Starting phenix.real_space_refine on Fri Jul 3 06:12:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e09_47353/07_2026/9e09_47353.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e09_47353/07_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_47353/07_2026/9e09_47353.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e09_47353/07_2026/9e09_47353.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e09_47353/07_2026/9e09_47353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e09_47353/07_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.13, per 1000 atoms: 0.17 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: 0.59 Conformation dependent library (CDL) restraints added in 253.5 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: 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: 1.40 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: 2.22 Time building geometry restraints manager: 0.87 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=" 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 bond pdb=" C3' DG J 5 " pdb=" C2' DG J 5 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.53e+00 bond pdb=" N ILE N 34 " pdb=" CA ILE N 34 " ideal model delta sigma weight residual 1.461 1.492 -0.032 1.19e-02 7.06e+03 7.04e+00 ... (remaining 13202 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 15732 1.30 - 2.59: 2983 2.59 - 3.89: 398 3.89 - 5.19: 47 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=" 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 angle pdb=" O4' DT I 157 " pdb=" C4' DT I 157 " pdb=" C3' DT I 157 " ideal model delta sigma weight residual 106.00 103.60 2.40 6.00e-01 2.78e+00 1.61e+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: 6.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.510 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.240 ------------------------------------------------------------------------------- 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= 0.553 Angle : 1.009 6.483 19170 Z= 0.773 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 / 0.55 (13207) covalent geometry : angle 1.00917 / 0.77 (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 : 0.276 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: 0.7434 (tt0) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1456 time to fit residues: 20.6448 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 : 0.187 ------------------------------------------------------------------------------- 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: 9.9990 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: 0.8980 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 = 0.159730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.128364 restraints weight = 18533.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.131057 restraints weight = 9034.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.132922 restraints weight = 5758.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.133788 restraints weight = 4402.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.134464 restraints weight = 3843.055| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 13207 Z= 0.228 Angle : 0.739 7.793 19170 Z= 0.424 Chirality : 0.049 0.263 2181 Planarity : 0.006 0.049 1344 Dihedral : 31.592 170.451 4231 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.81 % Allowed : 3.38 % Favored : 95.81 % 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: -0.17 (0.28), residues: 732 helix: 0.48 (0.20), residues: 544 sheet: None (None), residues: 0 loop : -1.66 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 77 TYR 0.032 0.004 TYR T 80 PHE 0.021 0.003 PHE Q 104 HIS 0.008 0.002 HIS O 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.23 (13207) covalent geometry : angle 0.73904 / 0.42 (19170) hydrogen bonds : bond 0.06229 / 4.10 ( 782) hydrogen bonds : angle 3.22318 / 2.31 ( 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 82 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.227 Fit side-chains REVERT: O 39 TYR cc_start: 0.8023 (m-80) cc_final: 0.7822 (m-80) REVERT: P 56 MET cc_start: 0.7651 (mmm) cc_final: 0.7143 (tpp) REVERT: Q 90 MET cc_start: 0.6739 (tpp) cc_final: 0.6477 (mpp) REVERT: T 44 GLN cc_start: 0.7606 (tt0) cc_final: 0.7400 (tt0) outliers start: 5 outliers final: 4 residues processed: 78 average time/residue: 0.1258 time to fit residues: 13.1609 Evaluate side-chains 75 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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: 0.7980 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 0.0970 chunk 4 optimal weight: 0.1980 chunk 14 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 25 ASN N 75 HIS P 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.154829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.122690 restraints weight = 18472.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125453 restraints weight = 8718.