Starting phenix.real_space_refine on Thu Aug 6 00:27:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e09_47353/08_2026/9e09_47353.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e09_47353/08_2026/9e09_47353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e09_47353/08_2026/9e09_47353.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e09_47353/08_2026/9e09_47353.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e09_47353/08_2026/9e09_47353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e09_47353/08_2026/9e09_47353.map" } resolution = 3.72 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= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 312 5.49 5 S 14 5.16 5 C 6779 2.51 5 N 2325 2.21 5 O 2925 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 12355 Number of models: 1 Model: "" Number of chains: 12 Chain: "M" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 820 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "N" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "O" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 755 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "P" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "Q" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 785 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "R" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "S" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 752 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "T" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3218 Classifications: {'DNA': 156} Link IDs: {'rna3p': 155} Chain: "J" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3178 Classifications: {'DNA': 156} Link IDs: {'rna3p': 155} Chain: "X" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 92 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "V" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 84 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Time building chain proxies: 2.71, per 1000 atoms: 0.22 Number of scatterers: 12355 At special positions: 0 Unit cell: (117.576, 116.748, 125.856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 312 15.00 O 2925 8.00 N 2325 7.00 C 6779 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 449.1 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: 1408 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 7 sheets defined 73.0% alpha, 2.1% beta 155 base pairs and 285 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'M' and resid 44 through 57 removed outlier: 3.645A pdb=" N GLN M 55 " --> pdb=" O ILE M 51 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS M 56 " --> pdb=" O ARG M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 77 removed outlier: 3.701A pdb=" N ASP M 77 " --> pdb=" O GLU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 114 removed outlier: 3.514A pdb=" N VAL M 89 " --> pdb=" O GLN M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 131 Processing helix chain 'N' and resid 30 through 42 Processing helix chain 'N' and resid 49 through 76 removed outlier: 3.905A pdb=" N GLU N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG N 67 " --> pdb=" O GLU N 63 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASP N 68 " --> pdb=" O ASN N 64 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR N 71 " --> pdb=" O ARG N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 92 removed outlier: 3.617A pdb=" N VAL N 86 " --> pdb=" O THR N 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 21 Processing helix chain 'O' and resid 26 through 38 removed outlier: 3.687A pdb=" N ASN O 38 " --> pdb=" O LEU O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 73 removed outlier: 3.594A pdb=" N ALA O 53 " --> pdb=" O VAL O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 89 removed outlier: 3.556A pdb=" N LEU O 83 " --> pdb=" O ILE O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 97 Processing helix chain 'P' and resid 34 through 46 Processing helix chain 'P' and resid 52 through 81 Processing helix chain 'P' and resid 87 through 99 Processing helix chain 'P' and resid 100 through 120 removed outlier: 3.598A pdb=" N LYS P 113 " --> pdb=" O SER P 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 55 Processing helix chain 'Q' and resid 63 through 79 removed outlier: 4.034A pdb=" N ASP Q 77 " --> pdb=" O GLU Q 73 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE Q 78 " --> pdb=" O ILE Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 114 Processing helix chain 'Q' and resid 120 through 131 Processing helix chain 'R' and resid 25 through 29 removed outlier: 3.699A pdb=" N ILE R 29 " --> pdb=" O ILE R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 42 