Starting phenix.real_space_refine on Sat Jul 4 11:16:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mlr_48378/07_2026/9mlr_48378.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mlr_48378/07_2026/9mlr_48378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mlr_48378/07_2026/9mlr_48378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mlr_48378/07_2026/9mlr_48378.map" model { file = "/net/cci-nas-00/data/ceres_data/9mlr_48378/07_2026/9mlr_48378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mlr_48378/07_2026/9mlr_48378.cif" } resolution = 3.1 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= 0.013 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: 6 Type Number sf(0) Gaussians P 252 5.49 5 S 14 5.16 5 C 6177 2.51 5 N 2076 2.21 5 O 2558 1.98 5 H 9048 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20125 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1626 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1291 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1693 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1460 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1585 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "F" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1291 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1691 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1494 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 3982 Classifications: {'DNA': 126} Link IDs: {'rna3p': 125} Chain: "J" Number of atoms: 4012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 4012 Classifications: {'DNA': 126} Link IDs: {'rna3p': 125} Time building chain proxies: 2.96, per 1000 atoms: 0.15 Number of scatterers: 20125 At special positions: 0 Unit cell: (79.12, 118.68, 121.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 14 16.00 P 252 15.00 O 2558 8.00 N 2076 7.00 C 6177 6.00 H 9048 1.00 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: 1.24 Conformation dependent library (CDL) restraints added in 434.5 milliseconds 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1388 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 9 sheets defined 72.3% alpha, 2.4% beta 124 base pairs and 227 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 86 through 115 removed outlier: 3.657A pdb=" N VAL A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 115 " --> pdb=" O CYS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'B' and resid 25 through 30 removed outlier: 3.714A pdb=" N GLN B 28 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 removed outlier: 3.719A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.450A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 93 through 98 Processing helix chain 'D' and resid 35 through 47 Processing helix chain 'D' and resid 53 through 82 removed outlier: 3.501A pdb=" N GLU D 69 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU D 74 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS D 80 " --> pdb=" O SER D 76 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 100 Processing helix chain 'D' and resid 101 through 122 removed outlier: 3.544A pdb=" N LYS D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.614A pdb=" N LEU E 49 " --> pdb=" O GLY E 45 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 86 through 115 removed outlier: 3.747A pdb=" N VAL E 90 " --> pdb=" O GLN E 86 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 132 removed outlier: 3.688A pdb=" N ILE E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 30 removed outlier: 3.666A pdb=" N GLN F 28 " --> pdb=" O ASP F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.575A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.556A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 47 through 74 Processing helix chain 'G' and resid 80 through 90 removed outlier: 3.532A pdb=" N LEU G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 98 Processing helix chain 'H' and resid 35 through 47 Processing helix chain 'H' and resid 53 through 82 removed outlier: 3.539A pdb=" N ASN H 65 " --> pdb=" O ASN H 61 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN H 82 " --> pdb=" O LEU H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 100 Processing helix chain 'H' and resid 101 through 123 removed outlier: 3.528A pdb=" N LYS H 106 " --> pdb=" O GLY H 102 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS H 123 " --> pdb=" O TYR H 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.681A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.004A pdb=" N ARG C 43 " --> pdb=" O ILE D 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103 removed outlier: 7.030A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 7.076A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.295A pdb=" N ARG G 43 " --> pdb=" O ILE H 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 78 through 79 383 hydrogen bonds defined for protein. 