Starting phenix.real_space_refine on Fri Aug 7 08:12:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mlr_48378/08_2026/9mlr_48378.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mlr_48378/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9mlr_48378/08_2026/9mlr_48378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mlr_48378/08_2026/9mlr_48378.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mlr_48378/08_2026/9mlr_48378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mlr_48378/08_2026/9mlr_48378.map" } 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-2.2rc3-6140/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: 2.69, per 1000 atoms: 0.13 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: 1.35 Conformation dependent library (CDL) restraints added in 256.0 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: 2.35 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: 3.80 Time building geometry restraints manager: 1.96 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: 32439 1.23 - 2.46: 4578 2.46 - 3.70: 542 3.70 - 4.93: 165 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: 1.910 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: 0.060 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.270 Find NCS groups from input model: 0.170 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:0.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.580 ------------------------------------------------------------------------------- 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= 0.604 Angle : 1.007 6.159 16989 Z= 0.836 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 1.00661 / 0.84 (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 : 0.261 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: 0.3038 time to fit residues: 55.4286 Evaluate side-chains 114 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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: 0.8980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.086736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.062050 restraints weight = 70217.427| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.89 r_work: 0.2823 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1616 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= 0.185 Angle : 0.696 7.345 16989 Z= 0.450 Chirality : 0.047 0.200 1932 Planarity : 0.005 0.044 1280 Dihedral : 28.991 103.296 3591 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.14 % Allowed : 6.98 % Favored : 91.88 % 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: 1.78 (0.29), residues: 732 helix: 1.77 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -0.38 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 70 TYR 0.009 0.001 TYR H 38 PHE 0.009 0.001 PHE A 68 HIS 0.005 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.19 (11784) covalent geometry : angle 0.69604 / 0.45 (16989) hydrogen bonds : bond 0.06810 / 4.57 ( 701) hydrogen bonds : angle 3.42146 / 2.48 ( 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 130 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: H 84 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.7870 (mtm-85) outliers start: 7 outliers final: 3 residues processed: 127 average time/residue: 0.2471 time to fit residues: 40.4726 Evaluate side-chains 119 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain H residue 84 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 16 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 52 optimal weight: 0.0050 chunk 8 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.085215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.060531 restraints weight = 70974.597| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.90 r_work: 0.2794 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 11784 Z= 0.200 Angle : 0.638 6.332 16989 Z= 0.424 Chirality : 0.042 0.199 1932 Planarity : 0.005 0.048 1280 Dihedral : 29.308 105.400 3591 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.79 % Allowed : 6.17 % 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: 2.09 (0.30), residues: 732 helix: 2.20 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.93 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 93 TYR 0.011 0.001 TYR H 38 PHE 0.008 0.001 PHE H 68 HIS 0.003 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.20 (11784) covalent geometry : angle 0.63811 / 0.42 (16989) hydrogen bonds : bond 0.06553 / 4.36 ( 701) hydrogen bonds : angle 3.28557 / 2.38 ( 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 126 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 60 GLU cc_start: 0.7783 (pt0) cc_final: 0.7405 (pm20) outliers start: 11 outliers final: 6 residues processed: 118 average time/residue: 0.2811 time to fit residues: 42.2394 Evaluate side-chains 113 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 31 ARG 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: 2.9990 chunk 91 optimal weight: 10.0000 chunk 17 optimal weight: 0.0670 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 overall best weight: 1.6124 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.085229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.060792 restraints weight = 70923.150| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.87 r_work: 0.2803 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2474 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= 0.170 Angle : 0.610 6.814 16989 Z= 0.397 Chirality : 0.041 0.212 1932 Planarity : 0.004 0.049 1280 Dihedral : 29.382 106.709 3591 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 0.82 % Favored : 99.04 % Rotamer: Outliers : 0.81 % Allowed : 7.79 % Favored : 91.40 % 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: 2.29 (0.30), residues: 732 helix: 2.46 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.22 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 