : bond 0.04614 / 3.09 ( 750) hydrogen bonds : angle 2.96979 / 2.15 ( 1879) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.342 Fit side-chains REVERT: A 40 ARG cc_start: 0.7517 (tpp80) cc_final: 0.7213 (tpp80) REVERT: B 35 ARG cc_start: 0.8117 (mtp180) cc_final: 0.7758 (mtm110) REVERT: E 105 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7756 (mt-10) REVERT: F 95 ARG cc_start: 0.7961 (mtt-85) cc_final: 0.7665 (mtm-85) REVERT: G 72 ASP cc_start: 0.8020 (m-30) cc_final: 0.7561 (m-30) REVERT: G 74 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8321 (mppt) outliers start: 17 outliers final: 10 residues processed: 94 average time/residue: 0.6976 time to fit residues: 70.3260 Evaluate side-chains 92 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain H residue 50 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 73 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.193839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.128116 restraints weight = 21242.131| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.96 r_work: 0.3338 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12841 Z= 0.173 Angle : 0.646 6.976 18575 Z= 0.368 Chirality : 0.046 0.237 2108 Planarity : 0.005 0.053 1346 Dihedral : 31.424 171.668 4001 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.55 % Allowed : 19.75 % Favored : 75.71 % 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: 1.25 (0.31), residues: 752 helix: 1.61 (0.23), residues: 545 sheet: None (None), residues: 0 loop : -1.29 (0.37), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 72 TYR 0.010 0.001 TYR A 54 PHE 0.012 0.002 PHE B 61 HIS 0.005 0.001 HIS H 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (12841) covalent geometry : angle 0.64569 / 0.37 (18575) hydrogen bonds : bond 0.04763 / 3.17 ( 750) hydrogen bonds : angle 2.94354 / 2.12 ( 1879) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.307 Fit side-chains REVERT: A 59 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6785 (pm20) REVERT: B 35 ARG cc_start: 0.8077 (mtp180) cc_final: 0.7832 (mtm110) REVERT: E 105 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7596 (mt-10) REVERT: F 95 ARG cc_start: 0.7993 (mtt-85) cc_final: 0.7672 (mtt-85) REVERT: C 92 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: G 72 ASP cc_start: 0.8128 (m-30) cc_final: 0.7678 (m-30) REVERT: G 74 LYS cc_start: 0.8706 (mmtt) cc_final: 0.8321 (mppt) outliers start: 29 outliers final: 10 residues processed: 100 average time/residue: 0.7347 time to fit residues: 78.5092 Evaluate side-chains 92 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 19 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 69 optimal weight: 20.0000 chunk 52 optimal weight: 50.0000 chunk 22 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 78 optimal weight: 30.0000 chunk 62 optimal weight: 30.0000 chunk 88 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.194098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.128432 restraints weight = 23795.276| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.11 r_work: 0.3324 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12841 Z= 0.157 Angle : 0.633 7.014 18575 Z= 0.362 Chirality : 0.045 0.238 2108 Planarity : 0.005 0.055 1346 Dihedral : 31.447 171.389 4001 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.08 % Allowed : 20.38 % Favored : 75.55 % 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: 1.34 (0.30), residues: 752 helix: 1.68 (0.23), residues: 545 sheet: None (None), residues: 0 loop : -1.24 (0.37), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 129 TYR 0.010 0.001 TYR A 54 PHE 0.013 0.002 PHE E 67 HIS 0.004 0.001 HIS H 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (12841) covalent geometry : angle 0.63264 / 0.36 (18575) hydrogen bonds : bond 0.04501 / 3.00 ( 750) hydrogen bonds : angle 2.90201 / 2.09 ( 1879) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.309 Fit side-chains REVERT: A 59 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6796 (pm20) REVERT: B 35 ARG cc_start: 0.8109 (mtp180) cc_final: 0.7867 (mtm110) REVERT: E 105 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7638 (mt-10) REVERT: E 120 MET cc_start: 0.8666 (mtt) cc_final: 0.8130 (mtm) REVERT: F 95 ARG cc_start: 0.7987 (mtt-85) cc_final: 0.7787 (mtm-85) REVERT: H 114 LYS cc_start: 0.8122 (tppp) cc_final: 0.7695 (ttmm) REVERT: C 92 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7999 (mt-10) REVERT: G 72 ASP cc_start: 0.8179 (m-30) cc_final: 0.7730 (m-30) REVERT: G 74 LYS cc_start: 0.8730 (mmtt) cc_final: 0.8357 (mppt) outliers start: 26 outliers final: 14 residues processed: 91 average time/residue: 0.6991 time to fit residues: 68.1229 Evaluate side-chains 96 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 70 optimal weight: 30.0000 chunk 38 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 54 optimal weight: 30.0000 chunk 22 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 53 optimal weight: 40.