1137 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 318 hydrogen bonds 636 hydrogen bond angles 0 basepair planarities 124 basepair parallelities 227 stacking parallelities Total time for adding SS restraints: 3.33 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9044 1.03 - 1.23: 95 1.23 - 1.42: 5033 1.42 - 1.61: 6636 1.61 - 1.81: 24 Bond restraints: 20832 Sorted by residual: bond pdb=" C3' DC I 69 " pdb=" C2' DC I 69 " ideal model delta sigma weight residual 1.516 1.554 -0.038 8.00e-03 1.56e+04 2.22e+01 bond pdb=" C3' DT I -26 " pdb=" C2' DT I -26 " ideal model delta sigma weight residual 1.516 1.553 -0.037 8.00e-03 1.56e+04 2.19e+01 bond pdb=" C3' DG J -69 " pdb=" C2' DG J -69 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.96e+01 bond pdb=" C3' DG I -7 " pdb=" C2' DG I -7 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.82e+01 bond pdb=" C3' DG I -37 " pdb=" C2' DG I -37 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.57e+01 ... (remaining 20827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 32502 1.23 - 2.46: 4542 2.46 - 3.70: 516 3.70 - 4.93: 164 4.93 - 6.16: 32 Bond angle restraints: 37756 Sorted by residual: angle pdb=" O4' DT J -16 " pdb=" C1' DT J -16 " pdb=" N1 DT J -16 " ideal model delta sigma weight residual 108.00 113.11 -5.11 7.00e-01 2.04e+00 5.33e+01 angle pdb=" O5' DT J -16 " pdb=" C5' DT J -16 " pdb=" C4' DT J -16 " ideal model delta sigma weight residual 109.40 115.04 -5.64 8.00e-01 1.56e+00 4.98e+01 angle pdb=" O5' DT I 68 " pdb=" C5' DT I 68 " pdb=" C4' DT I 68 " ideal model delta sigma weight residual 109.40 114.31 -4.91 8.00e-01 1.56e+00 3.76e+01 angle pdb=" O4' DA I -5 " pdb=" C1' DA I -5 " pdb=" N9 DA I -5 " ideal model delta sigma weight residual 108.00 103.72 4.28 7.00e-01 2.04e+00 3.74e+01 angle pdb=" O4' DC J -25 " pdb=" C1' DC J -25 " pdb=" N1 DC J -25 " ideal model delta sigma weight residual 108.00 112.26 -4.26 7.00e-01 2.04e+00 3.71e+01 ... (remaining 37751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 6280 17.68 - 35.37: 1105 35.37 - 53.05: 884 53.05 - 70.73: 427 70.73 - 88.42: 16 Dihedral angle restraints: 8712 sinusoidal: 6293 harmonic: 2419 Sorted by residual: dihedral pdb=" CA PRO H 101 " pdb=" C PRO H 101 " pdb=" N GLY H 102 " pdb=" CA GLY H 102 " ideal model delta harmonic sigma weight residual 180.00 155.08 24.92 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA GLY B 29 " pdb=" C GLY B 29 " pdb=" N ILE B 30 " pdb=" CA ILE B 30 " ideal model delta harmonic sigma weight residual 180.00 160.07 19.93 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ARG E 117 " pdb=" C ARG E 117 " pdb=" N VAL E 118 " pdb=" CA VAL E 118 " ideal model delta harmonic sigma weight residual 180.00 160.76 19.24 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 8709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1167 0.046 - 0.091: 471 0.091 - 0.137: 207 0.137 - 0.183: 78 0.183 - 0.228: 9 Chirality restraints: 1932 Sorted by residual: chirality pdb=" C4' DC I 69 " pdb=" C5' DC I 69 " pdb=" O4' DC I 69 " pdb=" C3' DC I 69 " both_signs ideal model delta sigma weight residual False -2.53 -2.30 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C4' DC I 21 " pdb=" C5' DC I 21 " pdb=" O4' DC I 21 " pdb=" C3' DC I 21 " both_signs ideal model delta sigma weight residual False -2.53 -2.32 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C1' DG I 54 " pdb=" O4' DG I 54 " pdb=" C2' DG I 54 " pdb=" N9 DG I 54 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1929 not shown) Planarity restraints: 2194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I -12 " -0.042 2.00e-02 2.50e+03 3.14e-02 2.71e+01 pdb=" N1 DC I -12 " 0.087 2.00e-02 2.50e+03 pdb=" C2 DC I -12 " -0.037 2.00e-02 2.50e+03 pdb=" O2 DC I -12 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DC I -12 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I -12 " -0.000 2.00e-02 2.50e+03 pdb=" N4 DC I -12 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DC I -12 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DC I -12 " 0.002 2.00e-02 2.50e+03 pdb=" H5 DC