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.127304 restraints weight = 5449.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.128364 restraints weight = 4130.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.128746 restraints weight = 3532.500| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13207 Z= 0.187 Angle : 0.656 6.783 19170 Z= 0.397 Chirality : 0.045 0.251 2181 Planarity : 0.005 0.043 1344 Dihedral : 31.395 171.377 4231 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.64 % Allowed : 4.67 % Favored : 94.69 % 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: 1.47 (0.30), residues: 732 helix: 1.79 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -1.50 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 77 TYR 0.030 0.002 TYR P 80 PHE 0.016 0.002 PHE Q 84 HIS 0.007 0.001 HIS S 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.19 (13207) covalent geometry : angle 0.65610 / 0.40 (19170) hydrogen bonds : bond 0.05971 / 3.76 ( 782) hydrogen bonds : angle 2.78945 / 1.97 ( 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 71 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.226 Fit side-chains REVERT: M 115 LYS cc_start: 0.8192 (mttm) cc_final: 0.7764 (mttm) REVERT: P 56 MET cc_start: 0.7493 (mmm) cc_final: 0.7169 (tpp) REVERT: Q 70 LEU cc_start: 0.7750 (tp) cc_final: 0.7446 (tt) REVERT: Q 90 MET cc_start: 0.6666 (tpp) cc_final: 0.6457 (mpp) REVERT: T 44 GLN cc_start: 0.7641 (tt0) cc_final: 0.7429 (tt0) REVERT: T 83 ARG cc_start: 0.7791 (mtp85) cc_final: 0.7498 (mtt90) outliers start: 4 outliers final: 1 residues processed: 68 average time/residue: 0.1762 time to fit residues: 14.9977 Evaluate side-chains 69 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 37 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.151357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.119415 restraints weight = 18220.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122186 restraints weight = 8574.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.124050 restraints weight = 5374.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125136 restraints weight = 4106.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125610 restraints weight = 3517.314| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13207 Z= 0.212 Angle : 0.677 11.478 19170 Z= 0.392 Chirality : 0.046 0.244 2181 Planarity : 0.005 0.037 1344 Dihedral : 31.666 172.992 4231 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.64 % Allowed : 4.83 % 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: 1.70 (0.30), residues: 732 helix: 1.95 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.38 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 45 TYR 0.035 0.002 TYR P 80 PHE 0.017 0.002 PHE N 100 HIS 0.005 0.001 HIS P 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.21 (13207) covalent geometry : angle 0.67678 / 0.39 (19170) hydrogen bonds : bond 0.05694 / 3.73 ( 782) hydrogen bonds : angle 2.75009 / 1.95 ( 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 67 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.316 Fit side-chains REVERT: M 115 LYS cc_start: 0.8240 (mttm) cc_final: 0.7831 (mttm) REVERT: M 120 MET cc_start: 0.6934 (mmm) cc_final: 0.6593 (mtt) REVERT: P 56 MET cc_start: 0.7508 (mmm) cc_final: 0.7260 (tpp) REVERT: Q 90 MET cc_start: 0.6608 (tpp) cc_final: 0.6360 (mpp) REVERT: S 20 ARG cc_start: 0.7727 (ttm110) cc_final: 0.7146 (ttm170) REVERT: S 99 ARG cc_start: 0.6826 (mtt180) cc_final: 0.6624 (mtp85) REVERT: T 83 ARG cc_start: 0.7762 (mtp85) cc_final: 0.7512 (mtt90) outliers start: 4 outliers final: 3 residues processed: 65 average time/residue: 0.1826 time to fit residues: 15.1211 Evaluate side-chains 63 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 38 ASN Chi-restraints excluded: chain Q residue 48 LEU 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: 0.9990 chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 59 optimal weight: 0.2980 chunk 97 optimal weight: 9.9990 chunk 60 optimal weight: 0.3980 chunk 6 optimal weight: 0.2980 chunk 44 optimal weight: 0.1980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 73 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 = 0.3811 r_free = 0.3811 target = 0.149619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.117747 restraints weight = 18375.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120340 restraints weight = 8829.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.122107 restraints weight = 5654.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.123259 restraints weight = 4342.