Processing helix chain 'R' and resid 49 through 76 removed outlier: 3.969A pdb=" N GLU R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG R 67 " --> pdb=" O GLU R 63 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP R 68 " --> pdb=" O ASN R 64 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR R 71 " --> pdb=" O ARG R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 92 removed outlier: 3.553A pdb=" N VAL R 86 " --> pdb=" O THR R 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 22 Processing helix chain 'S' and resid 26 through 37 removed outlier: 3.771A pdb=" N VAL S 30 " --> pdb=" O PRO S 26 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG S 35 " --> pdb=" O HIS S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 73 removed outlier: 4.554A pdb=" N VAL S 49 " --> pdb=" O ALA S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 90 removed outlier: 3.661A pdb=" N LEU S 83 " --> pdb=" O ILE S 79 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP S 90 " --> pdb=" O ALA S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 90 through 97 removed outlier: 3.524A pdb=" N LYS S 95 " --> pdb=" O GLU S 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 34 through 46 removed outlier: 3.598A pdb=" N LYS T 40 " --> pdb=" O ILE T 36 " (cutoff:3.500A) Processing helix chain 'T' and resid 52 through 81 Processing helix chain 'T' and resid 87 through 99 removed outlier: 3.610A pdb=" N ALA T 94 " --> pdb=" O GLU T 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 101 through 119 removed outlier: 3.600A pdb=" N LYS T 105 " --> pdb=" O GLY T 101 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER T 109 " --> pdb=" O LYS T 105 " (cutoff:3.500A) Processing helix chain 'X' and resid 741 through 746 Processing helix chain 'V' and resid 741 through 746 Processing sheet with id=AA1, first strand: chain 'M' and resid 83 through 84 removed outlier: 7.172A pdb=" N ARG M 83 " --> pdb=" O VAL N 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'N' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'O' and resid 42 through 43 removed outlier: 7.386A pdb=" N ARG O 42 " --> pdb=" O ILE P 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'O' and resid 100 through 102 removed outlier: 7.310A pdb=" N THR O 101 " --> pdb=" O TYR R 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'Q' and resid 83 through 84 removed outlier: 7.056A pdb=" N ARG Q 83 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'S' and resid 42 through 43 removed outlier: 7.578A pdb=" N ARG S 42 " --> pdb=" O ILE T 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 381 hydrogen bonds defined for protein. 1140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 401 hydrogen bonds 802 hydrogen bond angles 0 basepair planarities 155 basepair parallelities 285 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1789 1.33 - 1.45: 4807 1.45 - 1.57: 5963 1.57 - 1.69: 622 1.69 - 1.81: 26 Bond restraints: 13207 Sorted by residual: bond pdb=" N ILE R 46 " pdb=" CA ILE R 46 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.81e+00 bond pdb=" O3' DA I 60 " pdb=" P DA I 61 " ideal model delta sigma weight residual 1.607 1.571 0.036 1.20e-02 6.94e+03 8.79e+00 bond pdb=" O3' DA I 80 " pdb=" P DC I 81 " ideal model delta sigma weight residual 1.607 1.573 0.034 1.20e-02 6.94e+03 8.25e+00 bond pdb=" N ARG Q 63 " pdb=" CA ARG Q 63 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.22e-02 6.72e+03 7.94e+00 bond pdb=" C3' DC I 126 " pdb=" O3' DC I 126 " ideal model delta sigma weight residual 1.435 1.471 -0.036 1.30e-02 5.92e+03 7.73e+00 ... (remaining 13202 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 15706 1.30 - 2.59: 3007 2.59 - 3.89: 399 3.89 - 5.19: 48 5.19 - 6.48: 10 Bond angle restraints: 19170 Sorted by residual: angle pdb=" O5' DG I 92 " pdb=" C5' DG I 92 " pdb=" C4' DG I 92 " ideal model delta sigma weight residual 109.40 114.17 -4.77 8.00e-01 1.56e+00 3.55e+01 angle pdb=" O4' DA I 100 " pdb=" C4' DA I 100 " pdb=" C3' DA I 100 " ideal model delta sigma weight residual 106.00 103.45 2.55 6.00e-01 2.78e+00 1.80e+01 angle pdb=" C3' DC I 126 " pdb=" O3' DC I 126 " pdb=" P DC I 127 " ideal model delta sigma weight residual 119.70 124.73 -5.03 1.20e+00 6.94e-01 1.76e+01 angle pdb=" O4' DC J 76 " pdb=" C4' DC J 76 " pdb=" C3' DC J 76 " ideal model delta sigma weight residual 106.00 103.51 2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" O4' DA I 91 " pdb=" C4' DA I 91 " pdb=" C3' DA I 91 " ideal model delta sigma weight residual 106.00 103.54 2.46 6.00e-01 2.78e+00 1.68e+01 ... (remaining 19165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.70: 5623 34.70 - 69.41: 1476 69.41 - 104.11: 18 104.11 - 138.82: 0 138.82 - 173.52: 3 Dihedral angle restraints: 7120 sinusoidal: 4940 harmonic: 2180 Sorted by residual: dihedral pdb=" C4' DG I 152 " pdb=" C3' DG I 152 " pdb=" O3' DG I 152 " pdb=" P DC I 153 " ideal model delta sinusoidal sigma weight residual -140.00 33.52 -173.52 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC I 126 " pdb=" C3' DC I 126 " pdb=" O3' DC I 126 " pdb=" P DC I 127 " ideal model delta sinusoidal sigma weight residual 220.00 54.72 165.28 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DC J 9 " pdb=" C3' DC J 9 " pdb=" O3' DC J 9 " pdb=" P DC J 10 " ideal model delta sinusoidal sigma weight residual 220.00 81.07 138.93 1 3.50e+01 8.16e-04 1.37e+01 ... (remaining 7117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1666 0.061 - 0.123: 456 0.123 - 0.184: 54 0.184 - 0.245: 3 0.245 - 0.307: 2 Chirality restraints: 2181 Sorted by residual: chirality pdb=" C3' DC I 126 " pdb=" C4' DC I 126 " pdb=" O3' DC I 126 " pdb=" C2' DC I 126 " both_signs ideal model delta sigma weight residual False -2.73 -2.42 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C3' DG I 152 " pdb=" C4' DG I 152 " pdb=" O3' DG I 152 " pdb=" C2' DG I 152 " both_signs ideal model delta sigma weight residual False -2.73 -2.47 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C4' DG I 92 " pdb=" C5' DG I 92 " pdb=" O4' DG I 92 " pdb=" C3' DG I 92 " both_signs ideal model delta sigma weight residual False -2.53 -2.30 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 2178 not shown) Planarity restraints: 1344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 88 " -0.040 2.00e-02 2.50e+03 1.78e-02 7.88e+00 pdb=" N1 DT I 88 " 0.032 2.00e-02 2.50e+03 pdb=" C2 DT I 88 " 0.007 2.00e-02 2.50e+03 pdb=" O2 DT I 88 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DT I 88 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 88 " -0.007 2.00e-02 2.50e+03 pdb=" O4 DT I 88 " -0.015 2.00e-02 2.50e+03 pdb=" C5 DT I 88 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 88 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DT I 88 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 91 " -0.037 2.00e-02 2.50e+03 1.58e-02 6.90e+00 pdb=" N9 DA I 91 " 0.031 2.00e-02 2.50e+03 pdb=" C8 DA I 91 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA I 91 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DA I 91 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 91 " -0.007 2.00e-02 2.50e+03 pdb=" N6 DA I 91 " -0.014 2.00e-02 2.50e+03 pdb=" N1 DA I 91 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 91 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 91 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DA I 91 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 121 " -0.036 2.00e-02 2.50e+03 1.48e-02 6.00e+00 pdb=" N9 DA I 121 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DA I 121 " 0.008 2.00e-02 2.50e+03 pdb=" N7 DA I 121 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DA I 121 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 121 " -0.008 2.00e-02 2.50e+03 pdb=" N6 DA I 121 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I 121 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DA I 121 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA I 121 " 0.010 2.00e-02 2.50e+03 pdb=" C4 DA I 121 " 0.005 2.00e-02 2.50e+03 ... (remaining 1341 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2751 2.82 - 3.34: 10407 3.34 - 3.86: 24871 3.86 - 4.38: 28332 4.38 - 4.90: 38665 Nonbonded interactions: 105026 Sorted by model distance: nonbonded pdb=" OH TYR P 37 " pdb=" OP1 DG J 132 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR M 99 " pdb=" OE1 GLU M 133 " model vdw 2.358 3.040 nonbonded pdb=" OE2 GLU O 61 " pdb=" NH2 ARG V 743 " model vdw 2.376 3.120 nonbonded pdb=" OH TYR T 37 " pdb=" OP1 DG I 122 " model vdw 2.392 3.040 nonbonded pdb=" NH1 ARG O 81 " pdb=" O GLY O 105 " model vdw 2.392 3.120 ... (remaining 105021 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 'M' and resid 40 through 134) selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'R' } ncs_group { reference = (chain 'O' and (resid 14 through 72 or (resid 73 and (name N or name CA or name \ C or name O or name CB )) or resid 74 through 111)) selection = chain 'S' } ncs_group { reference = chain 'P' selection = (chain 'T' and resid 31 through 121) } ncs_group { reference = chain 'V' selection = (chain 'X' and resid 736 through 746) } 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 group one per residue 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: 11.360 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.650 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 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 