I -12 " -0.009 2.00e-02 2.50e+03 pdb=" H6 DC I -12 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 89 " 0.043 9.50e-02 1.11e+02 3.58e-02 2.43e+01 pdb=" NE ARG C 89 " -0.002 2.00e-02 2.50e+03 pdb=" CZ ARG C 89 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 89 " -0.049 2.00e-02 2.50e+03 pdb=" NH2 ARG C 89 " 0.049 2.00e-02 2.50e+03 pdb="HH11 ARG C 89 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG C 89 " 0.050 2.00e-02 2.50e+03 pdb="HH21 ARG C 89 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG C 89 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 49 " 0.042 2.00e-02 2.50e+03 2.97e-02 2.43e+01 pdb=" N1 DC I 49 " -0.082 2.00e-02 2.50e+03 pdb=" C2 DC I 49 " 0.034 2.00e-02 2.50e+03 pdb=" O2 DC I 49 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DC I 49 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 49 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC I 49 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DC I 49 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DC I 49 " -0.002 2.00e-02 2.50e+03 pdb=" H5 DC I 49 " 0.007 2.00e-02 2.50e+03 pdb=" H6 DC I 49 " 0.003 2.00e-02 2.50e+03 ... (remaining 2191 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.82: 14 1.82 - 2.52: 12408 2.52 - 3.21: 54110 3.21 - 3.91: 73354 3.91 - 4.60: 120243 Nonbonded interactions: 260129 Sorted by model distance: nonbonded pdb=" O ASN G 74 " pdb="HD21 ASN G 74 " model vdw 1.128 2.450 nonbonded pdb=" O PRO C 110 " pdb="HD21 ASN C 111 " model vdw 1.402 2.450 nonbonded pdb="HH21 ARG F 93 " pdb=" OE1 GLU H 74 " model vdw 1.482 2.450 nonbonded pdb="HH12 ARG H 84 " pdb=" OP2 DG J -33 " model vdw 1.535 2.450 nonbonded pdb=" OD2 ASP A 107 " pdb="HH11 ARG A 132 " model vdw 1.648 2.450 ... (remaining 260124 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' and resid 41 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = (chain 'G' and resid 13 through 118) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 31 through 122) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.990 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 11784 Z= 0.603 Angle : 0.995 6.159 16989 Z= 0.823 Chirality : 0.062 0.228 1932 Planarity : 0.011 0.104 1280 Dihedral : 26.045 88.417 5054 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.16 % Allowed : 5.84 % Favored : 93.99 % 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: 0.12 (0.27), residues: 732 helix: 0.20 (0.20), residues: 519 sheet: None (None), residues: 0 loop : 0.18 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG F 40 TYR 0.016 0.004 TYR G 58 PHE 0.011 0.002 PHE D 63 HIS 0.013 0.003 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.60 (11784) covalent geometry : angle 0.99497 / 0.82 (16989) hydrogen bonds : bond 0.13025 / 8.83 ( 701) hydrogen bonds : angle 3.89193 / 2.79 ( 1773) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 148 average time/residue: 0.3516 time to fit residues: 63.9298 Evaluate side-chains 113 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.086750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.062254 restraints weight = 69901.958| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.87 r_work: 0.2826 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11784 Z= 0.184 Angle : 0.698 7.090 16989 Z= 0.449 Chirality : 0.046 0.185 1932 Planarity : 0.005 0.044 1280 Dihedral : 28.988 105.020 3591 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.97 % Allowed : 6.98 % Favored : 92.05 % 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: 1.77 (0.29), residues: 732 helix: 1.76 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -0.39 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 70 TYR 0.008 0.001 TYR H 38 PHE 0.010 0.001 PHE F 62 HIS 0.005 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.18 (11784) covalent geometry : angle 0.69825 / 0.45 (16989) hydrogen bonds : bond 0.06687 / 4.48 ( 701) hydrogen bonds : angle 3.46620 / 2.51 ( 1773) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.404 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 125 average time/residue: 0.2715 time to fit residues: 44.3696 Evaluate side-chains 117 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain E residue 75 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 16 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.084610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.059836 restraints weight = 70501.087| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.88 r_work: 0.2778 