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.195489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.127606 restraints weight = 33113.390| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.31 r_work: 0.3344 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12841 Z= 0.126 Angle : 0.610 6.732 18575 Z= 0.354 Chirality : 0.045 0.239 2108 Planarity : 0.004 0.051 1346 Dihedral : 31.427 171.568 4001 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.29 % Allowed : 21.32 % Favored : 75.39 % 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: 1.62 (0.31), residues: 752 helix: 1.89 (0.23), residues: 545 sheet: None (None), residues: 0 loop : -1.19 (0.37), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 129 TYR 0.012 0.001 TYR H 38 PHE 0.013 0.001 PHE E 67 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.13 (12841) covalent geometry : angle 0.61046 / 0.35 (18575) hydrogen bonds : bond 0.04169 / 2.78 ( 750) hydrogen bonds : angle 2.83085 / 2.04 ( 1879) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.326 Fit side-chains REVERT: A 59 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6737 (pm20) REVERT: B 35 ARG cc_start: 0.8073 (mtp180) cc_final: 0.7837 (mtm110) REVERT: E 105 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7723 (mt-10) REVERT: F 95 ARG cc_start: 0.7927 (mtt-85) cc_final: 0.7725 (mtm-85) REVERT: H 114 LYS cc_start: 0.8282 (tppp) cc_final: 0.7737 (ttmm) REVERT: G 72 ASP cc_start: 0.8160 (m-30) cc_final: 0.7750 (m-30) outliers start: 21 outliers final: 12 residues processed: 90 average time/residue: 0.6842 time to fit residues: 66.0222 Evaluate side-chains 92 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 63 optimal weight: 30.0000 chunk 16 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.196395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.130991 restraints weight = 21453.948| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.83 r_work: 0.3387 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12841 Z= 0.127 Angle : 0.595 6.708 18575 Z= 0.346 Chirality : 0.043 0.238 2108 Planarity : 0.004 0.049 1346 Dihedral : 31.387 171.482 4001 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.61 % Allowed : 21.47 % Favored : 74.92 % 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: 1.85 (0.31), residues: 752 helix: 2.05 (0.23), residues: 545 sheet: None (None), residues: 0 loop : -1.07 (0.37), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 72 TYR 0.010 0.001 TYR H 38 PHE 0.014 0.001 PHE E 67 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.13 (12841) covalent geometry : angle 0.59455 / 0.35 (18575) hydrogen bonds : bond 0.03983 / 2.66 ( 750) hydrogen bonds : angle 2.76920 / 2.00 ( 1879) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.295 Fit side-chains REVERT: A 59 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6700 (pm20) REVERT: E 42 ARG cc_start: 0.7571 (mmt90) cc_final: 0.6092 (mmm160) REVERT: E 105 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7651 (mt-10) REVERT: E 120 MET cc_start: 0.8557 (mtt) cc_final: 0.8029 (mtm) REVERT: H 114 LYS cc_start: 0.8182 (tppp) cc_final: 0.7742 (ttpp) REVERT: G 72 ASP cc_start: 0.8158 (m-30) cc_final: 0.7759 (m-30) outliers start: 23 outliers final: 13 residues processed: 92 average time/residue: 0.7689 time to fit residues: 75.3770 Evaluate side-chains 94 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 4.9990 chunk 57 optimal weight: 30.0000 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 96 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 66 optimal weight: 50.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN D 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.193113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.128731 restraints weight = 31103.813| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.26 r_work: 0.3286 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12841 Z= 0.200 Angle : 0.663 7.333 18575 Z= 0.371 Chirality : 0.047 0.223 2108 Planarity : 0.005 0.047 1346 Dihedral : 31.548 169.870 4001 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.98 % Allowed : 22.26 % Favored : 74.76 % 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: 1.50 (0.30), residues: 752 helix: 1.78 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.14 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 35 TYR 0.011 0.002 TYR F 72 PHE 0.012 0.002 PHE E 67 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (12841) covalent geometry : angle 0.66276 / 0.37 (18575) hydrogen bonds : bond 0.04897 / 3.26 ( 750) hydrogen bonds : angle 2.94841 / 2.11 ( 1879) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.291 Fit side-chains REVERT: A 59 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6800 (pm20) REVERT: E 105 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7653 (mt-10) REVERT: H 114 LYS cc_start: 0.8213 (tppp) cc_final: 0.7674 (ttmm) REVERT: G 72 ASP cc_start: 0.8193 (m-30) cc_final: 0.7787 (m-30) outliers start: 19 outliers final: 12 residues processed: 90 average time/residue: 0.7190 time to fit residues: 69.1468 Evaluate side-chains 91 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 3.9990 chunk 56 optimal weight: 30.0000 chunk 16 optimal weight: 0.4980 chunk 48 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 78 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 63 optimal weight: 30.