Starting phenix.real_space_refine on Thu Feb 5 21:01:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mlr_48378/02_2026/9mlr_48378.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mlr_48378/02_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_48378/02_2026/9mlr_48378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mlr_48378/02_2026/9mlr_48378.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mlr_48378/02_2026/9mlr_48378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mlr_48378/02_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-2.0-5952/lib/python3.9/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: 3.70, per 1000 atoms: 0.18 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: 1.89 Conformation dependent library (CDL) restraints added in 392.5 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: 3.61 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: 4.77 Time building geometry restraints manager: 2.57 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 1.525 1.554 -0.029 2.00e-02 2.50e+03 2.06e+00 bond pdb=" C4' DC I 37 " pdb=" O4' DC I 37 " ideal model delta sigma weight residual 1.450 1.421 0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C3' DT I -26 " pdb=" C2' DT I -26 " ideal model delta sigma weight residual 1.525 1.553 -0.028 2.00e-02 2.50e+03 2.03e+00 bond pdb=" C4' DG I 27 " pdb=" O4' DG I 27 " ideal model delta sigma weight residual 1.450 1.422 0.028 2.00e-02 2.50e+03 1.98e+00 bond pdb=" C3' DG J -69 " pdb=" C2' DG J -69 " ideal model delta sigma weight residual 1.525 1.551 -0.026 2.00e-02 2.50e+03 1.75e+00 ... (remaining 20827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 32581 1.23 - 2.46: 4607 2.46 - 3.70: 505 3.70 - 4.93: 54 4.93 - 6.16: 9 Bond angle restraints: 37756 Sorted by residual: angle pdb=" C4' DC I 21 " pdb=" O4' DC I 21 " pdb=" C1' DC I 21 " ideal model delta sigma weight residual 109.70 104.26 5.44 1.50e+00 4.44e-01 1.32e+01 angle pdb=" C2' DG I -37 " pdb=" C1' DG I -37 " pdb=" N9 DG I -37 " ideal model delta sigma weight residual 113.50 118.59 -5.09 1.50e+00 4.44e-01 1.15e+01 angle pdb=" C4' DC J -27 " pdb=" O4' DC J -27 " pdb=" C1' DC J -27 " ideal model delta sigma weight residual 109.70 104.61 5.09 1.50e+00 4.44e-01 1.15e+01 angle pdb=" CA ASP A 82 " pdb=" CB ASP A 82 " pdb=" CG ASP A 82 " ideal model delta sigma weight residual 112.60 115.91 -3.31 1.00e+00 1.00e+00 1.09e+01 angle pdb=" C2' DT I -26 " pdb=" C1' DT I -26 " pdb=" N1 DT I -26 " ideal model delta sigma weight residual 113.50 118.44 -4.94 1.50e+00 4.44e-01 1.09e+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 - 0.044: 1249 0.044 - 0.089: 552 0.089 - 0.133: 112 0.133 - 0.177: 11 0.177 - 0.222: 8 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 -0.22 2.00e-01 2.50e+01 1.23e+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 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" C1' DC I 66 " pdb=" O4' DC I 66 " pdb=" C2' DC I 66 " pdb=" N1 DC I 66 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 9.41e-01 ... (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: 2.530 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: 0.110 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.630 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 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 : 0.005 0.030 11784 Z= 0.236 Angle : 0.915 6.159 16989 Z= 0.593 Chirality : 0.049 0.222 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 covalent geometry : bond 0.00493 (11784) covalent geometry : angle 0.91539 (16989) hydrogen bonds : bond 0.13025 ( 701) hydrogen bonds : angle 3.89193 ( 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 : 0.461 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: 0.4740 time to fit residues: 83.9350 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 : 0.426 ------------------------------------------------------------------------------- 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: 0.9980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.086539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.061808 restraints weight = 70672.115| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.91 r_work: 0.2830 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11784 Z= 0.189 Angle : 0.637 5.118 16989 Z= 0.399 Chirality : 0.039 0.125 1932 Planarity : 0.004 0.036 1280 Dihedral : 28.875 99.203 3591 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.65 % Allowed : 6.66 % Favored : 92.69 % 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: 2.10 (0.30), residues: 732 helix: 2.06 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.43 (0.38), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 31 TYR 0.010 0.001 TYR D 81 PHE 0.007 0.001 PHE D 63 HIS 0.005 0.001 HIS C 39 Details of bonding type rmsd covalent geometry : bond 0.00399 (11784) covalent geometry : angle 0.63744 (16989) hydrogen bonds : bond 0.05752 ( 701) hydrogen bonds : angle 3.11150 ( 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: 4 poor density : 124 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 60 GLU cc_start: 0.7675 (pt0) cc_final: 0.7370 (pm20) REVERT: H 66 ASP cc_start: 0.8743 (t0) cc_final: 0.8524 (t0) outliers start: 4 outliers final: 3 residues processed: 125 average time/residue: 0.3670 time to fit residues: 57.9820 Evaluate side-chains 113 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 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 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: 0.6980 chunk 89 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN F 26 ASN G 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.084427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.060061 restraints weight = 71910.484| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.93 r_work: 0.2782 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2710 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= 0.192 Angle : 0.608 4.873 16989 Z= 0.381 Chirality : 0.039 0.142 1932 Planarity : 0.005 0.066 1280 Dihedral : 28.751 96.928 3591 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.97 % Allowed : 8.28 % 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: 2.56 (0.31), residues: 732 helix: 2.60 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.94 (0.38), 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 B 62 HIS 0.005 0.001 HIS G 39 Details of bonding type rmsd covalent geometry : bond 0.00410 (11784) covalent geometry : angle 0.60762 (16989) hydrogen bonds : bond 0.05541 ( 701) hydrogen bonds : angle 2.96381 ( 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 123 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: C 65 GLU cc_start: 0.8303 (tp30) cc_final: 0.7932 (tp30) REVERT: E 60 GLU cc_start: 0.7885 (pt0) cc_final: 0.7677 (pm20) REVERT: G 91 ASP cc_start: 0.8268 (t0) cc_final: 0.8015 (t0) REVERT: H 66 ASP cc_start: 0.8919 (t0) cc_final: 0.8696 (t0) outliers start: 6 outliers final: 4 residues processed: 117 average time/residue: 0.4018 time to fit residues: 58.1933 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 : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 111 ASN 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: 4.9990 chunk 17 optimal weight: 0.0040 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.084763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.060232 restraints weight = 72042.335| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.97 r_work: 0.2794 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11784 Z= 0.171 Angle : 0.583 4.824 16989 Z= 0.367 Chirality : 0.038 0.146 1932 Planarity : 0.004 0.042 1280 Dihedral : 28.684 99.731 3591 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.32 % Allowed : 9.25 % 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: 2.81 (0.31), residues: 732 helix: 2.84 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.04 (0.38), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 93 TYR 0.009 0.001 TYR F 52 PHE 0.006 0.001 PHE B 62 HIS 0.004 0.001 HIS C 39 Details of bonding type rmsd covalent geometry : bond 0.00359 (11784) covalent geometry : angle 0.58344 (16989) hydrogen bonds : bond 0.04919 ( 701) hydrogen bonds : angle 2.82442 ( 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 116 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 77 GLN cc_start: 0.8904 (tt0) cc_final: 0.8673 (tm-30) REVERT: C 16 LYS cc_start: 0.8553 (tttm) cc_final: 0.8329 (tttp) REVERT: C 65 GLU cc_start: 0.8274 (tp30) cc_final: 0.7872 (tp30) REVERT: C 90 ASN cc_start: 0.8856 (m-40) cc_final: 0.8569 (m110) REVERT: E 60 GLU cc_start: 0.7901 (pt0) cc_final: 0.7609 (pm20) REVERT: G 91 ASP cc_start: 0.8229 (t0) cc_final: 0.7947 (t0) REVERT: H 66 ASP cc_start: 0.8916 (t0) cc_final: 0.8687 (t0) outliers start: 2 outliers final: 2 residues processed: 114 average time/residue: 0.3570 time to fit residues: 51.2611 Evaluate side-chains 112 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLU 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: 0.9980 chunk 83 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.082549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.057829 restraints weight = 71480.082| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.94 r_work: 0.2729 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 11784 Z= 0.226 Angle : 0.607 4.823 16989 Z= 0.379 Chirality : 0.041 0.145 1932 Planarity : 0.005 0.046 1280 Dihedral : 28.664 101.601 3591 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.65 % Allowed : 9.90 % 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: 2.46 (0.31), residues: 732 helix: 2.66 (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 0.003 0.000 ARG F 36 TYR 0.007 0.001 TYR H 38 PHE 0.010 0.001 PHE B 62 HIS 0.005 0.001 HIS C 39 Details of bonding type rmsd covalent geometry : bond 0.00489 (11784) covalent geometry : angle 0.60655 (16989) hydrogen bonds : bond 0.06112 ( 701) hydrogen bonds : angle 3.08067 ( 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 115 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 77 GLN cc_start: 0.8899 (tt0) cc_final: 0.8662 (tm-30) REVERT: C 16 LYS cc_start: 0.8700 (tttm) cc_final: 0.8380 (tttm) REVERT: C 65 GLU cc_start: 0.8338 (tp30) cc_final: 