Starting phenix.real_space_refine on Fri Jul 3 03:59:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3o_46542/07_2026/9d3o_46542.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3o_46542/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9d3o_46542/07_2026/9d3o_46542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3o_46542/07_2026/9d3o_46542.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d3o_46542/07_2026/9d3o_46542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3o_46542/07_2026/9d3o_46542.map" } 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): 0.00s 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: 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: 2.26, per 1000 atoms: 0.19 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: 0.95 Conformation dependent library (CDL) restraints added in 261.3 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: 1.66 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: 1.70 Time building geometry restraints manager: 1.29 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: 18371 2.54 - 5.08: 200 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: 0.600 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.720 Find NCS groups from input model: 0.150 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:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.170 ------------------------------------------------------------------------------- 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= 0.510 Angle : 0.770 12.708 18575 Z= 0.676 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 0.77030 / 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 : 0.311 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: 0.7620 time to fit residues: 77.8961 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 : 0.324 ------------------------------------------------------------------------------- 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... D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.194034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.124940 restraints weight = 28472.031| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.18 r_work: 0.3327 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 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 = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.0809 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= 0.230 Angle : 0.689 6.875 18575 Z= 0.397 Chirality : 0.048 0.241 2108 Planarity : 0.006 0.058 1346 Dihedral : 31.180 171.843 4001 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.45 % Allowed : 20.69 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.63 (0.30), residues: 752 helix: 1.12 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.41 (0.37), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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 0.00494 / 0.23 (12841) covalent geometry : angle 0.68887 / 0.40 (18575) hydrogen bonds : bond 0.05549 / 3.72 ( 750) hydrogen bonds : angle 3.19119 / 2.30 ( 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 111 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.201 Fit side-chains REVERT: A 40 ARG cc_start: 0.7613 (tpp80) cc_final: 0.7333 (tpp80) REVERT: B 35 ARG cc_start: 0.8101 (mtp180) cc_final: 0.7768 (mtm110) REVERT: B 92 ARG cc_start: 0.8647 (ptm-80) cc_final: 0.8398 (ptm-80) REVERT: D 76 GLU cc_start: 0.8546 (tp30) cc_final: 0.8344 (tp30) REVERT: E 65 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7926 (tp) REVERT: E 120 MET cc_start: 0.8730 (mtt) cc_final: 0.8360 (mtt) REVERT: H 40 TYR cc_start: 0.8191 (t80) cc_final: 0.7952 (t80) REVERT: G 72 ASP cc_start: 0.8053 (m-30) cc_final: 0.7582 (m-30) REVERT: G 74 LYS cc_start: 0.8623 (mmtt) cc_final: 0.8281 (mppt) outliers start: 22 outliers final: 8 residues processed: 101 average time/residue: 0.6579 time to fit residues: 71.0066 Evaluate side-chains 95 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 39 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 95 optimal weight: 0.3980 chunk 86 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 54 optimal weight: 30.0000 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 52 optimal weight: 50.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.193609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.128579 restraints weight = 24990.709| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.38 r_work: 0.3298 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12841 Z= 0.184 Angle : 0.645 7.086 18575 Z= 0.374 Chirality : 0.046 0.233 2108 Planarity : 0.005 0.054 1346 Dihedral : 31.320 171.461 4001 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.29 % Allowed : 21.47 % 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: 0.91 (0.30), residues: 752 helix: 1.35 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.37 (0.37), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 29 TYR 0.011 0.001 TYR B 51 PHE 0.015 0.002 PHE H 63 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (12841) covalent geometry : angle 0.64453 / 0.37 (18575) hydrogen bonds : bond 0.04928 / 3.30 ( 750) hydrogen bonds : angle 3.03337 / 2.19 ( 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 108 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.238 Fit side-chains REVERT: B 35 ARG cc_start: 0.8115 (mtp180) cc_final: 0.7759 (mtm110) REVERT: D 76 GLU cc_start: 0.8471 (tp30) cc_final: 0.8244 (tp30) REVERT: E 105 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7752 (mt-10) REVERT: F 95 ARG cc_start: 0.8013 (mtt-85) cc_final: 0.7690 (mtt-85) REVERT: G 72 ASP cc_start: 0.8009 (m-30) cc_final: 0.7504 (m-30) REVERT: G 74 