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123492 restraints weight = 3721.725| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4255 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= 0.160 Angle : 0.604 6.694 19170 Z= 0.363 Chirality : 0.042 0.236 2181 Planarity : 0.004 0.035 1344 Dihedral : 31.489 173.586 4231 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.48 % Allowed : 5.64 % 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: 2.25 (0.31), residues: 732 helix: 2.38 (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 0.012 0.001 ARG S 77 TYR 0.023 0.001 TYR P 80 PHE 0.011 0.002 PHE Q 67 HIS 0.005 0.001 HIS S 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.16 (13207) covalent geometry : angle 0.60432 / 0.36 (19170) hydrogen bonds : bond 0.05041 / 3.24 ( 782) hydrogen bonds : angle 2.56171 / 1.82 ( 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 62 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.220 Fit side-chains REVERT: M 115 LYS cc_start: 0.8224 (mttm) cc_final: 0.7806 (mttm) REVERT: M 120 MET cc_start: 0.6961 (mmm) cc_final: 0.6643 (mtt) REVERT: Q 90 MET cc_start: 0.6593 (tpp) cc_final: 0.6380 (mpp) REVERT: S 20 ARG cc_start: 0.7708 (ttm110) cc_final: 0.7165 (ttm110) outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 0.1801 time to fit residues: 13.3438 Evaluate side-chains 60 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 56 LYS Chi-restraints excluded: chain Q residue 48 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 0.0980 chunk 94 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 3 optimal weight: 0.3980 chunk 66 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 overall best weight: 0.2980 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.150687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118722 restraints weight = 18124.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121451 restraints weight = 8502.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.123329 restraints weight = 5319.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.124375 restraints weight = 4082.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.125151 restraints weight = 3500.011| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13207 Z= 0.149 Angle : 0.601 9.435 19170 Z= 0.357 Chirality : 0.041 0.244 2181 Planarity : 0.004 0.032 1344 Dihedral : 31.518 174.262 4231 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.64 % Allowed : 5.96 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.31), residues: 732 helix: 2.63 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.32 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 77 TYR 0.017 0.002 TYR P 80 PHE 0.009 0.001 PHE Q 67 HIS 0.003 0.001 HIS S 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.15 (13207) covalent geometry : angle 0.60081 / 0.36 (19170) hydrogen bonds : bond 0.04898 / 3.18 ( 782) hydrogen bonds : angle 2.51629 / 1.79 ( 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 80 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.183 Fit side-chains REVERT: M 72 ARG cc_start: 0.7795 (mtt-85) cc_final: 0.7365 (mtt-85) REVERT: M 115 LYS cc_start: 0.8238 (mttm) cc_final: 0.7828 (mttm) REVERT: M 120 MET cc_start: 0.7015 (mmm) cc_final: 0.6712 (mtt) REVERT: O 32 ARG cc_start: 0.8037 (ttp80) cc_final: 0.7661 (ttp-110) REVERT: S 20 ARG cc_start: 0.7703 (ttm110) cc_final: 0.7206 (ttm110) outliers start: 4 outliers final: 3 residues processed: 77 average time/residue: 0.2397 time to fit residues: 21.8738 Evaluate side-chains 78 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 38 ASN Chi-restraints excluded: chain Q residue 48 LEU 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: 0.9980 chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 62 optimal weight: 0.0870 chunk 45 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 0 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.143941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113029 restraints weight = 18148.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.115369 restraints weight = 9338.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.116950 restraints weight = 6206.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.117881 restraints weight = 4914.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.118291 restraints weight = 4275.287| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13207 Z= 0.216 Angle : 0.672 9.220 19170 Z= 0.389 Chirality : 0.046 0.235 2181 Planarity : 0.005 0.069 1344 Dihedral : 31.577 174.673 4231 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.81 % Allowed : 5.80 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.31), residues: 732 helix: 2.39 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.34 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG O 71 TYR 0.027 0.002 TYR P 80 PHE 0.018 0.002 PHE Q 84 HIS 0.009 0.001 HIS P 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.22 (13207) covalent geometry : angle 0.67231 / 0.39 (19170) hydrogen bonds : bond 0.05850 / 3.78 ( 782) hydrogen bonds : angle 2.74272 / 1.94 ( 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 75 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.286 Fit side-chains REVERT: M 72 ARG cc_start: 0.7856 (mtt-85) cc_final: 0.7412 (mtt-85) REVERT: M 120 MET cc_start: 0.7121 (mmm) cc_final: 0.6573 (mtt) REVERT: O 32 ARG cc_start: 0.8102 (ttp80) cc_final: 0.7824 (ttp-110) REVERT: O 71 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6540 (mtt90) REVERT: P 56 MET cc_start: 0.7485 (mmm) cc_final: 0.6676 (tpp) REVERT: Q 90 MET cc_start: 0.6363 (mpp) cc_final: 0.6049 (mpp) REVERT: S 20 ARG cc_start: 0.7714 (ttm110) cc_final: 0.7303 (ttm110) REVERT: T 59 MET cc_start: 0.7509 (mmm) cc_final: 0.6932 (mmm) outliers start: 5 outliers final: 1 residues processed: 71 average time/residue: 0.2641 time to fit residues: 22.1658 Evaluate side-chains 71 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 56 LYS Chi-restraints excluded: chain O residue 71 ARG 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: 0.6980 chunk 19 optimal weight: 0.4980 chunk 44 optimal weight: 0.0980 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 61 optimal weight: 0.0070 chunk 47 optimal weight: 0.9990 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 38 ASN O 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.144502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113106 restraints weight = 18159.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.115555 restraints weight = 9339.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.117174 restraints weight = 6161.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.118035 restraints weight = 4867.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.118598 restraints weight = 4249.268| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.5219 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= 0.152 Angle : 0.605 8.701 19170 Z= 0.360 Chirality : 0.042 0.241 2181 Planarity : 0.004 0.033 1344 Dihedral : 31.557 174.969 4231 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.64 % Allowed : 6.60 % Favored : 92.75 % 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: 2.63 (0.31), residues: 732 helix: 2.68 (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 O 35 TYR 0.019 0.002 TYR T 118 PHE 0.011 0.001 PHE Q 67 HIS 0.003 0.001 HIS P 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.15 (13207) covalent geometry : angle 0.60468 / 0.36 (19170) hydrogen bonds : bond 0.04938 / 3.19 ( 782) hydrogen bonds : angle 2.54679 / 1.81 ( 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 75 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.300 Fit side-chains REVERT: M 42 ARG cc_start: 0.7802 (mtp85) cc_final: 0.7528 (mtp85) REVERT: M 72 ARG cc_start: 0.7857 (mtt-85) cc_final: 0.7380 (mtt-85) REVERT: M 120 MET cc_start: 0.7083 (mmm) cc_final: 0.6812 (mtt) REVERT: N 44 LYS cc_start: 0.7850 (ttmm) cc_final: 0.7613 (ttmm) REVERT: O 32 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7724 (ttp-110) REVERT: O 71 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.6592 (mtt90) REVERT: P 56 MET cc_start: 0.7546 (mmm) cc_final: 0.6804 (tpp) REVERT: Q 90 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.6152 (mpp) REVERT: S 20 ARG cc_start: 0.7694 (ttm110) cc_final: 0.7305 (ttm110) outliers start: 4 outliers final: 2 residues processed: 71 average time/residue: 0.2572 time to fit residues: 21.6363 Evaluate side-chains 72 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain Q residue 90 MET 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: 0.4980 chunk 4 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 0.0870 chunk 88 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 25 ASN O 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.141334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.111098 restraints weight = 18256.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.113483 restraints weight = 9225.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.115127 restraints weight = 6063.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.115989 restraints weight = 4718.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.116472 restraints weight = 4110.947| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13207 Z= 0.195 Angle : 0.640 8.647 19170 Z= 0.375 Chirality : 0.044 0.238 2181 Planarity : 0.004 0.034 1344 Dihedral : 31.590 175.554 4231 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.64 % Allowed : 7.25 % Favored : 92.11 % 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: 2.45 (0.31), residues: 732 helix: 2.55 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.33 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 35 TYR 0.017 0.002 TYR T 118 PHE 0.016 0.002 PHE Q 84 HIS 0.004 0.001 HIS T 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.19 (13207) covalent geometry : angle 0.64009 / 0.38 (19170) hydrogen bonds : bond 0.05383 / 3.48 ( 782) hydrogen bonds : angle 2.66170 / 1.89 ( 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 72 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.231 Fit side-chains REVERT: M 42 ARG cc_start: 0.7801 (mtp85) cc_final: 0.7485 (mtp85) REVERT: M 72 ARG cc_start: 0.7902 (mtt-85) cc_final: 0.7433 (mtt-85) REVERT: M 120 MET cc_start: 0.7179 (mmm) cc_final: 