0.039 13207 Z= 0.560 Angle : 1.013 6.483 19170 Z= 0.776 Chirality : 0.054 0.307 2181 Planarity : 0.006 0.038 1344 Dihedral : 27.345 173.522 5712 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -2.42 (0.25), residues: 732 helix: -1.28 (0.18), residues: 519 sheet: None (None), residues: 0 loop : -2.04 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 88 TYR 0.023 0.003 TYR O 57 PHE 0.031 0.004 PHE S 25 HIS 0.005 0.002 HIS S 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00734 / 0.56 (13207) covalent geometry : angle 1.01340 / 0.78 (19170) hydrogen bonds : bond 0.13231 / 8.03 ( 782) hydrogen bonds : angle 4.87560 / 3.54 ( 1942) *********************** 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 108 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.223 Fit side-chains REVERT: M 59 GLU cc_start: 0.7475 (pt0) cc_final: 0.7191 (pt0) REVERT: M 115 LYS cc_start: 0.8085 (mttm) cc_final: 0.7812 (mttm) REVERT: O 33 LEU cc_start: 0.6918 (mt) cc_final: 0.6466 (mp) REVERT: R 59 LYS cc_start: 0.7299 (tttt) cc_final: 0.7023 (tttp) REVERT: R 80 THR cc_start: 0.7871 (m) cc_final: 0.7594 (t) REVERT: S 59 THR cc_start: 0.7232 (m) cc_final: 0.6885 (m) REVERT: T 44 GLN cc_start: 0.7709 (tt0) cc_final: 0.7433 (tt0) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1302 time to fit residues: 18.4302 Evaluate side-chains 99 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 39 HIS M 68 GLN O 31 HIS O 84 GLN Q 68 GLN S 31 HIS S 84 GLN T 46 HIS T 81 ASN T 106 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.159774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.128499 restraints weight = 18493.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.131190 restraints weight = 9009.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.132966 restraints weight = 5693.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.133933 restraints weight = 4385.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.134633 restraints weight = 3788.605| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13207 Z= 0.219 Angle : 0.759 8.837 19170 Z= 0.433 Chirality : 0.048 0.304 2181 Planarity : 0.006 0.064 1344 Dihedral : 31.535 170.492 4231 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.81 % Allowed : 3.22 % Favored : 95.97 % 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: -0.11 (0.28), residues: 732 helix: 0.52 (0.20), residues: 544 sheet: None (None), residues: 0 loop : -1.66 (0.39), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 77 TYR 0.029 0.004 TYR T 80 PHE 0.022 0.003 PHE O 25 HIS 0.008 0.002 HIS Q 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.22 (13207) covalent geometry : angle 0.75948 / 0.43 (19170) hydrogen bonds : bond 0.06481 / 4.29 ( 782) hydrogen bonds : angle 3.19644 / 2.28 ( 1942) *********************** 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 81 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.198 Fit side-chains REVERT: M 82 LEU cc_start: 0.8021 (mt) cc_final: 0.7772 (mt) REVERT: O 39 TYR cc_start: 0.8063 (m-80) cc_final: 0.7853 (m-80) REVERT: P 56 MET cc_start: 0.7641 (mmm) cc_final: 0.7161 (tpp) REVERT: Q 90 MET cc_start: 0.6698 (tpp) cc_final: 0.6446 (mpp) REVERT: T 44 GLN cc_start: 0.7604 (tt0) cc_final: 0.7393 (tt0) outliers start: 5 outliers final: 4 residues processed: 77 average time/residue: 0.1306 time to fit residues: 13.5959 Evaluate side-chains 73 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 88 ARG Chi-restraints excluded: chain T residue 56 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 60 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 4 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 HIS P 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.154675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.122522 restraints weight = 18439.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125248 restraints weight = 8797.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.127077 restraints weight = 5515.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.128133 restraints weight = 4216.