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8271 (mppt) outliers start: 21 outliers final: 11 residues processed: 97 average time/residue: 0.6263 time to fit residues: 65.0482 Evaluate side-chains 95 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 49 HIS 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 Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 19 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 25 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 91 optimal weight: 0.0980 chunk 73 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 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 = 0.4254 r_free = 0.4254 target = 0.194643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.129295 restraints weight = 21258.538| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.95 r_work: 0.3346 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- 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 = 0.49 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 = 0.48 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: 0.7943 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12841 Z= 0.146 Angle : 0.614 6.842 18575 Z= 0.360 Chirality : 0.045 0.236 2108 Planarity : 0.004 0.052 1346 Dihedral : 31.353 171.691 4001 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.61 % Allowed : 20.85 % 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: 1.22 (0.30), residues: 752 helix: 1.59 (0.23), residues: 543 sheet: None (None), residues: 0 loop : -1.29 (0.37), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 72 TYR 0.010 0.001 TYR B 51 PHE 0.013 0.002 PHE E 67 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (12841) covalent geometry : angle 0.61442 / 0.36 (18575) hydrogen bonds : bond 0.04576 / 3.06 ( 750) hydrogen bonds : angle 2.93226 / 2.11 ( 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 106 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.298 Fit side-chains REVERT: A 59 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6772 (pm20) REVERT: B 35 ARG cc_start: 0.8066 (mtp180) cc_final: 0.7798 (mtm110) REVERT: E 105 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: G 72 ASP cc_start: 0.8034 (m-30) cc_final: 0.7582 (m-30) REVERT: G 74 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8316 (mppt) outliers start: 23 outliers final: 14 residues processed: 92 average time/residue: 0.6520 time to fit residues: 64.1269 Evaluate side-chains 95 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 90 MET 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 49 HIS Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 90 THR 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 F residue 84 MET Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 ILE 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: 0.9980 chunk 74 optimal weight: 20.0000 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 78 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 88 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.4271 r_free = 0.4271 target = 0.196424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.132667 restraints weight = 23864.279| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.24 r_work: 0.3343 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12841 Z= 0.129 Angle : 0.587 6.484 18575 Z= 0.348 Chirality : 0.044 0.237 2108 Planarity : 0.004 0.048 1346 Dihedral : 31.378 171.840 4001 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: 1.53 (0.31), residues: 752 helix: 1.82 (0.23), residues: 543 sheet: None (None), residues: 0 loop : -1.17 (0.37), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 72 TYR 0.012 0.001 TYR H 38 PHE 0.013 0.001 PHE E 67 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.13 (12841) covalent geometry : angle 0.58728 / 0.35 (18575) hydrogen bonds : bond 0.04119 / 2.76 ( 750) hydrogen bonds : angle 2.81259 / 2.03 ( 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 108 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.291 Fit side-chains REVERT: A 59 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6679 (pm20) REVERT: B 35 ARG cc_start: 0.8072 (mtp180) cc_final: 0.7838 (mtm110) REVERT: E 105 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7731 (mt-10) REVERT: G 72 ASP cc_start: 0.8156 (m-30) cc_final: 0.7710 (m-30) REVERT: G 74 LYS cc_start: 0.8726 (mmtt) cc_final: 0.8355 (mppt) outliers start: 23 outliers final: 11 residues processed: 95 average time/residue: 0.6890 time to fit residues: 70.0872 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 : 0.309 ------------------------------------------------------------------------------- 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 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 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 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: 0.0870 chunk 24 optimal weight: 0.9990 chunk 70 optimal weight: 30.0000 chunk 38 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 54 optimal weight: 30.0000 chunk 22 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 53 optimal weight: 40.0000 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN B 93 GLN D 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.196207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.128383 restraints weight = 33182.980| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.36 r_work: 0.3348 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12841 Z= 0.134 Angle : 0.582 6.624 18575 Z= 0.342 Chirality : 0.043 0.232 2108 Planarity : 0.004 0.047 1346 Dihedral : 31.460 171.430 4001 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.45 % Allowed : 21.47 % Favored : 75.08 % 