93 TYR 0.008 0.001 TYR H 38 PHE 0.006 0.001 PHE F 62 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.17 (11784) covalent geometry : angle 0.60965 / 0.40 (16989) hydrogen bonds : bond 0.05835 / 3.86 ( 701) hydrogen bonds : angle 3.13386 / 2.26 ( 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 118 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: C 90 ASN cc_start: 0.8902 (m-40) cc_final: 0.8584 (m110) REVERT: E 60 GLU cc_start: 0.7862 (pt0) cc_final: 0.7612 (pm20) REVERT: E 106 GLU cc_start: 0.8384 (tt0) cc_final: 0.8154 (mt-10) REVERT: H 33 GLU cc_start: 0.8796 (mp0) cc_final: 0.8472 (mm-30) outliers start: 5 outliers final: 3 residues processed: 113 average time/residue: 0.3002 time to fit residues: 43.2055 Evaluate side-chains 112 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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=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: 1.9990 chunk 35 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.083569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.058845 restraints weight = 71722.283| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.92 r_work: 0.2756 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2604 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= 0.205 Angle : 0.611 6.093 16989 Z= 0.400 Chirality : 0.041 0.216 1932 Planarity : 0.004 0.049 1280 Dihedral : 29.389 107.779 3591 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.97 % Allowed : 8.12 % Favored : 90.91 % 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: 2.28 (0.30), residues: 732 helix: 2.50 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.41 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 70 TYR 0.009 0.001 TYR H 38 PHE 0.006 0.001 PHE H 63 HIS 0.007 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.20 (11784) covalent geometry : angle 0.61097 / 0.40 (16989) hydrogen bonds : bond 0.06255 / 4.15 ( 701) hydrogen bonds : angle 3.20804 / 2.32 ( 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 117 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: C 90 ASN cc_start: 0.8906 (m-40) cc_final: 0.8579 (m110) REVERT: E 60 GLU cc_start: 0.7932 (pt0) cc_final: 0.7696 (pm20) REVERT: E 106 GLU cc_start: 0.8399 (tt0) cc_final: 0.8176 (mt-10) REVERT: H 33 GLU cc_start: 0.8852 (mp0) cc_final: 0.8492 (mm-30) outliers start: 6 outliers final: 5 residues processed: 111 average time/residue: 0.3058 time to fit residues: 42.9672 Evaluate side-chains 114 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 31 ARG 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: 0.9980 chunk 76 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.084988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.060303 restraints weight = 71594.580| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.92 r_work: 0.2795 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 11784 Z= 0.142 Angle : 0.571 5.660 16989 Z= 0.378 Chirality : 0.040 0.189 1932 Planarity : 0.004 0.047 1280 Dihedral : 29.402 107.571 3591 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.65 % Allowed : 9.09 % Favored : 90.26 % 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: 2.60 (0.31), residues: 732 helix: 2.74 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.30 (0.38), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 36 TYR 0.008 0.001 TYR H 38 PHE 0.006 0.001 PHE F 62 HIS 0.004 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.14 (11784) covalent geometry : angle 0.57102 / 0.38 (16989) hydrogen bonds : bond 0.05293 / 3.51 ( 701) hydrogen bonds : angle 2.90314 / 2.09 ( 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 117 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: C 90 ASN cc_start: 0.8882 (m-40) cc_final: 0.8549 (m110) REVERT: E 106 GLU cc_start: 0.8385 (tt0) cc_final: 0.8139 (mt-10) REVERT: F 64 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8700 (mt-10) REVERT: H 33 GLU cc_start: 0.8881 (mp0) cc_final: 0.8519 (mm-30) outliers start: 4 outliers final: 2 residues processed: 113 average time/residue: 0.2842 time to fit residues: 41.3308 Evaluate side-chains 111 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 ARG 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: 10.0000 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 10.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.084255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.059565 restraints weight = 71657.371| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.93 r_work: 0.2777 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11784 Z= 0.175 Angle : 0.582 5.701 16989 Z= 0.381 Chirality : 0.040 0.206 1932 Planarity : 0.004 0.049 1280 Dihedral : 29.361 108.571 3591 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.14 % Allowed : 9.42 % Favored : 89.45 % 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: 2.57 (0.31), residues: 732 helix: 2.75 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.44 (0.38), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 36 TYR 0.009 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 0.00314 / 0.18 (11784) covalent geometry : angle 0.58212 / 0.38 (16989) hydrogen bonds : bond 0.05636 / 3.75 ( 701) hydrogen bonds : angle 2.99980 / 2.16 ( 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 118 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: C 90 ASN cc_start: 0.8895 (m-40) cc_final: 0.8564 (m110) REVERT: E 60 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7207 (pm20) REVERT: H 33 GLU cc_start: 0.8939 (mp0) cc_final: 0.8567 (mm-30) outliers start: 7 outliers final: 5 residues processed: 111 average time/residue: 0.2997 time to fit residues: 42.5945 Evaluate side-chains 114 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 75 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.083890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.059180 