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.128348 restraints weight = 3597.395| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13207 Z= 0.191 Angle : 0.678 7.013 19170 Z= 0.397 Chirality : 0.045 0.251 2181 Planarity : 0.005 0.034 1344 Dihedral : 31.390 172.746 4231 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.81 % Allowed : 4.35 % Favored : 94.85 % 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: 1.32 (0.30), residues: 732 helix: 1.67 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -1.49 (0.39), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG S 77 TYR 0.034 0.003 TYR P 80 PHE 0.013 0.002 PHE N 100 HIS 0.007 0.001 HIS S 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.19 (13207) covalent geometry : angle 0.67834 / 0.40 (19170) hydrogen bonds : bond 0.05802 / 3.70 ( 782) hydrogen bonds : angle 2.83111 / 2.00 ( 1942) *********************** 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 78 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.350 Fit side-chains REVERT: M 82 LEU cc_start: 0.8268 (mt) cc_final: 0.8013 (mt) REVERT: M 115 LYS cc_start: 0.8265 (mttm) cc_final: 0.7907 (mttm) REVERT: M 120 MET cc_start: 0.6857 (mmm) cc_final: 0.6200 (mtt) REVERT: P 56 MET cc_start: 0.7561 (mmm) cc_final: 0.7179 (tpp) REVERT: Q 90 MET cc_start: 0.6694 (tpp) cc_final: 0.6466 (mpp) outliers start: 5 outliers final: 2 residues processed: 74 average time/residue: 0.1822 time to fit residues: 17.1083 Evaluate side-chains 72 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 85 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 99 optimal weight: 7.9990 chunk 37 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 63 optimal weight: 0.1980 chunk 10 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.151510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.119503 restraints weight = 18275.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.122249 restraints weight = 8594.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.124141 restraints weight = 5391.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125097 restraints weight = 4082.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.125822 restraints weight = 3529.047| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13207 Z= 0.179 Angle : 0.658 8.319 19170 Z= 0.382 Chirality : 0.044 0.271 2181 Planarity : 0.005 0.041 1344 Dihedral : 31.516 173.669 4231 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.13 % Allowed : 4.35 % Favored : 94.52 % 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: 1.87 (0.30), residues: 732 helix: 2.08 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.35 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 77 TYR 0.020 0.002 TYR N 98 PHE 0.013 0.002 PHE O 25 HIS 0.005 0.001 HIS S 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.18 (13207) covalent geometry : angle 0.65757 / 0.38 (19170) hydrogen bonds : bond 0.05397 / 3.54 ( 782) hydrogen bonds : angle 2.65847 / 1.88 ( 1942) *********************** 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 66 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.217 Fit side-chains REVERT: M 115 LYS cc_start: 0.8272 (mttm) cc_final: 0.7916 (mttm) REVERT: M 120 MET cc_start: 0.6899 (mmm) cc_final: 0.6229 (mtt) REVERT: P 56 MET cc_start: 0.7485 (mmm) cc_final: 0.7247 (tpp) REVERT: Q 90 MET cc_start: 0.6582 (tpp) cc_final: 0.6366 (mpp) REVERT: R 30 THR cc_start: 0.7952 (OUTLIER) cc_final: 0.7745 (p) REVERT: S 20 ARG cc_start: 0.7719 (ttm110) cc_final: 0.7140 (ttm110) REVERT: S 99 ARG cc_start: 0.6868 (mtt180) cc_final: 0.6652 (mtp85) outliers start: 7 outliers final: 3 residues processed: 62 average time/residue: 0.1791 time to fit residues: 13.9418 Evaluate side-chains 62 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 38 ASN Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 85 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 0.1980 chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.146151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113957 restraints weight = 18364.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.116769 restraints weight = 8667.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.118510 restraints weight = 5418.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.119680 restraints weight = 4121.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.120138 restraints weight = 3579.836| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13207 Z= 0.199 Angle : 0.690 7.486 19170 Z= 0.397 Chirality : 0.047 0.252 2181 Planarity : 0.005 0.033 1344 Dihedral : 31.456 174.603 4231 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.45 % Allowed : 4.67 % Favored : 93.88 % 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: 1.97 (0.31), residues: 732 helix: 2.16 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.33 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 45 TYR 0.059 0.003 TYR P 80 PHE 0.022 0.002 PHE N 100 HIS 0.005 0.001 HIS S 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.20 (13207) covalent geometry : angle 0.68989 / 0.40 (19170) hydrogen bonds : bond 0.06053 / 3.84 ( 782) hydrogen bonds : angle 2.76295 / 1.95 ( 1942) *********************** 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 71 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.188 Fit