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: 1.83 (0.31), residues: 752 helix: 2.06 (0.23), residues: 543 sheet: None (None), residues: 0 loop : -1.12 (0.37), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 92 TYR 0.009 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 0.00237 / 0.13 (12841) covalent geometry : angle 0.58179 / 0.34 (18575) hydrogen bonds : bond 0.04122 / 2.75 ( 750) hydrogen bonds : angle 2.77111 / 1.99 ( 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 100 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.315 Fit side-chains REVERT: A 59 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6744 (pm20) REVERT: B 93 GLN cc_start: 0.8141 (mt0) cc_final: 0.7902 (mt0) REVERT: E 105 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7721 (mt-10) REVERT: E 120 MET cc_start: 0.8569 (mtt) cc_final: 0.7998 (mtm) REVERT: G 72 ASP cc_start: 0.8192 (m-30) cc_final: 0.7795 (m-30) outliers start: 22 outliers final: 13 residues processed: 89 average time/residue: 0.7049 time to fit residues: 67.0225 Evaluate side-chains 91 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS 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 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 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 107 VAL Chi-restraints excluded: chain G residue 19 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 63 optimal weight: 30.0000 chunk 16 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4274 r_free = 0.4274 target = 0.196707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.131687 restraints weight = 21462.787| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.90 r_work: 0.3390 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12841 Z= 0.122 Angle : 0.575 6.666 18575 Z= 0.340 Chirality : 0.043 0.232 2108 Planarity : 0.004 0.047 1346 Dihedral : 31.460 171.330 4001 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.82 % Allowed : 22.10 % Favored : 75.08 % 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: 1.94 (0.31), residues: 752 helix: 2.14 (0.23), residues: 543 sheet: None (None), residues: 0 loop : -1.08 (0.37), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 35 TYR 0.011 0.001 TYR H 38 PHE 0.012 0.001 PHE E 67 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.12 (12841) covalent geometry : angle 0.57496 / 0.34 (18575) hydrogen bonds : bond 0.03988 / 2.67 ( 750) hydrogen bonds : angle 2.74757 / 1.98 ( 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 97 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.313 Fit side-chains REVERT: A 59 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6663 (pm20) REVERT: B 93 GLN cc_start: 0.8075 (mt0) cc_final: 0.7826 (mt0) REVERT: E 42 ARG cc_start: 0.7464 (mmt90) cc_final: 0.6060 (mmm160) REVERT: E 105 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7668 (mt-10) REVERT: E 120 MET cc_start: 0.8501 (mtt) cc_final: 0.7948 (mtt) REVERT: F 52 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7848 (mm-30) REVERT: C 92 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: G 72 ASP cc_start: 0.8151 (m-30) cc_final: 0.7770 (m-30) outliers start: 18 outliers final: 14 residues processed: 88 average time/residue: 0.7238 time to fit residues: 68.0124 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 : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 59 GLU 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 80 LEU 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 H residue 52 ILE 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 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: 0.0770 chunk 96 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 31 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 66 optimal weight: 50.0000 overall best weight: 2.9944 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.193737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.129659 restraints weight = 31181.049| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.32 r_work: 0.3294 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1480 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= 0.186 Angle : 0.628 6.906 18575 Z= 0.359 Chirality : 0.045 0.218 2108 Planarity : 0.005 0.046 1346 Dihedral : 31.603 169.630 4001 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.76 % Allowed : 21.47 % 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: 1.64 (0.30), residues: 752 helix: 1.91 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -1.13 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 42 TYR 0.010 0.001 TYR F 72 PHE 0.012 0.002 PHE E 67 HIS 0.004 0.001 HIS H 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.19 (12841) covalent geometry : angle 0.62847 / 0.36 (18575) hydrogen bonds : bond 0.04738 / 3.16 ( 750) hydrogen bonds : angle 2.88920 / 2.07 ( 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 108 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.320 Fit side-chains REVERT: A 59 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6772 (pm20) REVERT: E 42 ARG cc_start: 0.7537 (mmt90) cc_final: 0.6156 (mmm160) REVERT: E 105 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7679 (mt-10) REVERT: F 52 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7890 (mm-30) REVERT: G 72 ASP cc_start: 0.8198 (m-30) cc_final: 0.7800 (m-30) outliers start: 24 outliers final: 15 residues processed: 97 average time/residue: 0.6805 time to fit residues: 70.5395 Evaluate side-chains 97 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS 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 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 51 MET 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: 0.6980 chunk 56 optimal weight: 30.0000 chunk 16 optimal weight: 0.1980 chunk 48 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 63 optimal weight: 30.