0.6890 (mtt) REVERT: N 44 LYS cc_start: 0.7863 (ttmm) cc_final: 0.7631 (ttmm) REVERT: O 32 ARG cc_start: 0.8046 (ttp80) cc_final: 0.7740 (ttp-110) REVERT: O 71 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.6602 (mtt90) REVERT: P 56 MET cc_start: 0.7539 (mmm) cc_final: 0.6779 (tpp) REVERT: Q 90 MET cc_start: 0.6442 (OUTLIER) cc_final: 0.6179 (mpp) REVERT: R 84 MET cc_start: 0.7396 (mmm) cc_final: 0.7032 (tpp) REVERT: S 20 ARG cc_start: 0.7726 (ttm110) cc_final: 0.7329 (ttm110) REVERT: S 85 LEU cc_start: 0.7959 (mp) cc_final: 0.7600 (mt) outliers start: 4 outliers final: 2 residues processed: 68 average time/residue: 0.2648 time to fit residues: 21.0330 Evaluate side-chains 72 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 90 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 chunk 54 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.141792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.111618 restraints weight = 18275.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.113994 restraints weight = 9259.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.115593 restraints weight = 6093.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.116551 restraints weight = 4763.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.116996 restraints weight = 4146.851| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13207 Z= 0.167 Angle : 0.616 6.952 19170 Z= 0.365 Chirality : 0.043 0.239 2181 Planarity : 0.004 0.033 1344 Dihedral : 31.581 175.576 4231 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.64 % Allowed : 7.25 % Favored : 92.11 % 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: 2.63 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.25 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 35 TYR 0.029 0.002 TYR T 118 PHE 0.010 0.001 PHE Q 67 HIS 0.003 0.001 HIS T 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.17 (13207) covalent geometry : angle 0.61579 / 0.37 (19170) hydrogen bonds : bond 0.05009 / 3.23 ( 782) hydrogen bonds : angle 2.57748 / 1.83 ( 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 73 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.231 Fit side-chains REVERT: M 42 ARG cc_start: 0.7808 (mtp85) cc_final: 0.7497 (mtp85) REVERT: M 72 ARG cc_start: 0.7868 (mtt-85) cc_final: 0.7422 (mtt-85) REVERT: M 120 MET cc_start: 0.7137 (mmm) cc_final: 0.6861 (mtt) REVERT: N 44 LYS cc_start: 0.7873 (ttmm) cc_final: 0.7637 (ttmm) REVERT: O 32 ARG cc_start: 0.8025 (ttp80) cc_final: 0.7728 (ttp-110) REVERT: O 71 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6622 (mtt90) REVERT: P 56 MET cc_start: 0.7548 (mmm) cc_final: 0.6770 (tpp) REVERT: Q 90 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.6187 (mpp) REVERT: R 84 MET cc_start: 0.7463 (mmm) cc_final: 0.7127 (tpp) REVERT: S 20 ARG cc_start: 0.7739 (ttm110) cc_final: 0.7362 (ttm110) REVERT: S 85 LEU cc_start: 0.7936 (mp) cc_final: 0.7582 (mt) REVERT: T 59 MET cc_start: 0.7495 (mmm) cc_final: 0.6911 (mmm) outliers start: 4 outliers final: 2 residues processed: 69 average time/residue: 0.2523 time to fit residues: 20.6006 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 : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 90 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 80 optimal weight: 3.9990 chunk 51 optimal weight: 0.2980 chunk 64 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 48 optimal weight: 0.0570 chunk 69 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 99 optimal weight: 50.0000 chunk 91 optimal weight: 2.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.139441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.109371 restraints weight = 18171.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.111784 restraints weight = 9169.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.113404 restraints weight = 5992.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.114237 restraints weight = 4699.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.114887 restraints weight = 4095.763| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.5924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13207 Z= 0.193 Angle : 0.647 6.881 19170 Z= 0.378 Chirality : 0.045 0.238 2181 Planarity : 0.005 0.041 1344 Dihedral : 31.631 176.251 4231 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.81 % Allowed : 7.09 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.31), residues: 732 helix: 2.60 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -1.34 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 35 TYR 0.020 0.002 TYR T 118 PHE 0.015 0.002 PHE Q 84 HIS 0.004 0.001 HIS S 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.19 (13207) covalent geometry : angle 0.64702 / 0.38 (19170) hydrogen bonds : bond 0.05433 / 3.52 ( 782) hydrogen bonds : angle 2.66658 / 1.90 ( 1942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1755.72 seconds wall clock time: 30 minutes 57.35 seconds (1857.35 seconds total)