side-chains REVERT: M 72 ARG cc_start: 0.7817 (mtt-85) cc_final: 0.7403 (mtt-85) REVERT: M 120 MET cc_start: 0.7123 (mmm) cc_final: 0.6845 (mtt) REVERT: P 56 MET cc_start: 0.7513 (mmm) cc_final: 0.7298 (tpp) REVERT: P 59 MET cc_start: 0.8247 (mmm) cc_final: 0.7874 (mmp) REVERT: Q 90 MET cc_start: 0.6609 (tpp) cc_final: 0.6370 (mpp) REVERT: S 20 ARG cc_start: 0.7690 (ttm110) cc_final: 0.7275 (ttm110) REVERT: S 23 LEU cc_start: 0.8166 (mt) cc_final: 0.7874 (mp) REVERT: S 85 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7601 (mt) outliers start: 9 outliers final: 4 residues processed: 64 average time/residue: 0.2183 time to fit residues: 16.9180 Evaluate side-chains 66 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 56 LYS Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 85 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 3 optimal weight: 0.0980 chunk 66 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 17 optimal weight: 0.0770 chunk 31 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 38 ASN P 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.145249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113845 restraints weight = 18186.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.116277 restraints weight = 9360.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117882 restraints weight = 6174.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.118993 restraints weight = 4825.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.119355 restraints weight = 4178.810| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13207 Z= 0.159 Angle : 0.627 7.587 19170 Z= 0.368 Chirality : 0.043 0.266 2181 Planarity : 0.004 0.032 1344 Dihedral : 31.487 174.657 4231 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.64 % Allowed : 5.80 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.31), residues: 732 helix: 2.48 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.23 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 77 TYR 0.028 0.002 TYR P 80 PHE 0.011 0.001 PHE Q 67 HIS 0.003 0.001 HIS T 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.16 (13207) covalent geometry : angle 0.62657 / 0.37 (19170) hydrogen bonds : bond 0.05101 / 3.30 ( 782) hydrogen bonds : angle 2.56199 / 1.81 ( 1942) *********************** 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 77 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.293 Fit side-chains REVERT: M 72 ARG cc_start: 0.7828 (mtt-85) cc_final: 0.7250 (mtt-85) REVERT: M 115 LYS cc_start: 0.8268 (mttm) cc_final: 0.7955 (mttm) REVERT: M 120 MET cc_start: 0.7004 (mmm) cc_final: 0.6676 (mtt) REVERT: N 40 ARG cc_start: 0.8619 (ttm170) cc_final: 0.8387 (ttm170) REVERT: O 32 ARG cc_start: 0.8047 (ttp80) cc_final: 0.7755 (tmm160) REVERT: P 59 MET cc_start: 0.8192 (mmm) cc_final: 0.7903 (mmp) REVERT: Q 90 MET cc_start: 0.6565 (tpp) cc_final: 0.6357 (mpp) REVERT: S 20 ARG cc_start: 0.7694 (ttm110) cc_final: 0.7260 (ttm110) REVERT: S 85 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7529 (mt) outliers start: 4 outliers final: 2 residues processed: 74 average time/residue: 0.2643 time to fit residues: 23.0770 Evaluate side-chains 74 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 85 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 0 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.141660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110728 restraints weight = 18122.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.113050 restraints weight = 9397.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.114544 restraints weight = 6250.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.115427 restraints weight = 4947.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115699 restraints weight = 4302.139| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13207 Z= 0.230 Angle : 0.703 9.489 19170 Z= 0.398 Chirality : 0.048 0.256 2181 Planarity : 0.005 0.036 1344 Dihedral : 31.507 175.334 4231 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.97 % Allowed : 5.80 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.31), residues: 732 helix: 2.35 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -1.41 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 35 TYR 0.036 0.002 TYR P 80 PHE 0.021 0.002 PHE Q 84 HIS 0.005 0.001 HIS T 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.23 (13207) covalent geometry : angle 0.70307 / 0.40 (19170) hydrogen bonds : bond 0.05818 / 3.77 ( 782) hydrogen bonds : angle 2.73094 / 1.93 ( 1942) *********************** 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 74 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.271 Fit side-chains REVERT: M 42 ARG cc_start: 