0.7985 (tp30) REVERT: C 90 ASN cc_start: 0.8893 (m-40) cc_final: 0.8600 (m110) REVERT: G 91 ASP cc_start: 0.8367 (t0) cc_final: 0.8106 (t0) REVERT: H 66 ASP cc_start: 0.9038 (t0) cc_final: 0.8822 (t0) outliers start: 4 outliers final: 2 residues processed: 111 average time/residue: 0.3511 time to fit residues: 49.6316 Evaluate side-chains 110 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 76 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.084417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.059930 restraints weight = 71759.098| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.94 r_work: 0.2789 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3413 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= 0.160 Angle : 0.577 4.672 16989 Z= 0.361 Chirality : 0.037 0.140 1932 Planarity : 0.004 0.047 1280 Dihedral : 28.563 101.290 3591 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.32 % Allowed : 10.55 % 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: 2.83 (0.31), residues: 732 helix: 2.97 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.43 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 36 TYR 0.008 0.001 TYR H 38 PHE 0.006 0.001 PHE D 63 HIS 0.003 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00337 (11784) covalent geometry : angle 0.57683 (16989) hydrogen bonds : bond 0.04617 ( 701) hydrogen bonds : angle 2.70922 ( 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 122 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: C 16 LYS cc_start: 0.8693 (tttm) cc_final: 0.8364 (tttm) REVERT: C 90 ASN cc_start: 0.8846 (m-40) cc_final: 0.8541 (m110) REVERT: E 60 GLU cc_start: 0.7705 (pm20) cc_final: 0.7308 (pm20) REVERT: H 66 ASP cc_start: 0.8965 (t0) cc_final: 0.8748 (t0) outliers start: 2 outliers final: 2 residues processed: 120 average time/residue: 0.3803 time to fit residues: 57.1225 Evaluate side-chains 114 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.082470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.057896 restraints weight = 71621.193| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.93 r_work: 0.2735 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 11784 Z= 0.231 Angle : 0.604 5.053 16989 Z= 0.376 Chirality : 0.041 0.134 1932 Planarity : 0.004 0.051 1280 Dihedral : 28.553 102.743 3591 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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: 2.57 (0.31), residues: 732 helix: 2.81 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.61 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 77 TYR 0.008 0.001 TYR H 38 PHE 0.008 0.001 PHE B 62 HIS 0.005 0.001 HIS C 39 Details of bonding type rmsd covalent geometry : bond 0.00502 (11784) covalent geometry : angle 0.60432 (16989) hydrogen bonds : bond 0.05793 ( 701) hydrogen bonds : angle 2.99344 ( 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 116 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.432 Fit side-chains REVERT: C 16 LYS cc_start: 0.8748 (tttm) cc_final: 0.8399 (tttm) REVERT: C 76 LYS cc_start: 0.9361 (mmtt) cc_final: 0.9137 (mmtp) REVERT: C 90 ASN cc_start: 0.8878 (m-40) cc_final: 0.8566 (m110) REVERT: E 60 GLU cc_start: 0.7889 (pm20) cc_final: 0.7333 (pm20) REVERT: H 66 ASP cc_start: 0.9051 (t0) cc_final: 0.8837 (t0) outliers start: 5 outliers final: 4 residues processed: 111 average time/residue: 0.3644 time to fit residues: 51.1596 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 : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain E residue 74 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: 0.8980 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 49 optimal weight: 0.2980 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.083522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.058888 restraints weight = 71611.064| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.95 r_work: 0.2761 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3506 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= 0.164 Angle : 0.583 4.712 16989 Z= 0.364 Chirality : 0.037 0.139 1932 Planarity : 0.004 0.050 1280 Dihedral : 28.568 102.779 3591 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.32 % Allowed : 10.88 % Favored : 88.80 % 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: 2.70 (0.31), residues: 732 helix: 2.91 (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 0.003 0.000 ARG H 77 TYR 0.008 0.001 TYR H 38 PHE 0.007 0.001 PHE D 63 HIS 0.003 0.001 HIS C 39 Details of bonding type rmsd covalent geometry : bond 0.00347 (11784) covalent geometry : angle 0.58298 (16989) hydrogen bonds : bond 0.05048 ( 701) hydrogen bonds : angle 2.80448 ( 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 116 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.475 Fit side-chains REVERT: C 16 LYS cc_start: 0.8699 (tttm) cc_final: 0.8412 (tttp) REVERT: C 65 GLU cc_start: 0.8343 (tp30) cc_final: 0.7924 (tp30) REVERT: C 76 LYS cc_start: 0.9360 (mmtt) cc_final: 0.9144 (mmtp) REVERT: C 90 ASN cc_start: 0.8868 (m-40) cc_final: 0.8555 (m110) REVERT: D 49 ASP cc_start: 0.8829 (p0) cc_final: 0.8608 (p0) REVERT: E 60 GLU cc_start: 0.7843 (pm20) cc_final: 0.7283 (pm20) REVERT: H 66 ASP cc_start: 0.9012 (t0) cc_final: 0.8790 (t0) outliers start: 2 outliers final: 2 residues processed: 114 average time/residue: 0.3521 time to fit residues: 50.8993 Evaluate side-chains 113 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain E residue 75 ILE 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: 0.