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11784 Z= 0.223 Angle : 0.646 6.218 16989 Z= 0.429 Chirality : 0.043 0.201 1932 Planarity : 0.005 0.049 1280 Dihedral : 29.282 107.627 3591 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.14 % Allowed : 6.49 % Favored : 92.37 % 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: 1.93 (0.30), residues: 732 helix: 2.08 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.99 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 70 TYR 0.011 0.001 TYR H 38 PHE 0.007 0.001 PHE D 63 HIS 0.004 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.22 (11784) covalent geometry : angle 0.64566 / 0.43 (16989) hydrogen bonds : bond 0.06915 / 4.60 ( 701) hydrogen bonds : angle 3.40206 / 2.47 ( 1773) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 60 GLU cc_start: 0.7814 (pt0) cc_final: 0.7423 (pm20) outliers start: 7 outliers final: 5 residues processed: 113 average time/residue: 0.2716 time to fit residues: 38.8972 Evaluate side-chains 109 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain E residue 75 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 3 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 26 ASN G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.085049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.060654 restraints weight = 70848.252| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.88 r_work: 0.2799 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11784 Z= 0.172 Angle : 0.605 6.214 16989 Z= 0.400 Chirality : 0.041 0.200 1932 Planarity : 0.004 0.048 1280 Dihedral : 29.379 108.338 3591 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.81 % Allowed : 7.63 % Favored : 91.56 % 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: 2.22 (0.30), residues: 732 helix: 2.37 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.15 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 97 TYR 0.008 0.001 TYR H 38 PHE 0.006 0.001 PHE D 63 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.17 (11784) covalent geometry : angle 0.60454 / 0.40 (16989) hydrogen bonds : bond 0.05954 / 3.94 ( 701) hydrogen bonds : angle 3.17367 / 2.29 ( 1773) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 90 ASN cc_start: 0.8904 (m-40) cc_final: 0.8593 (m110) REVERT: E 60 GLU cc_start: 0.7842 (pt0) cc_final: 0.7577 (pm20) REVERT: E 106 GLU cc_start: 0.8375 (tt0) cc_final: 0.8166 (mt-10) outliers start: 5 outliers final: 4 residues processed: 114 average time/residue: 0.2979 time to fit residues: 43.2632 Evaluate side-chains 113 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain E residue 75 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 60 optimal weight: 0.4980 chunk 88 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.084076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.059447 restraints weight = 71823.309| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.92 r_work: 0.2773 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11784 Z= 0.175 Angle : 0.596 5.611 16989 Z= 0.392 Chirality : 0.041 0.207 1932 Planarity : 0.004 0.047 1280 Dihedral : 29.412 109.738 3591 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.81 % Allowed : 8.44 % Favored : 90.75 % 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: 2.43 (0.30), residues: 732 helix: 2.61 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.33 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 93 TYR 0.009 0.001 TYR H 38 PHE 0.005 0.001 PHE E 68 HIS 0.003 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.17 (11784) covalent geometry : angle 0.59576 / 0.39 (16989) hydrogen bonds : bond 0.05876 / 3.91 ( 701) hydrogen bonds : angle 3.08089 / 2.23 ( 1773) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.418 Fit side-chains REVERT: C 90 ASN cc_start: 0.8876 (m-40) cc_final: 0.8539 (m110) REVERT: E 60 GLU cc_start: 0.7915 (pt0) cc_final: 0.7681 (pm20) REVERT: E 106 GLU cc_start: 0.8381 (tt0) cc_final: 0.8134 (mt-10) REVERT: H 33 GLU cc_start: 0.8828 (mp0) cc_final: 0.8574 (mm-30) outliers start: 5 outliers final: 4 residues processed: 113 average time/residue: 0.2914 time to fit residues: 41.9304 Evaluate side-chains 112 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain E residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 14 optimal weight: 0.0770 chunk 76 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.085113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.060446 restraints weight = 71873.166| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.94 