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.194250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.129176 restraints weight = 26553.887| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.46 r_work: 0.3274 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12841 Z= 0.145 Angle : 0.630 6.996 18575 Z= 0.359 Chirality : 0.045 0.225 2108 Planarity : 0.005 0.098 1346 Dihedral : 31.539 169.911 4001 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.45 % Allowed : 21.94 % Favored : 74.61 % 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: 1.57 (0.30), residues: 752 helix: 1.82 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.11 (0.38), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 35 TYR 0.011 0.001 TYR B 51 PHE 0.012 0.002 PHE E 67 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (12841) covalent geometry : angle 0.63011 / 0.36 (18575) hydrogen bonds : bond 0.04461 / 2.97 ( 750) hydrogen bonds : angle 2.88417 / 2.07 ( 1879) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.211 Fit side-chains REVERT: A 59 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6700 (pm20) REVERT: E 105 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7681 (mt-10) REVERT: H 114 LYS cc_start: 0.8217 (tppp) cc_final: 0.7678 (ttmm) REVERT: C 92 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7967 (mt-10) REVERT: G 72 ASP cc_start: 0.8179 (m-30) cc_final: 0.7773 (m-30) outliers start: 22 outliers final: 14 residues processed: 90 average time/residue: 0.7383 time to fit residues: 70.9813 Evaluate side-chains 94 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 83 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 68 optimal weight: 30.0000 chunk 25 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.194927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.129501 restraints weight = 28332.740| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.30 r_work: 0.3315 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12841 Z= 0.137 Angle : 0.613 6.892 18575 Z= 0.352 Chirality : 0.044 0.224 2108 Planarity : 0.005 0.062 1346 Dihedral : 31.489 169.879 4001 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.19 % Allowed : 23.35 % Favored : 74.45 % 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: 1.71 (0.31), residues: 752 helix: 1.94 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.08 (0.38), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 35 TYR 0.011 0.001 TYR F 72 PHE 0.014 0.002 PHE E 67 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (12841) covalent geometry : angle 0.61309 / 0.35 (18575) hydrogen bonds : bond 0.04203 / 2.80 ( 750) hydrogen bonds : angle 2.85190 / 2.05 ( 1879) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.309 Fit side-chains REVERT: A 59 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6719 (pm20) REVERT: E 105 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7670 (mt-10) REVERT: H 114 LYS cc_start: 0.8198 (tppp) cc_final: 0.7697 (ttmm) REVERT: G 72 ASP cc_start: 0.8182 (m-30) cc_final: 0.7791 (m-30) outliers start: 14 outliers final: 12 residues processed: 87 average time/residue: 0.7748 time to fit residues: 71.9973 Evaluate side-chains 92 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 63 optimal weight: 30.0000 chunk 56 optimal weight: 30.0000 chunk 66 optimal weight: 50.0000 chunk 30 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 76 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.194453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.127089 restraints weight = 28287.783| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.14 r_work: 0.3342 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12841 Z= 0.160 Angle : 0.625 6.905 18575 Z= 0.356 Chirality : 0.045 0.217 2108 Planarity : 0.005 0.060 1346 Dihedral : 31.469 169.676 4001 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.98 % Allowed : 22.26 % Favored : 74.76 % 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: 1.73 (0.30), residues: 752 helix: 1.96 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.10 (0.38), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 35 TYR 0.011 0.001 TYR F 72 PHE 0.012 0.002 PHE E 67 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 (12841) covalent geometry : angle 0.62455 / 0.36 (18575) hydrogen bonds : bond 0.04378 / 2.91 ( 750) hydrogen bonds : angle 2.84681 / 2.04 ( 1879) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3785.80 seconds wall clock time: 65 minutes 12.33 seconds (3912.33 seconds total)