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.196094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.131665 restraints weight = 26561.675| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.40 r_work: 0.3330 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 12841 Z= 0.124 Angle : 0.592 9.421 18575 Z= 0.345 Chirality : 0.043 0.221 2108 Planarity : 0.005 0.078 1346 Dihedral : 31.546 169.642 4001 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.51 % Allowed : 23.04 % 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: 1.90 (0.31), residues: 752 helix: 2.09 (0.23), residues: 543 sheet: None (None), residues: 0 loop : -1.01 (0.38), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 35 TYR 0.011 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 0.00201 / 0.12 (12841) covalent geometry : angle 0.59197 / 0.34 (18575) hydrogen bonds : bond 0.04037 / 2.70 ( 750) hydrogen bonds : angle 2.76487 / 1.99 ( 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 96 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.299 Fit side-chains REVERT: A 59 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6551 (pm20) REVERT: E 42 ARG cc_start: 0.7412 (mmt90) cc_final: 0.6063 (mmm160) REVERT: E 105 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7687 (mt-10) REVERT: F 52 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7885 (mm-30) REVERT: H 114 LYS cc_start: 0.8326 (tppp) cc_final: 0.7805 (ttmm) REVERT: G 72 ASP cc_start: 0.8173 (m-30) cc_final: 0.7763 (m-30) outliers start: 16 outliers final: 10 residues processed: 89 average time/residue: 0.7204 time to fit residues: 68.2931 Evaluate side-chains 90 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 59 GLU 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 51 MET Chi-restraints excluded: chain C residue 107 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 83 optimal weight: 0.0570 chunk 40 optimal weight: 0.6980 chunk 68 optimal weight: 30.0000 chunk 25 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.196085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.130401 restraints weight = 28390.994| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.37 r_work: 0.3328 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12841 Z= 0.132 Angle : 0.583 7.458 18575 Z= 0.341 Chirality : 0.043 0.215 2108 Planarity : 0.004 0.048 1346 Dihedral : 31.490 169.793 4001 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.51 % Allowed : 22.88 % 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: 2.00 (0.30), residues: 752 helix: 2.16 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -0.98 (0.38), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 42 TYR 0.010 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 0.00234 / 0.13 (12841) covalent geometry : angle 0.58279 / 0.34 (18575) hydrogen bonds : bond 0.04041 / 2.70 ( 750) hydrogen bonds : angle 2.75435 / 1.98 ( 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 97 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.282 Fit side-chains REVERT: A 59 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6568 (pm20) REVERT: B 35 ARG cc_start: 0.8075 (mtp180) cc_final: 0.7813 (mtm110) REVERT: E 42 ARG cc_start: 0.7490 (mmt90) cc_final: 0.6165 (mmm160) REVERT: E 76 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8467 (tp-100) REVERT: E 105 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7624 (mt-10) REVERT: F 52 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7885 (mm-30) REVERT: H 114 LYS cc_start: 0.8368 (tppp) cc_final: 0.7863 (ttmm) REVERT: G 72 ASP cc_start: 0.8170 (m-30) cc_final: 0.7818 (m-30) outliers start: 16 outliers final: 11 residues processed: 90 average time/residue: 0.7647 time to fit residues: 73.0525 Evaluate side-chains 93 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 59 GLU 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 76 GLN 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 51 MET 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: 0.0470 chunk 28 optimal weight: 6.9990 chunk 63 optimal weight: 30.0000 chunk 56 optimal weight: 30.0000 chunk 66 optimal weight: 50.0000 chunk 30 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 76 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.3484 ------------------------------------------------------------------------------- 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 = 0.4268 r_free = 0.4268 target = 0.195957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.130707 restraints weight = 28362.004| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.30 r_work: 0.3313 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.126 12841 Z= 0.177 Angle : 0.841 59.199 18575 Z= 0.497 Chirality : 0.046 0.753 2108 Planarity : 0.004 0.048 1346 Dihedral : 31.489 169.754 4001 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.19 % Allowed : 23.35 % Favored : 74.45 % Cbeta Deviations : 0.14 % 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: 1.98 (0.30), residues: 752 helix: 2.15 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -0.99 (0.38), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 42 TYR 0.009 0.001 TYR H 38 PHE 0.013 0.001 PHE E 67 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.18 (12841) covalent geometry : angle 0.84110 / 0.50 (18575) hydrogen bonds : bond 0.04088 / 2.73 ( 750) hydrogen bonds : angle 2.75723 / 1.98 ( 1879) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3423.62 seconds wall clock time: 58 minutes 59.18 seconds (3539.18 seconds total)