r_work: 0.2801 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11784 Z= 0.141 Angle : 0.563 5.416 16989 Z= 0.375 Chirality : 0.040 0.187 1932 Planarity : 0.004 0.046 1280 Dihedral : 29.423 109.991 3591 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.65 % Allowed : 8.93 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.31), residues: 732 helix: 2.82 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.29 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 43 TYR 0.007 0.001 TYR H 38 PHE 0.006 0.001 PHE D 63 HIS 0.005 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.14 (11784) covalent geometry : angle 0.56335 / 0.37 (16989) hydrogen bonds : bond 0.05187 / 3.45 ( 701) hydrogen bonds : angle 2.87028 / 2.06 ( 1773) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.265 Fit side-chains REVERT: C 90 ASN cc_start: 0.8857 (m-40) cc_final: 0.8530 (m110) REVERT: F 64 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8692 (mt-10) REVERT: H 33 GLU cc_start: 0.8845 (mp0) cc_final: 0.8557 (mm-30) outliers start: 4 outliers final: 3 residues processed: 113 average time/residue: 0.2945 time to fit residues: 42.6445 Evaluate side-chains 110 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain E residue 75 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 22 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 11.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.083983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.059398 restraints weight = 71661.835| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.95 r_work: 0.2771 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11784 Z= 0.184 Angle : 0.585 5.527 16989 Z= 0.383 Chirality : 0.040 0.209 1932 Planarity : 0.004 0.049 1280 Dihedral : 29.393 111.241 3591 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.65 % Allowed : 9.42 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.31), residues: 732 helix: 2.83 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.46 (0.38), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 93 TYR 0.009 0.001 TYR H 38 PHE 0.006 0.001 PHE H 63 HIS 0.006 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.18 (11784) covalent geometry : angle 0.58482 / 0.38 (16989) hydrogen bonds : bond 0.05751 / 3.83 ( 701) hydrogen bonds : angle 3.01972 / 2.18 ( 1773) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.418 Fit side-chains REVERT: C 90 ASN cc_start: 0.8875 (m-40) cc_final: 0.8552 (m110) REVERT: E 60 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7185 (pm20) REVERT: E 106 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8121 (mt-10) outliers start: 4 outliers final: 2 residues processed: 108 average time/residue: 0.2806 time to fit residues: 38.9435 Evaluate side-chains 109 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 106 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 63 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.084863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.060061 restraints weight = 71719.736| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.98 r_work: 0.2789 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11784 Z= 0.144 Angle : 0.560 5.456 16989 Z= 0.370 Chirality : 0.039 0.189 1932 Planarity : 0.004 0.074 1280 Dihedral : 29.391 111.575 3591 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.97 % Allowed : 9.09 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.31), residues: 732 helix: 2.92 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.42 (0.38), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.008 0.001 TYR H 38 PHE 0.007 0.001 PHE D 63 HIS 0.002 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.14 (11784) covalent geometry : angle 0.56023 / 0.37 (16989) hydrogen bonds : bond 0.05161 / 3.43 ( 701) hydrogen bonds : angle 2.85718 / 2.05 ( 1773) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: C 90 ASN cc_start: 0.8871 (m-40) cc_final: 0.8549 (m110) REVERT: E 60 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7194 (pm20) REVERT: E 106 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: H 33 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8161 (mm-30) outliers start: 6 outliers final: 2 residues processed: 110 average time/residue: 0.3087 time to fit residues: 43.2838 Evaluate side-chains 111 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 106 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 21 