0.7838 (mtp85) cc_final: 0.7594 (mtp85) REVERT: M 72 ARG cc_start: 0.7874 (mtt-85) cc_final: 0.7333 (mtt-85) REVERT: M 120 MET cc_start: 0.7174 (mmm) cc_final: 0.6877 (mtt) REVERT: O 32 ARG cc_start: 0.8086 (ttp80) cc_final: 0.7829 (tmm160) REVERT: O 99 ARG cc_start: 0.6810 (mtp180) cc_final: 0.6571 (mtp180) REVERT: P 46 HIS cc_start: 0.8382 (m90) cc_final: 0.8177 (m170) REVERT: P 56 MET cc_start: 0.7389 (mmm) cc_final: 0.7159 (tpp) REVERT: Q 90 MET cc_start: 0.6626 (tpp) cc_final: 0.6368 (mpp) REVERT: S 20 ARG cc_start: 0.7763 (ttm110) cc_final: 0.7365 (ttm110) outliers start: 6 outliers final: 4 residues processed: 69 average time/residue: 0.2716 time to fit residues: 21.9204 Evaluate side-chains 71 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 56 LYS Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 85 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 47 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.143470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111462 restraints weight = 18110.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.114214 restraints weight = 8507.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.116070 restraints weight = 5337.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.117081 restraints weight = 4103.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117827 restraints weight = 3532.431| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13207 Z= 0.165 Angle : 0.645 8.086 19170 Z= 0.374 Chirality : 0.044 0.260 2181 Planarity : 0.004 0.035 1344 Dihedral : 31.496 175.388 4231 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.48 % Allowed : 7.09 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.31), residues: 732 helix: 2.53 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.32 (0.40), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 77 TYR 0.023 0.002 TYR P 80 PHE 0.012 0.001 PHE Q 84 HIS 0.004 0.001 HIS T 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.16 (13207) covalent geometry : angle 0.64475 / 0.37 (19170) hydrogen bonds : bond 0.05132 / 3.31 ( 782) hydrogen bonds : angle 2.58901 / 1.83 ( 1942) *********************** 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 69 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.288 Fit side-chains REVERT: M 42 ARG cc_start: 0.7824 (mtp85) cc_final: 0.7573 (mtp85) REVERT: M 72 ARG cc_start: 0.7873 (mtt-85) cc_final: 0.7606 (mtt-85) REVERT: M 120 MET cc_start: 0.7107 (mmm) cc_final: 0.6571 (mtt) REVERT: O 32 ARG cc_start: 0.8064 (ttp80) cc_final: 0.7786 (tmm160) REVERT: Q 90 MET cc_start: 0.6562 (tpp) cc_final: 0.6344 (mpp) REVERT: S 20 ARG cc_start: 0.7745 (ttm110) cc_final: 0.7318 (ttm110) REVERT: S 85 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7600 (mt) outliers start: 3 outliers final: 2 residues processed: 67 average time/residue: 0.2724 time to fit residues: 21.3090 Evaluate side-chains 68 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 85 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 0.0050 chunk 54 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 43 optimal weight: 0.0470 chunk 88 optimal weight: 2.9990 overall best weight: 0.4292 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.143271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111357 restraints weight = 18052.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114122 restraints weight = 8527.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.116040 restraints weight = 5345.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.117012 restraints weight = 4048.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117736 restraints weight = 3494.278| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13207 Z= 0.166 Angle : 0.637 8.693 19170 Z= 0.370 Chirality : 0.044 0.260 2181 Planarity : 0.004 0.035 1344 Dihedral : 31.451 176.092 4231 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.48 % Allowed : 7.25 % Favored : 92.27 % 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: 2.54 (0.31), residues: 732 helix: 2.60 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.26 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 77 TYR 0.023 0.002 TYR P 80 PHE 0.013 0.001 PHE Q 84 HIS 0.003 0.001 HIS T 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.17 (13207) covalent geometry : angle 0.63721 / 0.37 (19170) hydrogen bonds : bond 0.04997 / 3.23 ( 782) hydrogen bonds : angle 2.56542 / 1.83 ( 1942) *********************** 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 71 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.273 Fit side-chains REVERT: M 42 ARG cc_start: 0.7817 (mtp85) cc_final: 0.7573 (mtp85) REVERT: M 72 ARG cc_start: 0.7901 (mtt-85) cc_final: 