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 41 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.084025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.059558 restraints weight = 71406.577| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.92 r_work: 0.2779 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11784 Z= 0.164 Angle : 0.586 6.873 16989 Z= 0.364 Chirality : 0.038 0.137 1932 Planarity : 0.004 0.051 1280 Dihedral : 28.522 102.644 3591 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.32 % Allowed : 11.36 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.31), residues: 732 helix: 3.00 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.55 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 36 TYR 0.008 0.001 TYR H 38 PHE 0.006 0.001 PHE D 63 HIS 0.003 0.001 HIS C 39 Details of bonding type rmsd covalent geometry : bond 0.00348 (11784) covalent geometry : angle 0.58568 (16989) hydrogen bonds : bond 0.04764 ( 701) hydrogen bonds : angle 2.73237 ( 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 115 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: C 16 LYS cc_start: 0.8731 (tttm) cc_final: 0.8441 (tttp) REVERT: C 76 LYS cc_start: 0.9359 (mmtt) cc_final: 0.9141 (mmtp) REVERT: C 90 ASN cc_start: 0.8908 (m-40) cc_final: 0.8598 (m110) REVERT: D 49 ASP cc_start: 0.8839 (p0) cc_final: 0.8623 (p0) REVERT: E 60 GLU cc_start: 0.7880 (pm20) cc_final: 0.7336 (pm20) REVERT: H 66 ASP cc_start: 0.9003 (t0) cc_final: 0.8785 (t0) outliers start: 2 outliers final: 2 residues processed: 113 average time/residue: 0.2975 time to fit residues: 43.0670 Evaluate side-chains 113 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain E residue 75 ILE 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: 1.9990 chunk 73 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.082556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.057914 restraints weight = 72091.762| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.93 r_work: 0.2738 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11784 Z= 0.217 Angle : 0.601 5.107 16989 Z= 0.373 Chirality : 0.041 0.132 1932 Planarity : 0.004 0.053 1280 Dihedral : 28.498 103.525 3591 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.32 % Allowed : 10.88 % Favored : 88.80 % 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: 2.84 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.71 (0.36), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 36 TYR 0.009 0.001 TYR H 38 PHE 0.008 0.001 PHE B 62 HIS 0.005 0.001 HIS C 39 Details of bonding type rmsd covalent geometry : bond 0.00470 (11784) covalent geometry : angle 0.60137 (16989) hydrogen bonds : bond 0.05586 ( 701) hydrogen bonds : angle 2.94417 ( 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 110 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.459 Fit side-chains REVERT: C 16 LYS cc_start: 0.8774 (tttm) cc_final: 0.8469 (tttp) REVERT: C 65 GLU cc_start: 0.8407 (tp30) cc_final: 0.8081 (tp30) REVERT: C 76 LYS cc_start: 0.9374 (mmtt) cc_final: 0.9165 (mmtp) REVERT: C 90 ASN cc_start: 0.8928 (m-40) cc_final: 0.8620 (m110) REVERT: D 49 ASP cc_start: 0.8827 (p0) cc_final: 0.8618 (p0) REVERT: E 60 GLU cc_start: 0.7963 (pm20) cc_final: 0.7417 (pm20) REVERT: H 66 ASP cc_start: 0.9047 (t0) cc_final: 0.8843 (t0) outliers start: 2 outliers final: 2 residues processed: 108 average time/residue: 0.3600 time to fit residues: 49.2189 Evaluate side-chains 110 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain E residue 75 ILE 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: 3.9990 chunk 79 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.082422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.057874 restraints weight = 71656.397| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.97 r_work: 0.2735 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 11784 Z= 0.214 Angle : 0.605 6.175 16989 Z= 0.375 Chirality : 0.040 0.135 1932 Planarity : 0.004 0.057 1280 Dihedral : 28.524 103.706 3591 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.32 % Allowed : 10.71 % 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: 2.52 (0.31), residues: 732 helix: 2.80 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.72 (0.36), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 36 TYR 0.008 0.001 TYR B 52 PHE 0.007 0.001 PHE B 62 HIS 0.004 0.001 HIS C 39 Details of bonding type rmsd covalent geometry : bond 0.00464 (11784) covalent geometry : angle 0.60459 (16989) hydrogen bonds : bond 0.05516 ( 701) hydrogen bonds : angle 2.94638 ( 1773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4870.74 seconds wall clock time: 83 minutes 16.45 seconds (4996.45 seconds total)