restraints weight = 71659.997| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.96 r_work: 0.2767 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3042 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 : 0.578 5.761 16989 Z= 0.378 Chirality : 0.039 0.197 1932 Planarity : 0.005 0.090 1280 Dihedral : 29.344 109.275 3591 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.30 % Allowed : 8.93 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.31), residues: 732 helix: 2.76 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.52 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 93 TYR 0.008 0.001 TYR H 38 PHE 0.007 0.001 PHE H 63 HIS 0.004 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.17 (11784) covalent geometry : angle 0.57829 / 0.38 (16989) hydrogen bonds : bond 0.05652 / 3.76 ( 701) hydrogen bonds : angle 3.00223 / 2.16 ( 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 118 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: C 90 ASN cc_start: 0.8866 (m-40) cc_final: 0.8543 (m110) REVERT: E 60 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7249 (pm20) REVERT: E 106 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8126 (mt-10) outliers start: 8 outliers final: 3 residues processed: 111 average time/residue: 0.3006 time to fit residues: 43.1576 Evaluate side-chains 113 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 31 ARG 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: 1.9990 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: 0.7980 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.084143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.059296 restraints weight = 71326.098| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.97 r_work: 0.2773 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11784 Z= 0.162 Angle : 0.570 5.637 16989 Z= 0.373 Chirality : 0.039 0.177 1932 Planarity : 0.004 0.054 1280 Dihedral : 29.287 110.104 3591 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.14 % Allowed : 9.42 % Favored : 89.45 % 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: 2.65 (0.31), residues: 732 helix: 2.84 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.49 (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 0.00281 / 0.16 (11784) covalent geometry : angle 0.57034 / 0.37 (16989) hydrogen bonds : bond 0.05405 / 3.59 ( 701) hydrogen bonds : angle 2.93511 / 2.10 ( 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 119 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: C 16 LYS cc_start: 0.8558 (tttm) cc_final: 0.8335 (tttp) REVERT: C 90 ASN cc_start: 0.8864 (m-40) cc_final: 0.8544 (m110) REVERT: E 60 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7344 (pm20) REVERT: E 106 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8109 (mt-10) REVERT: H 33 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8775 (mm-30) REVERT: H 74 GLU cc_start: 0.9050 (tp30) cc_final: 0.8746 (tp30) outliers start: 7 outliers final: 2 residues processed: 112 average time/residue: 0.2749 time to fit residues: 39.6010 Evaluate side-chains 114 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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: 0.9990 chunk 40 optimal weight: 1.9990 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: 0.7980 chunk 23 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.083655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.058890 restraints weight = 72221.903| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.94 r_work: 0.2768 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11784 Z= 0.165 Angle : 0.576 7.113 16989 Z= 0.374 Chirality : 0.039 0.164 1932 Planarity : 0.005 0.067 1280 Dihedral : 29.281 110.322 3591 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.65 % Allowed : 10.23 % 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: 2.65 (0.31), residues: 732 helix: 2.86 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.57 (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 0.004 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.17 (11784) covalent geometry : angle 0.57594 / 0.37 (16989) hydrogen bonds : bond 0.05428 / 3.61 ( 701) hydrogen bonds : angle 2.92573 / 2.10 ( 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 116 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: C 16 LYS cc_start: 0.8586 (tttm) cc_final: 0.8328 (tttp) REVERT: C 90 ASN cc_start: 0.8910 (m-40) cc_final: 0.8580 (m110) REVERT: E 60 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7353 (pm20) REVERT: E 106 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: H 33 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8707 (mm-30) outliers start: 4 outliers final: 2 residues processed: 112 average time/residue: 0.3359 time to fit residues: 47.8944 Evaluate side-chains 115 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 56 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 75 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.083563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.058888 restraints weight = 71700.925| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.92 r_work: 0.2768 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11784 Z= 0.168 Angle : 0.576 6.385 16989 Z= 0.374 Chirality : 0.039 0.153 1932 Planarity : 0.004 0.057 1280 Dihedral : 29.280 110.665 3591 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.97 % Allowed : 10.06 % Favored : 88.96 % 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: 2.61 (0.31), residues: 732 helix: 2.84 (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 0.00299 / 0.17 (11784) covalent geometry : angle 0.57632 / 0.37 (16989) hydrogen bonds : bond 0.05470 / 3.64 ( 701) hydrogen bonds : angle 2.94380 / 2.11 ( 1773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3945.67 seconds wall clock time: 67 minutes 25.95 seconds (4045.95 seconds total)