0.7562 (mtt180) REVERT: M 120 MET cc_start: 0.7102 (mmm) cc_final: 0.6528 (mtt) REVERT: O 32 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7809 (tmm160) REVERT: Q 90 MET cc_start: 0.6561 (tpp) cc_final: 0.6359 (mpp) REVERT: S 20 ARG cc_start: 0.7741 (ttm110) cc_final: 0.7332 (ttm110) REVERT: S 85 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7605 (mt) outliers start: 3 outliers final: 2 residues processed: 69 average time/residue: 0.2785 time to fit residues: 22.8039 Evaluate side-chains 71 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 85 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 47 optimal weight: 0.3980 chunk 31 optimal weight: 0.0970 chunk 8 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 54 optimal weight: 0.4980 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.143481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111779 restraints weight = 18033.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.114540 restraints weight = 8467.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.116403 restraints weight = 5284.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.117398 restraints weight = 4040.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.117948 restraints weight = 3464.556| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.5825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13207 Z= 0.154 Angle : 0.618 7.491 19170 Z= 0.363 Chirality : 0.043 0.262 2181 Planarity : 0.004 0.036 1344 Dihedral : 31.439 176.416 4231 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.48 % Allowed : 7.25 % Favored : 92.27 % 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: 2.68 (0.31), residues: 732 helix: 2.72 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.24 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 77 TYR 0.020 0.002 TYR P 80 PHE 0.011 0.001 PHE Q 67 HIS 0.011 0.001 HIS M 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.15 (13207) covalent geometry : angle 0.61836 / 0.36 (19170) hydrogen bonds : bond 0.04810 / 3.10 ( 782) hydrogen bonds : angle 2.51119 / 1.79 ( 1942) ********************** 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 71 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.246 Fit side-chains REVERT: M 42 ARG cc_start: 0.7812 (mtp85) cc_final: 0.7576 (mtp85) REVERT: M 72 ARG cc_start: 0.7904 (mtt-85) cc_final: 0.7574 (mtt180) REVERT: M 120 MET cc_start: 0.7094 (mmm) cc_final: 0.6801 (mtt) REVERT: N 44 LYS cc_start: 0.7937 (ttmt) cc_final: 0.7734 (ttmt) REVERT: O 23 LEU cc_start: 0.8136 (mp) cc_final: 0.7834 (mp) REVERT: O 32 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7788 (tmm160) REVERT: S 20 ARG cc_start: 0.7721 (ttm110) cc_final: 0.7312 (ttm110) REVERT: S 85 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7609 (mt) outliers start: 3 outliers final: 2 residues processed: 69 average time/residue: 0.2678 time to fit residues: 21.7040 Evaluate side-chains 70 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 85 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 80 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 48 optimal weight: 0.0670 chunk 69 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 99 optimal weight: 30.0000 chunk 91 optimal weight: 2.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.139922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.108670 restraints weight = 17993.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.111321 restraints weight = 8625.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113134 restraints weight = 5489.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.114069 restraints weight = 4219.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.114770 restraints weight = 3650.762| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.6174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13207 Z= 0.274 Angle : 0.750 9.367 19170 Z= 0.417 Chirality : 0.051 0.257 2181 Planarity : 0.005 0.039 1344 Dihedral : 31.629 176.305 4231 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.64 % Allowed : 7.57 % Favored : 91.79 % 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: 2.05 (0.31), residues: 732 helix: 2.27 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -1.41 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 45 TYR 0.025 0.002 TYR T 118 PHE 0.015 0.002 PHE M 84 HIS 0.006 0.002 HIS P 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.27 (13207) covalent geometry : angle 0.74999 / 0.42 (19170) hydrogen bonds : bond 0.06290 / 4.09 ( 782) hydrogen bonds : angle 2.84029 / 2.01 ( 1942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1785.19 seconds wall clock time: 31 minutes 19.97 seconds (1879.97 seconds total)