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.084547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.059824 restraints weight = 71434.073| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.98 r_work: 0.2786 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11784 Z= 0.157 Angle : 0.560 5.484 16989 Z= 0.370 Chirality : 0.039 0.192 1932 Planarity : 0.004 0.061 1280 Dihedral : 29.326 112.308 3591 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.65 % Allowed : 10.06 % Favored : 89.29 % 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: 2.82 (0.31), residues: 732 helix: 2.96 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.43 (0.38), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 96 TYR 0.008 0.001 TYR H 38 PHE 0.006 0.001 PHE H 63 HIS 0.004 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.16 (11784) covalent geometry : angle 0.56036 / 0.37 (16989) hydrogen bonds : bond 0.05244 / 3.49 ( 701) hydrogen bonds : angle 2.87735 / 2.06 ( 1773) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 0.314 Fit side-chains REVERT: A 77 GLN cc_start: 0.8866 (tt0) cc_final: 0.8650 (tm-30) REVERT: C 90 ASN cc_start: 0.8874 (m-40) cc_final: 0.8554 (m110) REVERT: E 60 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7293 (pm20) REVERT: E 106 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: H 33 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8249 (mm-30) outliers start: 4 outliers final: 2 residues processed: 109 average time/residue: 0.2887 time to fit residues: 40.2259 Evaluate side-chains 112 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 106 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.082605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.057946 restraints weight = 72290.214| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.91 r_work: 0.2742 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11784 Z= 0.220 Angle : 0.607 6.400 16989 Z= 0.389 Chirality : 0.040 0.202 1932 Planarity : 0.005 0.092 1280 Dihedral : 29.311 113.136 3591 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.91 % Favored : 97.95 % Rotamer: Outliers : 0.81 % Allowed : 10.06 % Favored : 89.12 % 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: 2.47 (0.31), residues: 732 helix: 2.74 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.65 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 96 TYR 0.008 0.001 TYR H 38 PHE 0.009 0.001 PHE H 63 HIS 0.005 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.22 (11784) covalent geometry : angle 0.60733 / 0.39 (16989) hydrogen bonds : bond 0.06222 / 4.14 ( 701) hydrogen bonds : angle 3.15789 / 2.27 ( 1773) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.425 Fit side-chains REVERT: C 16 LYS cc_start: 0.8620 (tttm) cc_final: 0.8367 (tttp) REVERT: C 65 GLU cc_start: 0.8398 (tp30) cc_final: 0.8074 (tp30) REVERT: C 90 ASN cc_start: 0.8937 (m-40) cc_final: 0.8612 (m110) REVERT: E 60 GLU cc_start: 0.7928 (pm20) cc_final: 0.7447 (pm20) REVERT: E 106 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8127 (mt-10) REVERT: H 33 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8277 (mm-30) outliers start: 5 outliers final: 3 residues processed: 108 average time/residue: 0.3059 time to fit residues: 42.1073 Evaluate side-chains 109 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 106 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 56 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 75 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.083307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.058787 restraints weight = 71634.738| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.92 r_work: 0.2758 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11784 Z= 0.161 Angle : 0.567 5.708 16989 Z= 0.372 Chirality : 0.038 0.178 1932 Planarity : 0.005 0.065 1280 Dihedral : 29.325 113.331 3591 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.81 % Allowed : 9.90 % Favored : 89.29 % 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: 2.59 (0.31), residues: 732 helix: 2.82 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.59 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.008 0.001 TYR H 38 PHE 0.007 0.001 PHE H 63 HIS 0.003 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.16 (11784) covalent geometry : angle 0.56740 / 0.37 (16989) hydrogen bonds : bond 0.05555 / 3.70 ( 701) hydrogen bonds : angle 2.97707 / 2.14 ( 1773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3964.22 seconds wall clock time: 67 minutes 47.83 seconds (4067.83 seconds total)